WorldWideScience

Sample records for arabidopsis thaliana interferes

  1. Sinapic acid or its derivatives interfere with abscisic acid homeostasis during Arabidopsis thaliana seed germination.

    Science.gov (United States)

    Bi, Baodi; Tang, Jingliang; Han, Shuang; Guo, Jinggong; Miao, Yuchen

    2017-06-06

    Sinapic acid and its esters have broad functions in different stages of seed germination and plant development and are thought to play a role in protecting against ultraviolet irradiation. To better understand the interactions between sinapic acid esters and seed germination processes in response to various stresses, we analyzed the role of the plant hormone abscisic acid (ABA) in the regulation of sinapic acid esters involved in seed germination and early seedling growth. We found that exogenous sinapic acid promotes seed germination in a dose-dependent manner in Arabidopsis thaliana. High-performance liquid chromatography mass spectrometry analysis showed that exogenous sinapic acid increased the sinapoylcholine content of imbibed seeds. Furthermore, sinapic acid affected ABA catabolism, resulting in reduced ABA levels and increased levels of the ABA-glucose ester. Using mutants deficient in the synthesis of sinapate esters, we showed that the germination of mutant sinapoylglucose accumulator 2 (sng2) and bright trichomes 1 (brt1) seeds was more sensitive to ABA than the wild-type. Moreover, Arabidopsis mutants deficient in either abscisic acid deficient 2 (ABA2) or abscisic acid insensitive 3 (ABI3) displayed increased expression of the sinapoylglucose:choline sinapoyltransferase (SCT) and sinapoylcholine esterase (SCE) genes with sinapic acid treatment. This treatment also affected the accumulation of sinapoylcholine and free choline during seed germination. We demonstrated that sinapoylcholine, which constitutes the major phenolic component in seeds among various minor sinapate esters, affected ABA homeostasis during seed germination and early seedling growth in Arabidopsis. Our findings provide insights into the role of sinapic acid and its esters in regulating ABA-mediated inhibition of Arabidopsis seed germination in response to drought stress.

  2. The DNA replication factor RFC1 is required for interference-sensitive meiotic crossovers in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Yingxiang Wang

    Full Text Available During meiotic recombination, induced double-strand breaks (DSBs are processed into crossovers (COs and non-COs (NCO; the former are required for proper chromosome segregation and fertility. DNA synthesis is essential in current models of meiotic recombination pathways and includes only leading strand DNA synthesis, but few genes crucial for DNA synthesis have been tested genetically for their functions in meiosis. Furthermore, lagging strand synthesis has been assumed to be unnecessary. Here we show that the Arabidopsis thaliana DNA replication factor C1 (RFC1 important for lagging strand synthesis is necessary for fertility, meiotic bivalent formation, and homolog segregation. Loss of meiotic RFC1 function caused abnormal meiotic chromosome association and other cytological defects; genetic analyses with other meiotic mutations indicate that RFC1 acts in the MSH4-dependent interference-sensitive pathway for CO formation. In a rfc1 mutant, residual pollen viability is MUS81-dependent and COs exhibit essentially no interference, indicating that these COs form via the MUS81-dependent interference-insensitive pathway. We hypothesize that lagging strand DNA synthesis is important for the formation of double Holliday junctions, but not alternative recombination intermediates. That RFC1 is found in divergent eukaryotes suggests a previously unrecognized and highly conserved role for DNA synthesis in discriminating between recombination pathways.

  3. Arabidopsis thaliana peroxidase N

    DEFF Research Database (Denmark)

    Mirza, Osman Asghar; Henriksen, A; Ostergaard, L

    2000-01-01

    The structure of the neutral peroxidase from Arabidopsis thaliana (ATP N) has been determined to a resolution of 1.9 A and a free R value of 20.5%. ATP N has the expected characteristic fold of the class III peroxidases, with a C(alpha) r.m.s.d. of 0.82 A when compared with horseradish peroxidase C...... (HRP C). HRP C is 54% identical to ATP N in sequence. When the structures of four class III plant peroxidases are superimposed, the regions with structural differences are non-randomly distributed; all are located in one half of the molecule. The architecture of the haem pocket of ATP N is very similar...... to that of HRP C, in agreement with the low small-molecule substrate specificity of all class III peroxidases. The structure of ATP N suggests that the pH dependence of the substrate turnover will differ from that of HRP C owing to differences in polarity of the residues in the substrate-access channel. Since...

  4. Brevicoryne brassicae aphids interfere with transcriptome responses of Arabidopsis thaliana to feeding by Plutella xylostella caterpillars in a density-dependent manner

    NARCIS (Netherlands)

    Kroes, Anneke; Broekgaarden, Colette; Castellanos Uribe, Marcos; May, Sean; van Loon, Joop J A; Dicke, Marcel

    2016-01-01

    Plants are commonly attacked by multiple herbivorous species. Yet, little is known about transcriptional patterns underlying plant responses to multiple insect attackers feeding simultaneously. Here, we assessed transcriptomic responses of Arabidopsis thaliana plants to simultaneous feeding by

  5. Bioavailability of nanoparticulate hematite to Arabidopsis thaliana

    International Nuclear Information System (INIS)

    Marusenko, Yevgeniy; Shipp, Jessie; Hamilton, George A.; Morgan, Jennifer L.L.; Keebaugh, Michael; Hill, Hansina; Dutta, Arnab; Zhuo, Xiaoding; Upadhyay, Nabin; Hutchings, James; Herckes, Pierre; Anbar, Ariel D.; Shock, Everett; Hartnett, Hilairy E.

    2013-01-01

    The environmental effects and bioavailability of nanoparticulate iron (Fe) to plants are currently unknown. Here, plant bioavailability of synthesized hematite Fe nanoparticles was evaluated using Arabidopsis thaliana (A. thaliana) as a model. Over 56-days of growing wild-type A. thaliana, the nanoparticle-Fe and no-Fe treatments had lower plant biomass, lower chlorophyll concentrations, and lower internal Fe concentrations than the Fe-treatment. Results for the no-Fe and nanoparticle-Fe treatments were consistently similar throughout the experiment. These results suggest that nanoparticles (mean diameter 40.9 nm, range 22.3–67.0 nm) were not taken up and therefore not bioavailable to A. thaliana. Over 14-days growing wild-type and transgenic (Type I/II proton pump overexpression) A. thaliana, the Type I plant grew more than the wild-type in the nanoparticle-Fe treatment, suggesting Type I plants cope better with Fe limitation; however, the nanoparticle-Fe and no-Fe treatments had similar growth for all plant types. -- Highlights: ► Iron nanoparticles were synthesized and assessed for bioavailability to Arabidopsis. ► Arabidopsis grew better in the presence of EDTA-bound iron than nanoparticulate iron. ► Arabidopsis grew the same in the presence of nanoparticulate iron compared to no iron. -- Synthesized iron nanoparticles were not bioavailable to Arabidopsis thaliana in agar nutrient media

  6. Die Regulation der Camalexinbiosynthese in Arabidopsis thaliana

    OpenAIRE

    Rauhut, Thomas

    2009-01-01

    Camalexin ist das charakteristische Phytoalexin von Arabidopsis thaliana. Bei Pathogeninfektion wird die Synthese von Camalexin z. B. durch die Erkennung von Peptidoglycan oder Nep1-artigen Proteinen (NLPs) ausgelöst. Pflanzen, welche ein NLP unter der Kontrolle eines Ethanol-induzierbaren Promotors exprimieren zeigten eine starke Induktion der Tryptophan- und Camalexinbiosynthesegene und eine reproduzierbare Camalexinakkumulation. Retrobiosynthetische NMR-Analysen und Markierungsexperimente ...

  7. Nitroreductase reactions of Arabidopsis thaliana thioredoxin reductase.

    Science.gov (United States)

    Miskiniene, V; Sarlauskas, J; Jacquot, J P; Cenas, N

    1998-09-07

    Arabidopsis thaliana NADPH:thioredoxin reductase (TR, EC 1.6.4.5) catalyzed redox cycling of aromatic nitrocompounds, including the explosives 2,4,6-trinitrotoluene and tetryl, and the herbicide 3,5-dinitro-o-cresol. The yield of nitro anion radicals was equal to 70-90%. Redox cycling of tetryl was accompanied by formation of N-methylpicramide. Bimolecular rate constants of nitroaromatic reduction (kcat/Km) and reaction catalytic constants (kcat) increased upon an increase in oxidant single-electron reduction potential (E(1)7). Using compounds with an unknown E(1)7 value, the reactivity of TR increased parallelly to the increase in reactivity of ferredoxin:NADP+ reductase of Anabaena PCC 7119 (EC 1.18.1.2). This indicated that the main factor determining reactivity of nitroaromatics towards TR was their energetics of single-electron reduction. Incubation of reduced TR in the presence of tetryl or 2,4-dinitrochlorobenzene resulted in a loss of thioredoxin reductase activity, most probably due to modification of reduced catalytic disulfide, whereas nitroreductase reaction rates were unchanged. This means that on the analogy of quinone reduction by TR (D. Bironaite, Z. Anusevicius, J.-P. Jacquot, N. Cenas, Biochim. Biophys. Acta 1383 (1998) 82-92), FAD and not catalytic disulfide of TR was responsible for the reduction of nitroaromatics. Tetryl, 2,4,6-trinitrotoluene and thioredoxin increased the FAD fluorescence intensity of TR. This finding suggests that nitroaromatics may bind close to the thioredoxin-binding site at the catalytic disulfide domain of TR, and induce a conformational change of enzymes (S.B. Mulrooney, C.H. Williams Jr., Protein Sci. 6 (1997) 2188-2195). Our data indicate that certain nitroaromatic herbicides, explosives and other classes of xenobiotics may interfere with the reduction of thioredoxin by plant TR, and confer prooxidant properties to this antioxidant enzyme.

  8. The pattern of polymorphism in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    2005-07-01

    Full Text Available We resequenced 876 short fragments in a sample of 96 individuals of Arabidopsis thaliana that included stock center accessions as well as a hierarchical sample from natural populations. Although A. thaliana is a selfing weed, the pattern of polymorphism in general agrees with what is expected for a widely distributed, sexually reproducing species. Linkage disequilibrium decays rapidly, within 50 kb. Variation is shared worldwide, although population structure and isolation by distance are evident. The data fail to fit standard neutral models in several ways. There is a genome-wide excess of rare alleles, at least partially due to selection. There is too much variation between genomic regions in the level of polymorphism. The local level of polymorphism is negatively correlated with gene density and positively correlated with segmental duplications. Because the data do not fit theoretical null distributions, attempts to infer natural selection from polymorphism data will require genome-wide surveys of polymorphism in order to identify anomalous regions. Despite this, our data support the utility of A. thaliana as a model for evolutionary functional genomics.

  9. Telomere-binding proteins of Arabidopsis thaliana.

    Science.gov (United States)

    Zentgraf, U

    1995-02-01

    The nucleoprotein structure of Arabidopsis thaliana telomeres was investigated. A protein specifically binding to telomeric sequences was characterized by gel mobility shift assays with synthetic oligonucleotides consisting of four 7 bp telomeric repeats of Arabidopsis (TTTAGGG) and crude nuclear protein extracts of Arabidopsis leaves. These DNA-protein binding studies revealed that the binding affinity of this telomere-binding protein to the G-rich single-strand as well as to the double-stranded telomeric DNA is much higher than to the C-rich single-strand. The molecular mass of the protein was identified by SDS-PAGE to be 67 kDa. The isoelectric points were determined to be 5.0, 4.85 and 4.7, respectively, indicating that either one protein with different modifications or three slightly different proteins have been isolated. An RNA component, possibly serving as a template for reverse transcription of a plant telomerase, does not mediate the DNA-protein contact because the DNA-protein interactions were not RNAse-sensitive.

  10. Identification of Polyadenylation Sites within Arabidopsis Thaliana

    KAUST Repository

    Kalkatawi, Manal

    2011-09-01

    Machine Learning (ML) is a field of artificial intelligence focused on the design and implementation of algorithms that enable creation of models for clustering, classification, prediction, ranking and similar inference tasks based on information contained in data. Many ML algorithms have been successfully utilized in a variety of applications. The problem addressed in this thesis is from the field of bioinformatics and deals with the recognition of polyadenylation (poly(A)) sites in the genomic sequence of the plant Arabidopsis thaliana. During the RNA processing, a tail consisting of a number of consecutive adenine (A) nucleotides is added to the terminal nucleotide of the 3’- untranslated region (3’UTR) of the primary RNA. The process in which these A nucleotides are added is called polyadenylation. The location in the genomic DNA sequence that corresponds to the start of terminal A nucleotides (i.e. to the end of 3’UTR) is known as a poly(A) site. Recognition of the poly(A) sites in DNA sequence is important for better gene annotation and understanding of gene regulation. In this study, we built an artificial neural network (ANN) for the recognition of poly(A) sites in the Arabidopsis thaliana genome. Our study demonstrates that this model achieves improved accuracy compared to the existing predictive models for this purpose. The key factor contributing to the enhanced predictive performance of our ANN model is a distinguishing set of features used in creation of the model. These features include a number of physico-chemical characteristics of relevance, such as dinucleotide thermodynamic characteristics, electron-ion interaction potential, etc., but also many of the statistical properties of the DNA sequences from the region surrounding poly(A) site, such as nucleotide and polynucleotide properties, common motifs, etc. Our ANN model was compared in performance with several other ML models, as well as with the PAC tool that is specifically developed for

  11. Ion channels in guard cells of Arabidopsis thaliana (L) Heynh

    NARCIS (Netherlands)

    Roelfsema, MRG; Prins, HBA

    Despite the availability of many mutants for signal transduction, Arabidopsis thaliana guard cells have so far not been used in electrophysiological research. Problems with the isolation of epidermal strips and the small size of A. thaliana guard cells were often prohibiting. In the present study

  12. Evolution and genetic differentiation among relatives of Arabidopsis thaliana.

    Science.gov (United States)

    Koch, Marcus A; Matschinger, Michaela

    2007-04-10

    Arabidopsis thaliana is one of the most intensively studied plant species. More recently, information is accumulating about its closest relatives, the former genus Cardaminopsis. A. thaliana diverged from these relatives, actually treated within three major lineages (Arabidopsis lyrata, Arabidopsis halleri, and Arabidopsis arenosa), approximately 5 mya. Significant karyotype evolution in A. thaliana with base chromosome number reduction from x=8 to x=5 might indicate and favor effective genetic isolation from these other species, although hybrids are occurring naturally and have been also constituted under controlled conditions. We tested the evolutionary significance to separate the x=5 from the x=8 lineage using DNA sequence data from the plastome and the nuclear ribosomal DNA based on an extensive, representative worldwide sampling of nearly all taxonomic entities. We conclude that (i) A. thaliana is clearly separated phylogenetically from the x=8 lineage, (ii) five major lineages outside A. thaliana can be identified (A. lyrata, A. arenosa, A. halleri, Arabidopsis croatica, and Arabidopsis pedemontana) together with Arabidopsis cebennensis, and (iii) centers of genetic and morphological diversity are mostly in congruence and are located close to the Balkans in Austria and Slovakia outside glaciated and permafrost regions with few notable exceptions.

  13. Building a hair: tip growth in Arabidopsis thaliana root hairs.

    OpenAIRE

    Carol, Rachel J; Dolan, Liam

    2002-01-01

    The Arabidopsis thaliana root hair is used as a model for studying tip growth in plants. We review recent advances, made using physiological and genetic approaches, which give rise to different, yet compatible, current views of the establishment and maintenance of tip growth in epidermal cells. For example, an active calcium influx channel localized at the tip of Arabidopsis root hairs has been identified by patch-clamp measurements. Actin has been visualized in vivo in Arabidopsis root hairs...

  14. Comparison of the spaceflight transcriptome of four commonly used Arabidopsis thaliana ecotypes

    Data.gov (United States)

    National Aeronautics and Space Administration — This experiment compared the spaceflight transcriptomes of four commonly used natural variants (ecotypes) of Arabidopsis thaliana using RNAseq. In nature Arabidopsis...

  15. Numerical and structural chromosome aberrations in cauliflower (Brassica oleracea var. botrytis) and Arabidopsis thaliana

    NARCIS (Netherlands)

    Ji, X.

    2014-01-01

    Numerical and structural chromosome aberrations in cauliflower (Brassica oleracea var. botrytis) and Arabidopsis thaliana. I studied numerical and structural chromosome aberrations in cauliflower (Brassica oleracea var. botrytis) and Arabidopsis thaliana. The large genomic changes are important for

  16. Gene networks controlling Arabidopsis thaliana flower development.

    Science.gov (United States)

    Ó'Maoiléidigh, Diarmuid Seosamh; Graciet, Emmanuelle; Wellmer, Frank

    2014-01-01

    The formation of flowers is one of the main models for studying the regulatory mechanisms that underlie plant development and evolution. Over the past three decades, extensive genetic and molecular analyses have led to the identification of a large number of key floral regulators and to detailed insights into how they control flower morphogenesis. In recent years, genome-wide approaches have been applied to obtaining a global view of the gene regulatory networks underlying flower formation. Furthermore, mathematical models have been developed that can simulate certain aspects of this process and drive further experimentation. Here, we review some of the main findings made in the field of Arabidopsis thaliana flower development, with an emphasis on recent advances. In particular, we discuss the activities of the floral organ identity factors, which are pivotal for the specification of the different types of floral organs, and explore the experimental avenues that may elucidate the molecular mechanisms and gene expression programs through which these master regulators of flower development act. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

  17. Salt-avoidance tropism in Arabidopsis thaliana.

    Science.gov (United States)

    Li, Xia; Zhang, Ws

    2008-05-01

    The orientation of plant root growth is modulated by developmental as well as environmental cues. Among the environmental factors, gravity has been extensively studied because of its overpowering effects in modulating root growth direction. However, our knowledge of the effects of other abiotic signals that influence root growth direction is largely unknown. Recently, we have shown that high salinity can modify root growth direction by inducing rapid amyloplast degradation in root columella cells of Arabidopsis thaliana. By exploiting salt overly sensitive (sos) mutants and PIN2 expression analyses, we have shown that the altered root growth direction in response to salt is mediated by ion disequilibrium and is correlated with PIN2 mRNA abundance and expression and localization of the protein. Our study demonstrates that the SOS pathway may mediate this process. Here we discuss our data from broader perspectives. We propose that salt-induced modification of root growth direction is a salt-avoidance behavior, which is an active adaptive mechanism for plants grown under saline conditions. Furthermore, high salinity also stimulates alteration of gravitropic growth of shoots. These findings illustrate that plants have a fine and sophisticated sensory and communication system that enable plants to dynamically and efficiently cope with rapidly changing environment.

  18. Light responses in Photoperiodism in Arabidopsis thaliana

    Energy Technology Data Exchange (ETDEWEB)

    Anthony R. Cashmore

    2006-08-01

    B. Nature 410, 487-490. Jarillo, J. A., Gabrys, H., Capel, J., Alonso, J. M., Ecker, J. R., and Cashmore, A. R. (2001b). Phototropin-related NPL1 controls chloroplast relocation induced by blue light. Nature 410, 952-954. Kinoshita, T., Doi, M., Suetsugu, N., Kagawa, T., Wada, M., and Shimazaki Ki, K. (2001). phot1 and phot2 mediate blue light regulation of stomatal opening. Nature 414, 656-660. Mas, P., Kim, W. Y., Somers, D. E., and Kay, S. A. (2003). Targeted degradation of TOC1 by ZTL modulates circadian function in Arabidopsis thaliana. Nature 426, 567-570.

  19. Infection and RNA recombination of Brome mosaic virus in Arabidopsis thaliana

    International Nuclear Information System (INIS)

    Dzianott, Aleksandra; Bujarski, Jozef J.

    2004-01-01

    Ecotypes of Arabidopsis thaliana supported the replication and systemic spread of Brome mosaic virus (BMV) RNAs. Infection was induced either by manual inoculation with viral RNA or by BMV virions, demonstrating that virus disassembly did not prevent infection. When in vitro-transcribed BMV RNAs 1-3 were used, production of subgenomic RNA4 was observed, showing that BMV RNA replication and transcription had occurred. Furthermore, inoculations of the transgenic Arabidopsis line that expressed a suppressor of RNA interference (RNAi) pathway markedly increased the BMV RNA concentrations. Inoculations with designed BMV RNA3 recombination vectors generated both homologous and nonhomologous BMV RNA-RNA recombinants. Thus, all cellular factors essential for BMV RNA replication, transcription, and RNA recombination were shown to be present in Arabidopsis. The current scope of understanding of the model Arabidopsis plant system should facilitate the identification of these factors governing the BMV life cycle

  20. Metabolic changes in Arabidopsis thaliana plants overexpressing chalcone synthase

    NARCIS (Netherlands)

    Dao, Thi Thanh Hien

    2010-01-01

    The study has shown that it is possible to introduce the heterologous CHS gene in Arabidopsis thaliana and common multicopies of transgenes containing plants were obtained. Analysis of the change in metabolome of CHS transgenic plants, high expression transgenic lines can be identified by markers

  1. Magnetic field effects in Arabidopsis thaliana Cryptochrome-1

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Chandler, Danielle E.; Schulten, Klaus

    2007-01-01

    of cryptochrome-1 in Arabidopsis thaliana is enhanced by the presence of a weak external magnetic field, confirming the ability of cryptochrome to mediate magnetic field responses. Cryptochrome's signaling is tied to the photoreduction of an internally bound chromophore, flavin adenine dinucleotide. The spin...

  2. Highlights of meiotic genes in Arabidopsis thaliana | Consiglio ...

    African Journals Online (AJOL)

    Meiosis is a fascinating and complex phenomenon and, despite its central role in sexual plant reproduction, little is known on the molecular mechanisms involved in this process. We review the progress made in recent years using Arabidopsis thaliana mutants for isolating meiotic genes. In particular, emphasis is given on ...

  3. Reduction of mineral nutrient availability accelerates flowering of Arabidopsis thaliana

    Czech Academy of Sciences Publication Activity Database

    Kolář, Jan; Seňková, J.

    2008-01-01

    Roč. 165, č. 15 (2008), s. 1601-1609 ISSN 0176-1617 R&D Projects: GA AV ČR KJB600380510 Institutional research plan: CEZ:AV0Z50380511 Keywords : Arabidopsis thaliana * Flowering * Landsberg erecta Subject RIV: EF - Botanics Impact factor: 2.437, year: 2008

  4. Adaptation response of Arabidopsis thaliana to random positioning

    NARCIS (Netherlands)

    Kittang, A.I.; Winge, P.; van Loon, J.J.W.A.; Bones, A.M.; Iversen, T.H.

    2013-01-01

    Arabidopsis thaliana seedlings were exposed on a Random Positioning Machine (RPM) under light conditions for 16 h and the samples were analysed using microarray techniques as part of a preparation for a space experiment on the International Space Station (ISS). The results demonstrated a moderate to

  5. The influences of Hygromycin B on growth of Arabidopsis thaliana ...

    African Journals Online (AJOL)

    In this article, growth and development of Arabidopsis thaliana seedling cotyledon and leaf were evidently affected by Hygromycin B. As compared to the control, cotyledon of seedling on Murashige and Skoog (MS) with Hygromycin B was very small and its leaf was not formed. Along with increase in culture time, cells in the ...

  6. Changes in leaf proteome profile of Arabidopsis thaliana in ...

    Indian Academy of Sciences (India)

    2013-04-25

    Apr 25, 2013 ... soluble proteins of Arabidopsis thaliana leaves by proteomic analysis. An initial study at transcript level has been performed on temporal landscape, which revealed that induction of most of the SA-responsive genes occurs within 3 to 6 h post treatment (HPT) and the expression peaked within 24 HPT.

  7. Cytological events in explants of Arabidopsis thaliana during early callogenesis.

    Science.gov (United States)

    Fras, A; Juchimiuk, J; Siwinska, D; Maluszynska, J

    2007-11-01

    Leaf explants of diploid (2n = 2x = 10) and autotetraploid (2n = 4x = 20) plants of Arabidopsis thaliana ecotype Columbia were cytologically and cytogenetically analysed to determine the time and the mechanisms of the process of polyploidization. The first polyploid cells were observed after the third day of culture in both genotypes of explants. Polyploid cells were the result of pre-existing mixoploidy in explants of A. thaliana. Other factors such as endoreduplication, endomitosis, abnormal microtubules arrangement and DNA damage may have induced polyploidization during early stages of callogenesis.

  8. Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Keshavaiah Channa

    2011-02-01

    Full Text Available Abstract Background All sequenced genomes contain a proportion of lineage-specific genes, which exhibit no sequence similarity to any genes outside the lineage. Despite their prevalence, the origins and functions of most lineage-specific genes remain largely unknown. As more genomes are sequenced opportunities for understanding evolutionary origins and functions of lineage-specific genes are increasing. Results This study provides a comprehensive analysis of the origins of lineage-specific genes (LSGs in Arabidopsis thaliana that are restricted to the Brassicaceae family. In this study, lineage-specific genes within the nuclear (1761 genes and mitochondrial (28 genes genomes are identified. The evolutionary origins of two thirds of the lineage-specific genes within the Arabidopsis thaliana genome are also identified. Almost a quarter of lineage-specific genes originate from non-lineage-specific paralogs, while the origins of ~10% of lineage-specific genes are partly derived from DNA exapted from transposable elements (twice the proportion observed for non-lineage-specific genes. Lineage-specific genes are also enriched in genes that have overlapping CDS, which is consistent with such novel genes arising from overprinting. Over half of the subset of the 958 lineage-specific genes found only in Arabidopsis thaliana have alignments to intergenic regions in Arabidopsis lyrata, consistent with either de novo origination or differential gene loss and retention, with both evolutionary scenarios explaining the lineage-specific status of these genes. A smaller number of lineage-specific genes with an incomplete open reading frame across different Arabidopsis thaliana accessions are further identified as accession-specific genes, most likely of recent origin in Arabidopsis thaliana. Putative de novo origination for two of the Arabidopsis thaliana-only genes is identified via additional sequencing across accessions of Arabidopsis thaliana and closely

  9. Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana

    Science.gov (United States)

    2011-01-01

    Background All sequenced genomes contain a proportion of lineage-specific genes, which exhibit no sequence similarity to any genes outside the lineage. Despite their prevalence, the origins and functions of most lineage-specific genes remain largely unknown. As more genomes are sequenced opportunities for understanding evolutionary origins and functions of lineage-specific genes are increasing. Results This study provides a comprehensive analysis of the origins of lineage-specific genes (LSGs) in Arabidopsis thaliana that are restricted to the Brassicaceae family. In this study, lineage-specific genes within the nuclear (1761 genes) and mitochondrial (28 genes) genomes are identified. The evolutionary origins of two thirds of the lineage-specific genes within the Arabidopsis thaliana genome are also identified. Almost a quarter of lineage-specific genes originate from non-lineage-specific paralogs, while the origins of ~10% of lineage-specific genes are partly derived from DNA exapted from transposable elements (twice the proportion observed for non-lineage-specific genes). Lineage-specific genes are also enriched in genes that have overlapping CDS, which is consistent with such novel genes arising from overprinting. Over half of the subset of the 958 lineage-specific genes found only in Arabidopsis thaliana have alignments to intergenic regions in Arabidopsis lyrata, consistent with either de novo origination or differential gene loss and retention, with both evolutionary scenarios explaining the lineage-specific status of these genes. A smaller number of lineage-specific genes with an incomplete open reading frame across different Arabidopsis thaliana accessions are further identified as accession-specific genes, most likely of recent origin in Arabidopsis thaliana. Putative de novo origination for two of the Arabidopsis thaliana-only genes is identified via additional sequencing across accessions of Arabidopsis thaliana and closely related sister species

  10. Mining the active proteome of Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Renier A. L. Van Der Hoorn

    2011-11-01

    Full Text Available Assigning functions to the >30.000 proteins encoded by the Arabidopsis genome is a challenging task of the Arabidopsis Functional Genomics Network. Although genome-wide technologies like proteomics and transcriptomics have generated a wealth of information that significantly accelerated gene annotation, protein activities are poorly predicted by transcript or protein levels as protein activities are post-translationally regulated. To directly display protein activities in Arabidopsis proteomes, we developed and applied Activity-based Protein Profiling (ABPP. ABPP is based on the use of small molecule probes that react with the catalytic residues of distinct protein classes in an activity-dependent manner. Labeled proteins are separated and detected from proteins gels and purified and identified by mass spectrometry. Using probes of six different chemotypes we have displayed of activities of 76 Arabidopsis proteins. These proteins represent over ten different protein classes that contain over 250 Arabidopsis proteins, including cysteine- serine- and metallo-proteases, lipases, acyltransferases, and the proteasome. We have developed methods for identification of in vivo labeled proteins using click-chemistry and for in vivo imaging with fluorescent probes. In vivo labeling has revealed novel protein activities and unexpected subcellular activities of the proteasome. Labeling of extracts displayed several differential activities e.g. of the proteasome during immune response and methylesterases during infection. These studies illustrate the power of ABPP to display the functional proteome and testify to a successful interdisciplinary collaboration involving chemical biology, organic chemistry and proteomics.

  11. Collection of apoplastic fluids from Arabidopsis thaliana leaves

    DEFF Research Database (Denmark)

    Madsen, Svend Roesen; Nour-Eldin, Hussam Hassan; Halkier, Barbara Ann

    2016-01-01

    The leaf apoplast comprises the extracellular continuum outside cell membranes. A broad range of processes take place in the apoplast, including intercellular signaling, metabolite transport, and plant-microbe interactions. To study these processes, it is essential to analyze the metabolite conte...... in apoplastic fluids. Due to the fragile nature of leaf tissues, it is a challenge to obtain apoplastic fluids from leaves. Here, methods to collect apoplastic washing fluid and guttation fluid from Arabidopsis thaliana leaves are described....

  12. Functional genetics of intraspecific ecological interactions in Arabidopsis thaliana

    OpenAIRE

    Wolf, Jason B.; Mutic, Joshua J.; Kover, Paula X.

    2011-01-01

    Studying the genetic basis of traits involved in ecological interactions is a fundamental part of elucidating the connections between evolutionary and ecological processes. Such knowledge allows one to link genetic models of trait evolution with ecological models describing interactions within and between species. Previous work has shown that connections between genetic and ecological processes in Arabidopsis thaliana may be mediated by the fact that quantitative trait loci (QTL) with ‘direct...

  13. Quantitative trait loci for floral morphology in Arabidopsis thaliana.

    OpenAIRE

    Juenger, T; Purugganan, M; Mackay, T F

    2000-01-01

    A central question in biology is how genes control the expression of quantitative variation. We used statistical methods to estimate genetic variation in eight Arabidopsis thaliana floral characters (fresh flower mass, petal length, petal width, sepal length, sepal width, long stamen length, short stamen length, and pistil length) in a cosmopolitan sample of 15 ecotypes. In addition, we used genome-wide quantitative trait locus (QTL) mapping to evaluate the genetic basis of variation in these...

  14. New cytokinin metabolites in IPT transgenic Arabidopsis thaliana plants

    Czech Academy of Sciences Publication Activity Database

    Werner, Tomáš; Hanuš, Jan; Holub, Jan; Schmülling, T.; Onckelen, H. V.; Strnad, Miroslav

    2003-01-01

    Roč. 118, č. 1 (2003), s. 127-137 ISSN 0031-9317 R&D Projects: GA ČR GA301/02/0475 Grant - others: Volkswagen Stiftung(DE) I/76 86:153100008; - - -(BE) IUAP P5/13 Institutional research plan: CEZ:AV0Z5038910 Keywords : transgenic Arabidopsis thaliana * cytokinin * zeatin-O-glucoside Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.767, year: 2003

  15. The structure of the major anthocyanin in Arabidopsis thaliana.

    Science.gov (United States)

    Bloor, Stephen J; Abrahams, Sharon

    2002-02-01

    The major anthocyanin in the leaves and stems of Arabidopsis thaliana has been isolated and shown to be cyanidin 3-O-[2-O(2-O-(sinapoyl)-beta-D-xylopyranosyl)-6-O-(4-O-(beta-D-glucopyranosyl)-p-coumaroyl-beta-D-glucopyranoside] 5-O-[6-O-(malonyl) beta-D-glucopyranoside]. This anthocyanin is a glucosylated version of one of the anthocyanins found in the flowers of the closely related Matthiola incana.

  16. Nucleosome structure incorporated histone acetylation site prediction in Arabidopsis thaliana.

    Science.gov (United States)

    Zhao, Chen; Liu, Hui; Li, Jiang; Deng, Youping; Shi, Tieliu

    2010-11-02

    Acetylation is a crucial post-translational modification for histones, and plays a key role in gene expression regulation. Due to limited data and lack of a clear acetylation consensus sequence, a few researches have focused on prediction of lysine acetylation sites. Several systematic prediction studies have been conducted for human and yeast, but less for Arabidopsis thaliana. Concerning the insufficient observation on acetylation site, we analyzed contributions of the peptide-alignment-based distance definition and 3D structure factors in acetylation prediction. We found that traditional structure contributes little to acetylation site prediction. Identified acetylation sites of histones in Arabidopsis thaliana are conserved and cross predictable with that of human by peptide based methods. However, the predicted specificity is overestimated, because of the existence of non-observed acetylable site. Here, by performing a complete exploration on the factors that affect the acetylability of lysines in histones, we focused on the relative position of lysine at nucleosome level, and defined a new structure feature to promote the performance in predicting the acetylability of all the histone lysines in A. thaliana. We found a new spacial correlated acetylation factor, and defined a ε-N spacial location based feature, which contains five core spacial ellipsoid wired areas. By incorporating the new feature, the performance of predicting the acetylability of all the histone lysines in A. Thaliana was promoted, in which the previous mispredicted acetylable lysines were corrected by comparing to the peptide-based prediction.

  17. Polyamines and Paraquat Toxicity in Arabidopsis thaliana

    OpenAIRE

    Jasmina, Kurepa; Jan, Smalle; Marc Van, Montagu; Dirk, Inze; Laboratorium voor Genetica, Department of Genetics, Flanders Interuniversity Institute for Biotechnology, Universiteit Gent; Laboratorium voor Genetica, Department of Genetics, Flanders Interuniversity Institute for Biotechnology, Universiteit Gent; Laboratorium voor Genetica, Department of Genetics, Flanders Interuniversity Institute for Biotechnology, Universiteit Gent; Laboratorium voor Genetica, Department of Genetics, Flanders Interuniversity Institute for Biotechnology, Universiteit Gent:Laboratoire Associe de l'Institut National de la Recherche Agronomique(France), Universiteit Gent

    1998-01-01

    The relationship between paraquat toxicity and polyamine levels was analyzed in Arabidopsis wild-type and gi-3 plants. Paraquat treatment led to an increase in putrescine, but not of spermidine and spermine content. Additionally, polyamine feeding offered high levels of protection against paraquat toxicity with spermidine being the most effective protectant.

  18. Characterization Of Laccase T-DNA Mutants In Arabidopsis thaliana

    DEFF Research Database (Denmark)

    Andersen, Jeppe R; Asp, Torben; Mansfield, Shawn

    Laccases (P-diphenol:O2 oxidoreductase; EC 1.10.3.2), also termed laccase-like multicopper oxidases, are blue copper-containing oxidases which comprise multigene families in plants. In the Arabidopsis thaliana genome, 17 laccase genes (LAC1 to LAC17) have been annotated. To identify laccases...... involved in cell wall biosynthesis in Arabidopsis primary stems we have developed homozygous T-DNA mutants for 14 individual laccases. Six laccases are highly expressed in the wild type primary stem, four of which (LAC2, LAC4, LAC12, and LAC17) show correlated gene expression with one to several genes (e...... different and distinct biochemical pathways and that laccases might be involved in polymerization of both polysaccharides and monolignols in the Arabidopsis cell wall....

  19. The scale of population structure in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Alexander Platt

    2010-02-01

    Full Text Available The population structure of an organism reflects its evolutionary history and influences its evolutionary trajectory. It constrains the combination of genetic diversity and reveals patterns of past gene flow. Understanding it is a prerequisite for detecting genomic regions under selection, predicting the effect of population disturbances, or modeling gene flow. This paper examines the detailed global population structure of Arabidopsis thaliana. Using a set of 5,707 plants collected from around the globe and genotyped at 149 SNPs, we show that while A. thaliana as a species self-fertilizes 97% of the time, there is considerable variation among local groups. This level of outcrossing greatly limits observed heterozygosity but is sufficient to generate considerable local haplotypic diversity. We also find that in its native Eurasian range A. thaliana exhibits continuous isolation by distance at every geographic scale without natural breaks corresponding to classical notions of populations. By contrast, in North America, where it exists as an exotic species, A. thaliana exhibits little or no population structure at a continental scale but local isolation by distance that extends hundreds of km. This suggests a pattern for the development of isolation by distance that can establish itself shortly after an organism fills a new habitat range. It also raises questions about the general applicability of many standard population genetics models. Any model based on discrete clusters of interchangeable individuals will be an uneasy fit to organisms like A. thaliana which exhibit continuous isolation by distance on many scales.

  20. The fate of retrotransposed processed genes in Arabidopsis thaliana.

    Science.gov (United States)

    Abdelkarim, Basma T M; Maranda, Vincent; Drouin, Guy

    2017-04-20

    Processed genes are functional genes that have arisen as a result of the retrotransposition of mRNA molecules. We found 6 genes that generated processed genes in the common ancestor of five Brassicaceae species (Arabidopsis thaliana, Arabidopsis lyrata, Capsella rubella, Brassica rapa and Thellungiella parvula). These processed genes have therefore been kept for at least 30millionyears. Analyses of the Ka/Ks ratio of these genes, and of those having given rise to them, show that they evolve relatively slowly and suggest that the processed genes maintained the same function as that of their parental gene. There is a significant negative correlation between the number of ESTs and transcripts produced and the Ka/Ks ratios of the parental genes but not of the processed genes. This suggests that selection has not yet adapted the selective pressure the processed genes experience to their expression level. However, the A. thaliana processed genes tend to be expressed in the same tissues as that of their parental genes. Furthermore, most have a CAATT-box, a TATA-box and are located about 1kb from another protein-coding gene. Altogether, our results suggest that the processed genes found in the A. thaliana genome have been kept to produce more of the same product, and in the same tissues, as that encoded by their parental gene. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

  1. Diuretics Prime Plant Immunity in Arabidopsis thaliana

    Science.gov (United States)

    Noutoshi, Yoshiteru; Ikeda, Mika; Shirasu, Ken

    2012-01-01

    Plant activators are agrochemicals that activate the plant immune system, thereby enhancing disease resistance. Due to their prophylactic and durable effects on a wide spectrum of diseases, plant activators can provide synergistic crop protection when used in combination with traditional pest controls. Although plant activators have achieved great success in wet-rice farming practices in Asia, their use is still limited. To isolate novel plant activators applicable to other crops, we screened a chemical library using a method that can selectively identify immune-priming compounds. Here, we report the isolation and characterization of three diuretics, bumetanide, bendroflumethiazide and clopamide, as immune-priming compounds. These drugs upregulate the immunity-related cell death of Arabidopsis suspension-cultured cells induced with an avirulent strain of Pseudomonas syringae pv. tomato in a concentration-dependent manner. The application of these compounds to Arabidopsis plants confers disease resistance to not only the avirulent but also a virulent strain of the pathogen. Unlike salicylic acid, an endogenous phytohormone that governs disease resistance in response to biotrophic pathogens, the three diuretic compounds analyzed here do not induce PR1 or inhibit plant growth, showing potential as lead compounds in a practical application. PMID:23144763

  2. Identification of a novel group of putative Arabidopsis thaliana beta-(1,3)-galactosyltransferases

    DEFF Research Database (Denmark)

    Qu, Yongmei; Egelund, Jack; Gilson, Paul R

    2008-01-01

    -(1,3)-Gal linkage from CAZy GT-family-31 from Arabidopsis thaliana. These analyses confirmed that 20 members of the GT-31 family contained domains/motifs typical of biochemically characterised beta-(1,3)-GTs from mammalian systems. Microarray data confirm that members of this family are expressed......-glycans in Arabidopsis thaliana....

  3. Involvement of NRAMP1 from Arabidopsis thaliana in iron transport.

    Science.gov (United States)

    Curie, C; Alonso, J M; Le Jean, M; Ecker, J R; Briat, J F

    2000-05-01

    Nramp genes code for a widely distributed class of proteins involved in a variety of processes, ranging from the control of susceptibility to bacterial infection in mammalian cells and taste behaviour in Drosophila to manganese uptake in yeast. Some of the NRAMP proteins in mammals and in yeast are capable of transporting metal ions, including iron. In plants, iron transport was shown to require a reduction/Fe(II) transport system. In Arabidopsis thaliana this process involves the IRT1 and Fro2 genes. Here we report the sequence of five NRAMP proteins from A. thaliana. Sequence comparison suggests that there are two classes of NRAMP proteins in plants: A. thaliana (At) NRAMP1 and Oriza sativa (Os) NRAMP1 and 3 (two rice isologues) represent one class, and AtNRAMP2-5 and OsNRAMP2 the other. AtNramp1 and OsNramp1 are able to complement the fet3fet4 yeast mutant defective both in low- and high-affinity iron transports, whereas AtNramp2 and OsNramp2 fail to do so. In addition, AtNramp1 transcript, but not AtNramp2 transcript, accumulates in response to iron deficiency in roots but not in leaves. Finally, overexpression of AtNramp1 in transgenic A. thaliana plants leads to an increase in plant resistance to toxic iron concentration. Taken together, these results demonstrate that AtNramp1 participates in the control of iron homoeostasis in plants.

  4. Adaptation of Arabidopsis thaliana to the Yangtze River basin.

    Science.gov (United States)

    Zou, Yu-Pan; Hou, Xing-Hui; Wu, Qiong; Chen, Jia-Fu; Li, Zi-Wen; Han, Ting-Shen; Niu, Xiao-Min; Yang, Li; Xu, Yong-Chao; Zhang, Jie; Zhang, Fu-Min; Tan, Dunyan; Tian, Zhixi; Gu, Hongya; Guo, Ya-Long

    2017-12-28

    Organisms need to adapt to keep pace with a changing environment. Examining recent range expansion aids our understanding of how organisms evolve to overcome environmental constraints. However, how organisms adapt to climate changes is a crucial biological question that is still largely unanswered. The plant Arabidopsis thaliana is an excellent system to study this fundamental question. Its origin is in the Iberian Peninsula and North Africa, but it has spread to the Far East, including the most south-eastern edge of its native habitats, the Yangtze River basin, where the climate is very different. We sequenced 118 A. thaliana strains from the region surrounding the Yangtze River basin. We found that the Yangtze River basin population is a unique population and diverged about 61,409 years ago, with gene flows occurring at two different time points, followed by a population dispersion into the Yangtze River basin in the last few thousands of years. Positive selection analyses revealed that biological regulation processes, such as flowering time, immune and defense response processes could be correlated with the adaptation event. In particular, we found that the flowering time gene SVP has contributed to A. thaliana adaptation to the Yangtze River basin based on genetic mapping. A. thaliana adapted to the Yangtze River basin habitat by promoting the onset of flowering, a finding that sheds light on how a species can adapt to locales with very different climates.

  5. Cleaning the GenBank Arabidopsis thaliana data set

    DEFF Research Database (Denmark)

    Korning, Peter G.; Hebsgaard, Stefan M.; Rouze, Pierre

    1996-01-01

    Data driven computational biology relies on the large quantities of genomic data stored in international sequence data banks. However, the possibilities are drastically impaired if the stored data is unreliable. During a project aiming to predict splice sites in the dicot Arabidopsis thaliana, we...... extracted a data set from the A. thaliana entries in GenBank. A number of simple `sanity' checks, based on the nature of the data, revealed an alarmingly high error rate. More than 15% of the most important entries extracted did contain erroneous information. In addition, a number of entries had directly...... conflicting assignments of exons and introns, not stemming from alternative splicing. In a few cases the errors are due to mere typographical misprints, which may be corrected by comparison to the original papers, but errors caused by wrong assignments of splice sites from experimental data are the most...

  6. CB5C affects the glucosinolate profile in Arabidopsis thaliana

    DEFF Research Database (Denmark)

    Vik, Daniel; Crocoll, Christoph; Andersen, Tonni Grube

    2016-01-01

    proteins support the cytochrome P450 enzymes of plant specialized metabolism and found CB5C from Arabidopsis thaliana to co-express with glucosinolate biosynthetic genes. We characterized the glucosinolate profiles of two T-DNA insertion mutants of CB5C, and found that long-chained aliphatic glucosinolates...... were reduced in one of the mutant lines - a phenotype that was exaggerated upon methyl-jasmonate treatment. These results support the hypothesis, that CB5C influences glucosinolate biosynthesis, however, the mode of action remains unknown. Furthermore, the mutants differed in their biomass response...

  7. The Arabidopsis thaliana ABC protein superfamily, a complete inventory.

    Science.gov (United States)

    Sánchez-Fernández, R; Davies, T G; Coleman, J O; Rea, P A

    2001-08-10

    We describe the first complete inventory of ATP-binding cassette (ABC) proteins from a multicellular organism, the model plant Arabidopsis thaliana. By the application of several search criteria, Arabidopsis was found to contain a total of 129 open reading frames (ORFs) capable of encoding ABC proteins, of which 103 possessed contiguous transmembrane spans and were identified as putative intrinsic membrane proteins. Fifty-two of the putative intrinsic membrane proteins contained at least two transmembrane domains (TMDs) and two nucleotide-binding folds (NBFs) and could be classified as belonging to one of five subfamilies of full-molecule transporters. The other 51 putative membrane proteins, all of which were half-molecule transporters, fell into five subfamilies. Of the remaining ORFs identified, all of which encoded proteins lacking TMDs, 11 could be classified into three subfamilies. There were no obvious homologs in other organisms for 15 of the ORFs which encoded a heterogeneous group of non-intrinsic ABC proteins (NAPs). Unrooted phylogenetic analyses substantiated the subfamily designations. Notable features of the Arabidopsis ABC superfamily was the presence of a large yeast-like PDR subfamily, and the absence of genes encoding bona fide cystic fibrosis transmembrane conductance regulator (CFTR), sulfonylurea receptor (SUR), and heavy metal tolerance factor 1 (HMT1) homologs. Arabidopsis was unusual in its large allocation of ORFs (a minimum of 0.5%) to members of the ABC protein superfamily.

  8. Multiple reference genomes and transcriptomes for Arabidopsis thaliana

    KAUST Repository

    Gan, Xiangchao

    2011-08-28

    Genetic differences between Arabidopsis thaliana accessions underlie the plants extensive phenotypic variation, and until now these have been interpreted largely in the context of the annotated reference accession Col-0. Here we report the sequencing, assembly and annotation of the genomes of 18 natural A. thaliana accessions, and their transcriptomes. When assessed on the basis of the reference annotation, one-third of protein-coding genes are predicted to be disrupted in at least one accession. However, re-annotation of each genome revealed that alternative gene models often restore coding potential. Gene expression in seedlings differed for nearly half of expressed genes and was frequently associated with cis variants within 5 kilobases, as were intron retention alternative splicing events. Sequence and expression variation is most pronounced in genes that respond to the biotic environment. Our data further promote evolutionary and functional studies in A. thaliana, especially the MAGIC genetic reference population descended from these accessions. ©2011 Macmillan Publishers Limited. All rights reserved.

  9. AtPIN: Arabidopsis thaliana Protein Interaction Network

    Directory of Open Access Journals (Sweden)

    Silva-Filho Marcio C

    2009-12-01

    Full Text Available Abstract Background Protein-protein interactions (PPIs constitute one of the most crucial conditions to sustain life in living organisms. To study PPI in Arabidopsis thaliana we have developed AtPIN, a database and web interface for searching and building interaction networks based on publicly available protein-protein interaction datasets. Description All interactions were divided into experimentally demonstrated or predicted. The PPIs in the AtPIN database present a cellular compartment classification (C3 which divides the PPI into 4 classes according to its interaction evidence and subcellular localization. It has been shown in the literature that a pair of genuine interacting proteins are generally expected to have a common cellular role and proteins that have common interaction partners have a high chance of sharing a common function. In AtPIN, due to its integrative profile, the reliability index for a reported PPI can be postulated in terms of the proportion of interaction partners that two proteins have in common. For this, we implement the Functional Similarity Weight (FSW calculation for all first level interactions present in AtPIN database. In order to identify target proteins of cytosolic glutamyl-tRNA synthetase (Cyt-gluRS (AT5G26710 we combined two approaches, AtPIN search and yeast two-hybrid screening. Interestingly, the proteins glutamine synthetase (AT5G35630, a disease resistance protein (AT3G50950 and a zinc finger protein (AT5G24930, which has been predicted as target proteins for Cyt-gluRS by AtPIN, were also detected in the experimental screening. Conclusions AtPIN is a friendly and easy-to-use tool that aggregates information on Arabidopsis thaliana PPIs, ontology, and sub-cellular localization, and might be a useful and reliable strategy to map protein-protein interactions in Arabidopsis. AtPIN can be accessed at http://bioinfo.esalq.usp.br/atpin.

  10. Building a hair: tip growth in Arabidopsis thaliana root hairs.

    Science.gov (United States)

    Carol, Rachel J; Dolan, Liam

    2002-06-29

    The Arabidopsis thaliana root hair is used as a model for studying tip growth in plants. We review recent advances, made using physiological and genetic approaches, which give rise to different, yet compatible, current views of the establishment and maintenance of tip growth in epidermal cells. For example, an active calcium influx channel localized at the tip of Arabidopsis root hairs has been identified by patch-clamp measurements. Actin has been visualized in vivo in Arabidopsis root hairs by using a green-fluorescent-protein-talin reporter and shown to form a dense mesh in the apex of the growing tip. The kojak gene, which encodes a protein similar to the catalytic subunit of cellulose synthase, is needed in the first stages of hair growth. A role for LRX1, a leucine-rich repeat extensin, in determining the morphology of the cell wall of root hairs has been established using reverse genetics. The new information can be integrated into a general and more advanced view of how these specialized plant cells grow.

  11. Redox Impact on Starch Biosynthetic Enzymes in Arabidopsis thaliana

    DEFF Research Database (Denmark)

    Skryhan, Katsiaryna

    Summary The thesis provides new insight into the influence of the plant cell redox state on the transient starch metabolism in Arabidopsis thaliana with a focus on starch biosynthetic enzymes. Two main hypotheses forms the basis of this thesis: 1) photosynthesis and starch metabolism...... are coordinated by the redox state of the cell via post-translational modification of the starch metabolic enzymes containing redox active cysteine residues and these cysteine residues became cross-linked upon oxidation providing a conformational change leading to activity loss; 2) cysteine residues...... of chloroplast enzymes can play a role not only in enzyme activity and redox sensitivity but also in protein folding and stability upon oxidation. Several redox sensitive enzymes identified in this study can serve as potential targets to control the carbon flux to and from starch during the day and night...

  12. Multimodal nonlinear imaging of arabidopsis thaliana root cell

    Science.gov (United States)

    Jang, Bumjoon; Lee, Sung-Ho; Woo, Sooah; Park, Jong-Hyun; Lee, Myeong Min; Park, Seung-Han

    2017-07-01

    Nonlinear optical microscopy has enabled the possibility to explore inside the living organisms. It utilizes ultrashort laser pulse with long wavelength (greater than 800nm). Ultrashort pulse produces high peak power to induce nonlinear optical phenomenon such as two-photon excitation fluorescence (TPEF) and harmonic generations in the medium while maintaining relatively low average energy pre area. In plant developmental biology, confocal microscopy is widely used in plant cell imaging after the development of biological fluorescence labels in mid-1990s. However, fluorescence labeling itself affects the sample and the sample deviates from intact condition especially when labelling the entire cell. In this work, we report the dynamic images of Arabidopsis thaliana root cells. This demonstrates the multimodal nonlinear optical microscopy is an effective tool for long-term plant cell imaging.

  13. A Regulatory Network Analysis of Orphan Genes in Arabidopsis Thaliana

    Science.gov (United States)

    Singh, Pramesh; Chen, Tianlong; Arendsee, Zebulun; Wurtele, Eve S.; Bassler, Kevin E.

    Orphan genes, which are genes unique to each particular species, have recently drawn significant attention for their potential usefulness for organismal robustness. Their origin and regulatory interaction patterns remain largely undiscovered. Recently, methods that use the context likelihood of relatedness to infer a network followed by modularity maximizing community detection algorithms on the inferred network to find the functional structure of regulatory networks were shown to be effective. We apply improved versions of these methods to gene expression data from Arabidopsis thaliana, identify groups (clusters) of interacting genes with related patterns of expression and analyze the structure within those groups. Focusing on clusters that contain orphan genes, we compare the identified clusters to gene ontology (GO) terms, regulons, and pathway designations and analyze their hierarchical structure. We predict new regulatory interactions and unravel the structure of the regulatory interaction patterns of orphan genes. Work supported by the NSF through Grants DMR-1507371 and IOS-1546858.

  14. Human intrinsic factor expressed in the plant Arabidopsis thaliana

    DEFF Research Database (Denmark)

    Fedosov, Sergey N; Laursen, Niels B; Nexø, Ebba

    2003-01-01

    Intrinsic factor (IF) is the gastric protein that promotes the intestinal uptake of vitamin B12. Gastric IF from animal sources is used in diagnostic tests and in vitamin pills. However, administration of animal IF to humans becomes disadvantageous because of possible pathogenic transmission...... and contamination by other B12 binders. We tested the use of recombinant plants for large-scale production of pathogen-free human recombinant IF. Human IF was successfully expressed in the recombinant plant Arabidopsis thaliana. Extract from fresh plants possessed high B12-binding capacity corresponding to 70 mg...... to recombinant IF and gastric IF were alike, as was the interaction of recombinant and native IF with the specific receptor cubilin. The data presented show that recombinant plants have a great potential as a large-scale source of human IF for analytical and therapeutic purposes....

  15. Gravitropism in leaves of Arabidopsis thaliana (L.) Heynh.

    Science.gov (United States)

    Mano, Eriko; Horiguchi, Gorou; Tsukaya, Hirokazu

    2006-02-01

    In higher plants, stems and roots show negative and positive gravitropism, respectively. However, current knowledge on the graviresponse of leaves is lacking. In this study, we analyzed the positioning and movement of rosette leaves of Arabidopsis thaliana under light and dark conditions. We found that the radial positioning of rosette leaves was not affected by the direction of gravity under continuous white light. In contrast, when plants were shifted to darkness, the leaves moved upwards, suggesting negative gravitropism. Analysis of the phosphoglucomutase and shoot gravitropism 2-1 mutants revealed that the sedimenting amyloplasts in the leaf petiole are important for gravity perception, as is the case in stems and roots. In addition, our detailed physiological analyses revealed a unique feature of leaf movement after the shift to darkness, i.e. movement could be divided into negative gravitropism and nastic movement. The orientation of rosette leaves is ascribed to a combination of these movements.

  16. Signals of speciation within Arabidopsis thaliana in comparison with its relatives

    NARCIS (Netherlands)

    Alcazar, R.; Pecinka, A.; Aarts, M.G.M.; Fransz, P.F.; Koornneef, M.

    2012-01-01

    The species within the now well-defined Arabidopsis genus provide biological materials suitable to investigate speciation and the development of reproductive isolation barriers between related species. Even within the model species A. thaliana, genetic differentiation between populations due to

  17. Adsorption and inhibition of CuO nanoparticles on Arabidopsis thaliana root

    Science.gov (United States)

    Xu, Lina

    2018-02-01

    CuO NPs, the size ranging from 20 to 80 nm were used to detect the adsorption and inhibition on the Arabidopsis thaliana roots. In this study, CuO NPs were adsorbed and agglomerated on the surface of root top after exposed for 7 days. With the increasing of CuO NPs concentrations, CuO NPs also adsorbed on the meristernatic zone. The growth of Arabidopsis thaliana lateral roots were also inhibited by CuO NPs exposure. The Inhibition were concentration dependent. The number of root top were 246, 188 and 123 per Arabidopsis thaliana, respectively. The number of root tops after CuO NPs exposure were significantly decreased compared with control groups. This results suggested the phytotoxicity of CuO NPs on Arabidopsis thaliana roots.

  18. Partial Purification and Characterization of RNase P from Arabidopsis Thaliana Tissue

    National Research Council Canada - National Science Library

    2000-01-01

    ...) molecules to give mature 5, ends has been isolated from Arabidopsis thaliana tissue. The RNase P activity was isolated by ammonium sulfate precipitation of a tissue homogenate and further purified by anion exchange chromatography...

  19. Ethylene-induced hyponastic growth in Arabidopsis thaliana is controlled by ERECTA

    NARCIS (Netherlands)

    Zanten, van M.; Snoek, L.B.; Eck-Stouten, van E.; Proveniers, M.C.G.; Torii, K.U.; Voesenek, L.A.C.J.; Peeters, A.J.M.; Millenaar, F.F.

    2010-01-01

    Plants can respond quickly and profoundly to detrimental changes in their environment. For example, Arabidopsis thaliana can induce an upward leaf movement response through differential petiole growth (hyponastic growth) to outgrow complete submergence. This response is induced by accumulation of

  20. Isolation and characterization of CNGC17 gene from Arabidopsis thaliana

    International Nuclear Information System (INIS)

    Yamagami, Mutsumi; Kobayashi, Daisuke; Hisamatsu, Shun'ichi

    2007-01-01

    Phytoremediation is a possible countermeasure for cleaning up soil contaminated by 137 Cs, and development of plants which can effectively absorb 137 Cs is important for it. It is expected that capability of Cs extraction from soil can be strengthened by genetic alteration of the Cs + root-uptake mechanism of plants. This study aimed at elucidating the uptake mechanism of Cs + for future genetic engineering. Plant roots take up Cs + from the soil solution via transport proteins at the plasma membrane of root cells. Voltage-insensitive cation channels (VICCs) are a possible transfer route of Cs + , and they are encoded by cyclic-nucleotide gated channel (CNGC) and glutamate receptor (GLR) gene families. The genome of Arabidopsis thaliana contains 20 CNGC genes. We have cloned a putative AtCNGC17 gene from cDNAs which were generated with total-RNA obtained from leaves of Arabidopsis thaliana by RT-PCR. The cDNA contained 2163 bp with an ORF that encoded a protein consisting of 721 amino acids residues. The plasmid prepared by the insertion of the gene under a Taq promoter was used to transform an E. coli deficient in the three major K + uptake systems (Kdp, Trk, and Kup). Only the E. coli with AtCNGC17 gene grew in low K + concentration minimal medium. This result suggested that the AtCNGC17 protein has a function of K + uptake. Growth rates of the E. coli cells expressing the gene were strongly inhibited by CsCl in low K + concentration minimal medium, suggesting that the AtCNGC17 transporter also carries Cs + . (author)

  1. Quantification of camalexin, a phytoalexin from Arabidopsis thaliana: a comparison of five analytical methods.

    Science.gov (United States)

    Beets, Caryn; Dubery, Ian

    2011-12-15

    Camalexin is a phytoalexin of Arabidopsis thaliana and an important component of inducible defenses. Accurate quantification of low concentrations suffers from interference by structurally related metabolites. A. thaliana plants were induced with silver nitrate and camalexin was extracted using methanol and identified and quantified by (i) TLC as a blue fluorescent band, (ii) microtiter plate-based fluorescence spectroscopy, (iii) GC on a midpolar column coupled to flame ionization detection, (iv) C(18) HPLC coupled to a photodiode detector, and (v) UPLC coupled to a mass spectrometer detector. Standard curves over the range of 0.1-15 μg ml(-1) gave R(2) values from 0.996 to 0.999. The different methods were compared and evaluated for their ability to detect and quantify increasing concentrations (camalexin. Each of the techniques presented advantages and disadvantages with regard to accuracy, precision, interference, analytical sensitivity, and limits of detection. TLC is a good qualitative technique for the identification of camalexin and fluorescence spectroscopy is subject to quenching when performed on crude extracts. Comparable results were obtained with GC-FID, HPLC-PDA, and UPLC-MS, with UPLC-MS having the added advantage of short analysis times and detection based on accurate mass. Copyright © 2011 Elsevier Inc. All rights reserved.

  2. Novel Ribonuclease Activity Differs between Fibrillarins from Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Ulises Rodriguez-Corona

    2017-10-01

    Full Text Available Fibrillarin is one of the most important nucleolar proteins that have been shown as essential for life. Fibrillarin localizes primarily at the periphery between fibrillar center and dense fibrillar component as well as in Cajal bodies. In most plants there are at least two different genes for fibrillarin. In Arabidopsis thaliana both genes show high level of expression in transcriptionally active cells. Here, we focus on two important differences between A. thaliana fibrillarins. First and most relevant is the enzymatic activity by AtFib2. The AtFib2 shows a novel ribonuclease activity that is not seen with AtFib1. Second is a difference in the ability to interact with phosphoinositides and phosphatidic acid between both proteins. We also show that the novel ribonuclease activity as well as the phospholipid binding region of fibrillarin is confine to the GAR domain. The ribonuclease activity of fibrillarin reveals in this study represents a new role for this protein in rRNA processing.

  3. Exploring Arabidopsis thaliana Root Endophytes via Single-Cell Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Lundberg, Derek; Woyke, Tanja; Tringe, Susannah; Dangl, Jeff

    2014-03-19

    Land plants grow in association with microbial communities both on their surfaces and inside the plant (endophytes). The relationships between microbes and their host can vary from pathogenic to mutualistic. Colonization of the endophyte compartment occurs in the presence of a sophisticated plant immune system, implying finely tuned discrimination of pathogens from mutualists and commensals. Despite the importance of the microbiome to the plant, relatively little is known about the specific interactions between plants and microbes, especially in the case of endophytes. The vast majority of microbes have not been grown in the lab, and thus one of the few ways of studying them is by examining their DNA. Although metagenomics is a powerful tool for examining microbial communities, its application to endophyte samples is technically difficult due to the presence of large amounts of host plant DNA in the sample. One method to address these difficulties is single-cell genomics where a single microbial cell is isolated from a sample, lysed, and its genome amplified by multiple displacement amplification (MDA) to produce enough DNA for genome sequencing. This produces a single-cell amplified genome (SAG). We have applied this technology to study the endophytic microbes in Arabidopsis thaliana roots. Extensive 16S gene profiling of the microbial communities in the roots of multiple inbred A. thaliana strains has identified 164 OTUs as being significantly enriched in all the root endophyte samples compared to their presence in bulk soil.

  4. Endophytic actinobacteria induce defense pathways in Arabidopsis thaliana.

    Science.gov (United States)

    Conn, V M; Walker, A R; Franco, C M M

    2008-02-01

    Endophytic actinobacteria, isolated from healthy wheat tissue, which are capable of suppressing a number wheat fungal pathogens both in vitro and in planta, were investigated for the ability to activate key genes in the systemic acquired resistance (SAR) or the jasmonate/ethylene (JA/ET) pathways in Arabidopsis thaliana. Inoculation of A. thaliana (Col-0) with selected endophytic strains induced a low level of SAR and JA/ET gene expression, measured using quantitative polymerase chain reaction. Upon pathogen challenge, endophyte-treated plants demonstrated a higher abundance of defense gene expression compared with the non-endophyte-treated controls. Resistance to the bacterial pathogen Erwinia carotovora subsp. carotovora required the JA/ET pathway. On the other hand, resistance to the fungal pathogen Fusarium oxysporum involved primarily the SAR pathway. The endophytic actinobacteria appear to be able to "prime" both the SAR and JA/ET pathways, upregulating genes in either pathway depending on the infecting pathogen. Culture filtrates of the endophytic actinobacteria were investigated for the ability to also activate defense pathways. The culture filtrate of Micromonospora sp. strain EN43 grown in a minimal medium resulted in the induction of the SAR pathway; however, when grown in a complex medium, the JA/ET pathway was activated. Further analysis using Streptomyces sp. strain EN27 and defense-compromised mutants of A. thaliana indicated that resistance to E. carotovora subsp. carotovora occurred via an NPR1-independent pathway and required salicylic acid whereas the JA/ET signaling molecules were not essential. In contrast, resistance to F. oxysporum mediated by Streptomyces sp. strain EN27 occurred via an NPR1-dependent pathway but also required salicylic acid and was JA/ET independent.

  5. Functional diversification of thylakoidal processing peptidases in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Shih-Chi Hsu

    Full Text Available Thylakoidal processing peptidase (TPP is responsible for removing amino-terminal thylakoid-transfer signals from several proteins in the thylakoid lumen. Three TPP isoforms are encoded by the nuclear genome of Arabidopsis thaliana. Previous studies showed that one of them termed plastidic type I signal peptidase 1 (Plsp1 was necessary for processing three thylakoidal proteins and one protein in the chloroplast envelope in vivo. The lack of Plsp1 resulted in seedling lethality, apparently due to disruption of proper thylakoid development. The physiological roles of the other two TPP homologs remain unknown. Here we show that the three A. thaliana TPP isoforms evolved to acquire diverse functions. Phylogenetic analysis revealed that TPP may have originated before the endosymbiotic event, and that there are two groups of TPP in seed plants: one includes Plsp1 and another comprises the other two A. thaliana TPP homologs, which are named as Plsp2A and Plsp2B in this study. The duplication leading to the two groups predates the gymnosperm-angiosperm divergence, and the separation of Plsp2A and Plsp2B occurred after the Malvaceae-Brassicaceae diversification. Quantitative reverse transcription-PCR assay revealed that the two PLSP2 genes were co-expressed in both photosynthetic tissues and roots, whereas the PLSP1 transcript accumulated predominantly in photosynthetic tissues. Both PLSP2 genes were expressed in the aerial parts of the plsp1-null mutant at levels comparable to those in wild-type plants. The seedling-lethal phenotype of the plsp1-null mutant could be rescued by a constitutive expression of Plsp1 cDNA but not by that of Plsp2A or Plsp2B. These results indicate that Plsp1 and Plsp2 evolved to function differently, and that neither of the Plsp2 isoforms is necessary for proper thylakoid development in photosynthetic tissues.

  6. Homeopathic Treatment of Arabidopsis thaliana Plants Infected with Pseudomonas syringae

    Directory of Open Access Journals (Sweden)

    Devika Shah-Rossi

    2009-01-01

    Full Text Available Homeopathic basic research is still in the screening phase to identify promising model systems that are adapted to the needs and peculiarities of homeopathic medicine and pharmacy. We investigated the potential of a common plant-pathogen system, Arabidopsis thaliana infected with the virulent bacteria Pseudomonas syringae, regarding its response towards a homeopathic treatment. A. thaliana plants were treated with homeopathic preparations before and after infection. Outcome measure was the number of P. syringae bacteria in the leaves of A. thaliana, assessed in randomized and blinded experiments. After a screening of 30 homeopathic preparations, we investigated the effect of Carbo vegetabilis 30x, Magnesium phosphoricum 30x, Nosode 30x, Biplantol (a homeopathic complex remedy, and Biplantol 30x on the infection rate in five or six independent experiments in total. The screening yielded significant effects for four out of 30 tested preparations. In the repeated experimental series, only the homeopathic complex remedy Biplantol induced a significant reduction of the infection rate (p = 0.01; effect size, d = 0.38. None of the other four repeatedly tested preparations (Carbo vegetabilis 30x, Magnesium phosphoricum 30x, Nosode 30x, Biplantol 30x yielded significant effects in the overall evaluation. This phytopathological model yielded a small to medium effect size and thus might be of interest for homeopathic basic research after further improvement. Compared to Bion (a common SAR inducer used as positive control, the magnitude of the treatment effect of Biplantol was about 50%. Thus, homeopathic formulations might have a potential for the treatment of plant diseases after further optimization. However, the ecological impact should be investigated more closely before widespread application.

  7. The RNA-binding protein repertoire of Arabidopsis thaliana

    KAUST Repository

    Marondedze, Claudius

    2016-07-11

    RNA-binding proteins (RBPs) have essential roles in determining the fate of RNA from synthesis to decay and have been studied on a protein-by-protein basis, or computationally based on a number of well-characterised RNA-binding domains. Recently, high-throughput methods enabled the capture of mammalian RNA-binding proteomes. To gain insight into the role of Arabidopsis thaliana RBPs at the systems level, we have employed interactome capture techniques using cells from different ecotypes grown in cultures and leaves. In vivo UV-crosslinking of RNA to RBPs, oligo(dT) capture and mass spectrometry yielded 1,145 different proteins including 550 RBPs that either belong to the functional category ‘RNA-binding’, have known RNA-binding domains or have orthologs identified in mammals, C. elegans, or S. cerevisiae in addition to 595 novel candidate RBPs. We noted specific subsets of RBPs in cultured cells and leaves and a comparison of Arabidopsis, mammalian, C. elegans, and S. cerevisiae RBPs reveals a common set of proteins with a role in intermediate metabolism, as well as distinct differences suggesting that RBPs are also species and tissue specific. This study provides a foundation for studies that will advance our understanding of the biological significance of RBPs in plant developmental and stimulus specific responses.

  8. Arabidopsis thaliana and Thlaspi caerulescens respond comparably to low zinc supply

    NARCIS (Netherlands)

    Talukdar, S.; Aarts, M.G.M.

    2008-01-01

    The main objective of this research was to study the response of Arabidopsis thaliana L. and Thlaspi caerulescens J. & C. Presl to different Zn supplies. The A. thaliana plants were exposed to Zn-deficiency (0 and 0.05 ¿M Zn) and compared to the plants grown on media containing standard Zn (2

  9. Crystallization and preliminary X-ray analysis of immunophilin-like FKBP42 from Arabidopsis thaliana

    Energy Technology Data Exchange (ETDEWEB)

    Eckhoff, Andreas; Granzin, Joachim [Institut für Biologische Informationsverarbeitung (IBI-2, Biologische Strukturforschung), Forschungszentrum Jülich GmbH, D-52425 Jülich (Germany); Kamphausen, Thilo [Max-Planck-Forschungsstelle für Enzymologie der Proteinfaltung, D-06120 Halle (Germany); Büldt, Georg [Institut für Biologische Informationsverarbeitung (IBI-2, Biologische Strukturforschung), Forschungszentrum Jülich GmbH, D-52425 Jülich (Germany); Schulz, Burkhard [Universität Tübingen, ZMBP, D-72076 Tübingen (Germany); Purdue University, Department of Horticulture and Landscape Architecture, West Lafayette, IN 47907 (United States); Weiergräber, Oliver H., E-mail: o.h.weiergraeber@fz-juelich.de [Institut für Biologische Informationsverarbeitung (IBI-2, Biologische Strukturforschung), Forschungszentrum Jülich GmbH, D-52425 Jülich (Germany)

    2005-04-01

    The crystallization of FKBP42, a multi-domain member of the FK506-binding protein family, from the plant A. thaliana is reported. Two fragments of FKBP42 from Arabidopsis thaliana covering differing lengths of the molecule have been expressed, purified and crystallized. For each construct, crystals belonging to two different space groups were obtained and subjected to preliminary X-ray analysis.

  10. Crystallization and preliminary X-ray analysis of immunophilin-like FKBP42 from Arabidopsis thaliana

    International Nuclear Information System (INIS)

    Eckhoff, Andreas; Granzin, Joachim; Kamphausen, Thilo; Büldt, Georg; Schulz, Burkhard; Weiergräber, Oliver H.

    2005-01-01

    The crystallization of FKBP42, a multi-domain member of the FK506-binding protein family, from the plant A. thaliana is reported. Two fragments of FKBP42 from Arabidopsis thaliana covering differing lengths of the molecule have been expressed, purified and crystallized. For each construct, crystals belonging to two different space groups were obtained and subjected to preliminary X-ray analysis

  11. Structure and organ specificity of an anionic peroxidase from Arabidopsis thaliana cell suspension culture

    DEFF Research Database (Denmark)

    Ostergaard, L; Abelskov, A K; Mattsson, O

    1996-01-01

    The predominant peroxidase (pI 3.5) (E.C. 1.11.1.7) of an Arabidopsis thaliana cell suspension culture was purified and partially sequenced. Oligonucleotides were designed and a specific probe was obtained. A cDNA clone was isolated from an Arabidopsis cell suspension cDNA library and completely...

  12. FYVE zinc-finger proteins in the plant model Arabidopsis thaliana

    DEFF Research Database (Denmark)

    Jensen, R B; La Cour, T; Albrethsen, J

    2001-01-01

    Classic FYVE zinc-finger domains recognize the phosphoinositide signal PtdIns3P and share the basic (R/K)(1)(R/K)HHCR(6) (single-letter amino acid codes) consensus sequence. This domain is present in predicted PtdIns3P 5-kinases and lipases from Arabidopsis thaliana. Other Arabidopsis proteins...

  13. Multi-element bioimaging of Arabidopsis thaliana roots

    DEFF Research Database (Denmark)

    Persson, Daniel Olof; Chen, Anle; Aarts, Mark G.M.

    2016-01-01

    Better understanding of root function is central for the development of plants with more efficient nutrient uptake and translocation. We here present a method for multielement bioimaging at the cellular level in roots of the genetic model system Arabidopsis (Arabidopsis thaliana). Using conventio...

  14. Expression pattern of the Arabidopsis thaliana AtEP3/AtchitIV endocitinase gene

    NARCIS (Netherlands)

    Passarinho, P.A.; Hengel, van A.J.; Fransz, P.F.; Vries, de S.C.

    2001-01-01

    The carrot (Daucus carota L.) EP3 chitinase was shown to be essential for somatic embryo formation in a carrot mutant cell line. We identified the Arabidopsis thaliana (L.) Heynh. ortholog of the carrot EP3-3 chitinase gene, designated as AtEP3/AtchitIV and analyzed its expression in Arabidopsis by

  15. Specific Arabidopsis thaliana malic enzyme isoforms can provide anaplerotic pyruvate carboxylation function in Saccharomyces cerevisiae

    NARCIS (Netherlands)

    Badia, Mariana Beatriz; Mans, R.; Lis, A.V.; Tronconi, Marcos Ariel; Arias, Cintia Lucía; Maurino, Verónica Graciela; Andreo, Carlos Santiago; Drincovich, María Fabiana; van Maris, A.J.A.; Gerrard Wheeler, Mariel Claudia

    2017-01-01

    NAD(P)-malic enzyme (NAD(P)-ME) catalyzes the reversible oxidative decarboxylation of malate to pyruvate, CO2, and NAD(P)H and is present as a multigene family in Arabidopsis thaliana. The carboxylation reaction catalyzed by purified recombinant Arabidopsis NADP-ME proteins is faster

  16. Arabidopsis thaliana mTERF proteins: evolution and functional classification

    Directory of Open Access Journals (Sweden)

    Tatjana eKleine

    2012-10-01

    Full Text Available Organellar gene expression (OGE is crucial for plant development, photosynthesis and respiration, but our understanding of the mechanisms that control it is still relatively poor. Thus, OGE requires various nucleus-encoded proteins that promote transcription, splicing, trimming and editing of organellar RNAs, and regulate translation. In metazoans, proteins of the mitochondrial Transcription tERmination Factor (mTERF family interact with the mitochondrial chromosome and regulate transcriptional initiation and termination. Sequencing of the Arabidopsis thaliana genome led to the identification of a diversified MTERF gene family but, in contrast to mammalian mTERFs, knowledge about the function of these proteins in photosynthetic organisms is scarce. In this hypothesis article, I show that tandem duplications and one block duplication contributed to the large number of MTERF genes in A. thaliana, and propose that the expansion of the family is related to the evolution of land plants. The MTERF genes - especially the duplicated genes - display a number of distinct mRNA accumulation patterns, suggesting functional diversification of mTERF proteins to increase adaptability to environmental changes. Indeed, hypothetical functions for the different mTERF proteins can be predicted using co-expression analysis and gene ontology annotations. On this basis, mTERF proteins can be sorted into five groups. Members of the chloroplast and chloroplast-associated clusters are principally involved in chloroplast gene expression, embryogenesis and protein catabolism, while representatives of the mitochondrial cluster seem to participate in DNA and RNA metabolism in that organelle. Moreover, members of the mitochondrion-associated cluster and the low expression group may act in the nucleus and/or the cytosol. As proteins involved in OGE and presumably nuclear gene expression, mTERFs are ideal candidates for the coordination of the expression of organelle and nuclear

  17. Characterization of carbon ion-induced mutations in Arabidopsis thaliana

    International Nuclear Information System (INIS)

    Shikazono, N.; Suzuki, C.; Kitamura, S.; Watanabe, H.; Tano, S.; Tanaka, A.

    2003-01-01

    Full text: Irradiation of Arabidopsis thaliana by carbon ions was carried out to investigate the mutational effect of ion particles in higher plants. The averaged mutation rate of carbon ions was 2.0 X 10 -6 / Gy, which was 18-fold higher than that of electrons. PCR analysis of the carbon ion-induced mutants showed that, out of 28 mutant alleles, 14 had point-like mutations within the gene, while 14 contained large structural alterations. In the case of 12 electron-induced mutants, 9 had point-like mutations within the gene, while 3 contained large structural alterations. These results suggest that carbon ions are more likely to induce large structural alterations compared with electrons. Further sequence analysis revealed that most of the point-like mutations induced by carbon ions were short deletions. In the case of rearrangements, DNA strand breaks were found to be rejoined using, if present, short homologous sequences for both types of radiation. After carbon ion-irradiation, small deletions were frequently observed around the breakpoints, whereas duplications of terminal sequence were found after electron-irradiation. These results suggest that non-homologous end joining (NHEJ) pathway operates after plant cells are exposed to both ion particles and electrons but that different mode of rejoining deals with the broken ends produced by each radiation. From the present results, it seems reasonable to assume that carbon ions could predominantly induce null mutations in Arabidopsis. The fact that the molecular nature of carbon ion-induced mutation was different from that of electrons and that the molecular mechanisms of cells to induce mutations appeared to be also different implicates that ion particle is not only valuable as a new mutagen but also useful as a new tool to study repair mechanisms of certain types of DNA damage

  18. Control of seed development in Arabidopsis thaliana by atmospheric oxygen

    Science.gov (United States)

    Kuang, A.; Crispi, M.; Musgrave, M. E.

    1998-01-01

    Seed development is known to be inhibited completely when plants are grown in oxygen concentrations below 5.1 kPa, but apart from reports of decreased seed weight little is known about embryogenesis at subambient oxygen concentrations above this critical level. Arabidopsis thaliana (L.) Heynh. plants were grown full term under continuous light in premixed atmospheres with oxygen partial pressures of 2.5, 5.1, 10.1, 16.2 and 21.3 kPa O2, 0.035 kPa CO2 and the balance nitrogen. Seeds were harvested for germination tests and microscopy when siliques had yellowed. Seed germination was depressed in O2 treatments below 16.2 kPa, and seeds from plants grown in 2.5 kPa O2 did not germinate at all. Fewer than 25% of the seeds from plants grown in 5.1 kPa oxygen germinated and most of the seedlings appeared abnormal. Light and scanning electron microscopic observation of non-germinated seeds showed that these embryos had stopped growing at different developmental stages depending upon the prevailing oxygen level. Embryos stopped growing at the heart-shaped to linear cotyledon stage in 5.1 kPa O2, at around the curled cotyledon stage in 10.1 kPa O2, and at the premature stage in 16.2 kPa O2. Globular and heart-shaped embryos were observed in sectioned seeds from plants grown in 2.5 kPa O2. Tissue degeneration caused by cell autolysis and changes in cell structure were observed in cotyledons and radicles. Transmission electron microscopy of mature seeds showed that storage substances, such as protein bodies, were reduced in subambient oxygen treatments. The results demonstrate control of embryo development by oxygen in Arabidopsis.

  19. Transcriptional responses of Arabidopsis thaliana plants to As (V stress

    Directory of Open Access Journals (Sweden)

    Yuan Joshua S

    2008-08-01

    Full Text Available Abstract Background Arsenic is toxic to plants and a common environmental pollutant. There is a strong chemical similarity between arsenate [As (V] and phosphate (Pi. Whole genome oligonucleotide microarrays were employed to investigate the transcriptional responses of Arabidopsis thaliana plants to As (V stress. Results Antioxidant-related genes (i.e. coding for superoxide dismutases and peroxidases play prominent roles in response to arsenate. The microarray experiment revealed induction of chloroplast Cu/Zn superoxide dismutase (SOD (at2g28190, Cu/Zn SOD (at1g08830, as well as an SOD copper chaperone (at1g12520. On the other hand, Fe SODs were strongly repressed in response to As (V stress. Non-parametric rank product statistics were used to detect differentially expressed genes. Arsenate stress resulted in the repression of numerous genes known to be induced by phosphate starvation. These observations were confirmed with qRT-PCR and SOD activity assays. Conclusion Microarray data suggest that As (V induces genes involved in response to oxidative stress and represses transcription of genes induced by phosphate starvation. This study implicates As (V as a phosphate mimic in the cell by repressing genes normally induced when available phosphate is scarce. Most importantly, these data reveal that arsenate stress affects the expression of several genes with little or unknown biological functions, thereby providing new putative gene targets for future research.

  20. Desensitization and recovery of phototropic responsiveness in Arabidopsis thaliana

    International Nuclear Information System (INIS)

    Janoudi, A.K.; Poff, K.L.

    1993-01-01

    Phototropism is induced by blue light, which also induces desensitization, a partial or total loss of phototropic responsiveness. The fluence and fluence-rate dependence of densensitization and recovery from desensitization have been measured for etiolated and red light (669-nm) preirradiated Arabidopsis thaliana seedlings. The extent of desensitization increased as the fluence of the desensitizing 450-nm light was increased from 0.3 to 60 μmol m -2 s -1 . At equal fluences, blue light caused more desensitization when given at a fluence rate of 1.0 μmol m -2 s -1 than at 0.3 μmol m -2 s -1 . In addition, seedlings irradiated with blue light at the higher fluence rate required a longer recovery time than seedlings irradiated at the lower fluence rate. A red light preirradiation, probably mediated via phytochrome, decreased the time required for recovery from desensitization. The minimum time for detectable recovery was about 65 s, and the maximum time observed was about 10 min. It is proposed that the descending arm of the fluence-response relationship for first positive phototropism is a consequence of desensitization, and that the time threshold for second positive phototropism establishes a period during which recovery from desensitization occurs. 11 refs., 6 figs

  1. Adaptation response of Arabidopsis thaliana to random positioning

    Science.gov (United States)

    Kittang, A.-I.; Winge, P.; van Loon, J. J. W. A.; Bones, A. M.; Iversen, T.-H.

    2013-10-01

    Arabidopsis thaliana seedlings were exposed on a Random Positioning Machine (RPM) under light conditions for 16 h and the samples were analysed using microarray techniques as part of a preparation for a space experiment on the International Space Station (ISS). The results demonstrated a moderate to low regulation of 55 genes (genes). Genes encoding proteins associated with the chaperone system (e.g. heat shock proteins, HSPs) and enzymes in the flavonoid biosynthesis were induced. Most of the repressed genes were associated with light and sugar responses. Significant up-regulation of selected HSP genes was found by quantitative Real-Time PCR in 1 week old plants after the RPM exposure both in light and darkness. Higher quantity of DPBA (diphenylboric acid 2-amino-ethyl ester) staining was observed in the whole root and in the root elongation zone of the seedlings exposed on the RPM by use of fluorescent microscopy, indicating higher flavonoid content. The regulated genes and an increase of flavonoids are related to several stresses, but increased occurrence of HSPs and flavonoids are also representative for normal growth (e.g. gravitropism). The response could be a direct stress response or an integrated response of the two signal pathways of light and gravity resulting in an overall light response.

  2. Molecule mechanism of stem cells in Arabidopsis thaliana.

    Science.gov (United States)

    Zhang, Wenjin; Yu, Rongming

    2014-07-01

    Plants possess the ability to continually produce new tissues and organs throughout their life. Unlike animals, plants are exposed to extreme variations in environmental conditions over the course of their lives. The vitality of plants is so powerful that they can survive several hundreds of years or even more making it an amazing miracle that comes from plant stem cells. The stem cells continue to divide to renew themselves and provide cells for the formation of leaves, stems, and flowers. Stem cells are not only quiescent but also immortal, pluripotent and homeostatic. Stem cells are the magic cells that repair tissues and regenerate organs. During the past decade, scholars around the world have paid more and more attention toward plant stem cells. At present, the major challenge is in relating molecule action mechanism to root apical meristem, shoot apical meristem and vascular system. The coordination between stem cells maintenance and differentiation is critical for normal plant growth and development. Elements such as phytohormones, transcription factors and some other known or unknown genes cooperate to balance this process. In this review, Arabidopsis thaliana as a pioneer system, we highlight recent developments in molecule modulating, illustrating how plant stem cells generate new mechanistic insights into the regulation of plants growth and development.

  3. Lagging adaptation to warming climate in Arabidopsis thaliana.

    Science.gov (United States)

    Wilczek, Amity M; Cooper, Martha D; Korves, Tonia M; Schmitt, Johanna

    2014-06-03

    If climate change outpaces the rate of adaptive evolution within a site, populations previously well adapted to local conditions may decline or disappear, and banked seeds from those populations will be unsuitable for restoring them. However, if such adaptational lag has occurred, immigrants from historically warmer climates will outperform natives and may provide genetic potential for evolutionary rescue. We tested for lagging adaptation to warming climate using banked seeds of the annual weed Arabidopsis thaliana in common garden experiments in four sites across the species' native European range: Valencia, Spain; Norwich, United Kingdom; Halle, Germany; and Oulu, Finland. Genotypes originating from geographic regions near the planting site had high relative fitness in each site, direct evidence for broad-scale geographic adaptation in this model species. However, genotypes originating in sites historically warmer than the planting site had higher average relative fitness than local genotypes in every site, especially at the northern range limit in Finland. This result suggests that local adaptive optima have shifted rapidly with recent warming across the species' native range. Climatic optima also differed among seasonal germination cohorts within the Norwich site, suggesting that populations occurring where summer germination is common may have greater evolutionary potential to persist under future warming. If adaptational lag has occurred over just a few decades in banked seeds of an annual species, it may be an important consideration for managing longer-lived species, as well as for attempts to conserve threatened populations through ex situ preservation.

  4. Multiple paths to similar germination behavior in Arabidopsis thaliana.

    Science.gov (United States)

    Burghardt, Liana T; Edwards, Brianne R; Donohue, Kathleen

    2016-02-01

    Germination timing influences plant fitness, and its sensitivity to temperature may cause it to change as climate shifts. These changes are likely to be complex because temperatures that occur during seed maturation and temperatures that occur post-dispersal interact to define germination timing. We used the model organism Arabidopsis thaliana to determine how flowering time (which defines seed-maturation temperature) and post-dispersal temperature influence germination and the expression of genetic variation for germination. Germination responses to temperature (germination envelopes) changed as seeds aged, or after-ripened, and these germination trajectories depended on seed-maturation temperature and genotype. Different combinations of genotype, seed-maturation temperature, and after-ripening produced similar germination envelopes. Likewise, different genotypes and seed-maturation temperatures combined to produce similar germination trajectories. Differences between genotypes were most likely to be observed at high and low germination temperatures. The germination behavior of some genotypes responds weakly to maternal temperature but others are highly plastic. We hypothesize that weak dormancy induction could synchronize germination of seeds dispersed at different times. By contrast, we hypothesize that strongly responsive genotypes may spread offspring germination over several possible germination windows. Considering germination responses to temperature is important for predicting phenology expression and evolution in future climates. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  5. Functional bias in molecular evolution rate of Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Anandakrishnan Ramu

    2010-05-01

    Full Text Available Abstract Background Characteristics derived from mutation and other mechanisms that are advantageous for survival are often preserved during evolution by natural selection. Some genes are conserved in many organisms because they are responsible for fundamental biological function, others are conserved for their unique functional characteristics. Therefore one would expect the rate of molecular evolution for individual genes to be dependent on their biological function. Whether this expectation holds for genes duplicated by whole genome duplication is not known. Results We empirically demonstrate here, using duplicated genes generated from the Arabidopsis thaliana α-duplication event, that the rate of molecular evolution of genes duplicated in this event depend on biological function. Using functional clustering based on gene ontology annotation of gene pairs, we show that some duplicated genes, such as defense response genes, are under weaker purifying selection or under stronger diversifying selection than other duplicated genes, such as protein translation genes, as measured by the ratio of nonsynonymous to synonymous divergence (dN/dS. Conclusions These results provide empirical evidence indicating that molecular evolution rate for genes duplicated in whole genome duplication, as measured by dN/dS, may depend on biological function, which we characterize using gene ontology annotation. Furthermore, the general approach used here provides a framework for comparative analysis of molecular evolution rate for genes based on their biological function.

  6. Arabidopsis thaliana cells: a model to evaluate the virulence of Pectobacterium carotovorum.

    Science.gov (United States)

    Terta, Meriam; Kettani-Halabi, Mohamed; Ibenyassine, Khadija; Tran, Daniel; Meimoun, Patrice; M'hand, Raja Ait; El-Maarouf-Bouteau, Hayat; Val, Florence; Ennaji, M Mustapha; Bouteau, François

    2010-02-01

    Pectobacterium carotovorum are economically important plant pathogens that cause plant soft rot. These enterobacteria display high diversity world-wide. Their pathogenesis depends on production and secretion of virulence factors such as plant cell wall-degrading enzymes, type III effectors, a necrosis-inducing protein, and a secreted virulence factor from Xanthomonas spp., which are tightly regulated by quorum sensing. Pectobacterium carotovorum also present pathogen-associated molecular patterns that could participate in their pathogenicity. In this study, by using suspension cells of Arabidopsis thaliana, we correlate plant cell death and pectate lyase activities during coinfection with different P. carotovorum strains. When comparing soft rot symptoms induced on potato slices with pectate lyase activities and plant cell death observed during coculture with Arabidopsis thaliana cells, the order of strain virulence was found to be the same. Therefore, Arabidopsis thaliana cells could be an alternative tool to evaluate rapidly and efficiently the virulence of different P. carotovorum strains.

  7. Effects of pH on uranium uptake and oxidative stress responses induced in Arabidopsis thaliana

    OpenAIRE

    Saenen, Eline; Horemans, Nele; Vanhoudt, Nathalie; Vandenhove, Hildegarde; Biermans, Geert; Van Hees, May; Wannijn, Jean; Vangronsveld, Jaco; Cuypers, Ann

    2013-01-01

    Uranium (U) causes oxidative stress in Arabidopsis thaliana plants grown at pH 5.5. However, U speciation and its toxicity strongly depend on environmental parameters, for example pH. It is unknown how different U species determine U uptake and translocation within plants and how they might affect the oxidative defense mechanisms of these plants. The present study analyzed U uptake and oxidative stress-related responses in A. thaliana (Columbia ecotype) under contrasted U chemical speciation ...

  8. Functional genetics of intraspecific ecological interactions in Arabidopsis thaliana.

    Science.gov (United States)

    Wolf, Jason B; Mutic, Joshua J; Kover, Paula X

    2011-05-12

    Studying the genetic basis of traits involved in ecological interactions is a fundamental part of elucidating the connections between evolutionary and ecological processes. Such knowledge allows one to link genetic models of trait evolution with ecological models describing interactions within and between species. Previous work has shown that connections between genetic and ecological processes in Arabidopsis thaliana may be mediated by the fact that quantitative trait loci (QTL) with 'direct' effects on traits of individuals also have pleiotropic 'indirect' effects on traits expressed in neighbouring plants. Here, we further explore these connections by examining functional relationships between traits affected directly and indirectly by the same QTL. We develop a novel approach using structural equation models (SEMs) to determine whether observed pleiotropic effects result from traits directly affected by the QTL in focal individuals causing the changes in the neighbours' phenotypes. This hypothesis was assessed using SEMs to test whether focal plant phenotypes appear to mediate the connection between the focal plants' genotypes and the phenotypes of their neighbours, or alternatively, whether the connection between the focal plants' genotypes and the neighbours' phenotypes is mediated by unmeasured traits. We implement this analysis using a QTL of major effect that maps to the well-characterized flowering locus, FRIGIDA. The SEMs support the hypothesis that the pleiotropic indirect effects of this locus arise from size and developmental timing-related traits in focal plants affecting the expression of developmental traits in their neighbours. Our findings provide empirical insights into the genetics and nature of intraspecific ecological interactions. Our technique holds promise in directing future work into the genetic basis and functional relationship of traits mediating and responding to ecological interactions.

  9. Alanine aminotransferase variants conferring diverse NUE phenotypes in Arabidopsis thaliana.

    Science.gov (United States)

    McAllister, Chandra H; Good, Allen G

    2015-01-01

    Alanine aminotransferase (AlaAT, E.C. 2.6.1.2), is a pyridoxal-5'-phosphate-dependent (PLP) enzyme that catalyzes the reversible transfer of an amino group from alanine to 2-oxoglutarate to produce glutamate and pyruvate, or vice versa. It has been well documented in both greenhouse and field studies that tissue-specific over-expression of AlaAT from barley (Hordeum vulgare, HvAlaAT) results in a significant increase in plant NUE in both canola and rice. While the physical phenotypes associated with over-expression of HvAlaAT have been well characterized, the role this enzyme plays in vivo to create a more N efficient plant remains unknown. Furthermore, the importance of HvAlaAT, in contrast to other AlaAT enzyme homologues in creating this phenotype has not yet been explored. To address the role of AlaAT in NUE, AlaAT variants from diverse sources and different subcellular locations, were expressed in the wild-type Arabidopsis thaliana Col-0 background and alaat1;2 (alaat1-1;alaat2-1) knockout background in various N environments. The analysis and comparison of both the physical and physiological properties of AlaAT over-expressing transgenic plants demonstrated significant differences between plants expressing the different AlaAT enzymes under different external conditions. This analysis indicates that the over-expression of AlaAT variants other than HvAlaAT in crop plants could further increase the NUE phenotype(s) previously observed.

  10. Adaptive diversification of growth allometry in the plant Arabidopsis thaliana.

    Science.gov (United States)

    Vasseur, François; Exposito-Alonso, Moises; Ayala-Garay, Oscar J; Wang, George; Enquist, Brian J; Vile, Denis; Violle, Cyrille; Weigel, Detlef

    2018-03-27

    Seed plants vary tremendously in size and morphology; however, variation and covariation in plant traits may be governed, at least in part, by universal biophysical laws and biological constants. Metabolic scaling theory (MST) posits that whole-organismal metabolism and growth rate are under stabilizing selection that minimizes the scaling of hydrodynamic resistance and maximizes the scaling of resource uptake. This constrains variation in physiological traits and in the rate of biomass accumulation, so that they can be expressed as mathematical functions of plant size with near-constant allometric scaling exponents across species. However, the observed variation in scaling exponents calls into question the evolutionary drivers and the universality of allometric equations. We have measured growth scaling and fitness traits of 451 Arabidopsis thaliana accessions with sequenced genomes. Variation among accessions around the scaling exponent predicted by MST was correlated with relative growth rate, seed production, and stress resistance. Genomic analyses indicate that growth allometry is affected by many genes associated with local climate and abiotic stress response. The gene with the strongest effect, PUB4 , has molecular signatures of balancing selection, suggesting that intraspecific variation in growth scaling is maintained by opposing selection on the trade-off between seed production and abiotic stress resistance. Our findings suggest that variation in allometry contributes to local adaptation to contrasting environments. Our results help reconcile past debates on the origin of allometric scaling in biology and begin to link adaptive variation in allometric scaling to specific genes. Copyright © 2018 the Author(s). Published by PNAS.

  11. The Hidden Geometries of the Arabidopsis thaliana Epidermis

    KAUST Repository

    Staff, Lee

    2012-09-11

    The quest for the discovery of mathematical principles that underlie biological phenomena is ancient and ongoing. We present a geometric analysis of the complex interdigitated pavement cells in the Arabidopsis thaliana (Col.) adaxial epidermis with a view to discovering some geometric characteristics that may govern the formation of this tissue. More than 2,400 pavement cells from 10, 17 and 24 day old leaves were analyzed. These interdigitated cells revealed a number of geometric properties that remained constant across the three age groups. In particular, the number of digits per cell rarely exceeded 15, irrespective of cell area. Digit numbers per 100 ?m2 cell area reduce with age and as cell area increases, suggesting early developmental programming of digits. Cell shape proportions as defined by length:width ratios were highly conserved over time independent of the size and, interestingly, both the mean and the medians were close to the golden ratio 1.618034. With maturity, the cell area:perimeter ratios increased from a mean of 2.0 to 2.4. Shape properties as defined by the medial axis transform (MAT) were calculated and revealed that branch points along the MAT typically comprise one large and two small angles. These showed consistency across the developmental stages considered here at 140° (± 5°) for the largest angles and 110° (± 5°) for the smaller angles. Voronoi diagram analyses of stomatal center coordinates revealed that giant pavement cells (?500 ?m2) tend to be arranged along Voronoi boundaries suggesting that they could function as a scaffold of the epidermis. In addition, we propose that pavement cells have a role in spacing and positioning of the stomata in the growing leaf and that they do so by growing within the limits of a set of \\'geometrical rules\\'. © 2012 Staff et al.

  12. Multiwall carbon nanotubes modulate paraquat toxicity in Arabidopsis thaliana.

    Science.gov (United States)

    Fan, Xiaoji; Xu, Jiahui; Lavoie, Michel; Peijnenburg, W J G M; Zhu, Youchao; Lu, Tao; Fu, Zhengwei; Zhu, Tingheng; Qian, Haifeng

    2018-02-01

    Carbon nanotubes can be either toxic or beneficial to plant growth and can also modulate toxicity of organic contaminants through surface sorption. The complex interacting toxic effects of carbon nanotubes and organic contaminants in plants have received little attention in the literature to date. In this study, the toxicity of multiwall carbon nanotubes (MWCNT, 50 mg/L) and paraquat (MV, 0.82 mg/L), separately or in combination, were evaluated at the physiological and the proteomic level in Arabidopsis thaliana for 7-14 days. The results revealed that the exposure to MWCNT had no inhibitory effect on the growth of shoots and leaves. Rather, MWCNT stimulated the relative electron transport rate and the effective photochemical quantum yield of PSII value as compared to the control by around 12% and lateral root production up to nearly 4-fold as compared to the control. The protective effect of MWCNT on MV toxicity on the root surface area could be quantitatively explained by the extent of MV adsorption on MWCNT and was related to stimulation of photosynthesis, antioxidant protection and number and area of lateral roots which in turn helped nutrient assimilation. The influence of MWCNT and MV on photosynthesis and oxidative stress at the physiological level was consistent with the proteomics analysis, with various over-expressed photosynthesis-related proteins (by more than 2 folds) and various under-expressed oxidative stress related proteins (by about 2-3 folds). This study brings new insights into the interactive effects of two xenobiotics (MWCNT and MV) on the physiology of a model plant. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. The hidden geometries of the Arabidopsis thaliana epidermis.

    Directory of Open Access Journals (Sweden)

    Lee Staff

    Full Text Available The quest for the discovery of mathematical principles that underlie biological phenomena is ancient and ongoing. We present a geometric analysis of the complex interdigitated pavement cells in the Arabidopsis thaliana (Col. adaxial epidermis with a view to discovering some geometric characteristics that may govern the formation of this tissue. More than 2,400 pavement cells from 10, 17 and 24 day old leaves were analyzed. These interdigitated cells revealed a number of geometric properties that remained constant across the three age groups. In particular, the number of digits per cell rarely exceeded 15, irrespective of cell area. Digit numbers per 100 µm(2 cell area reduce with age and as cell area increases, suggesting early developmental programming of digits. Cell shape proportions as defined by length:width ratios were highly conserved over time independent of the size and, interestingly, both the mean and the medians were close to the golden ratio 1.618034. With maturity, the cell area:perimeter ratios increased from a mean of 2.0 to 2.4. Shape properties as defined by the medial axis transform (MAT were calculated and revealed that branch points along the MAT typically comprise one large and two small angles. These showed consistency across the developmental stages considered here at 140° (± 5° for the largest angles and 110° (± 5° for the smaller angles. Voronoi diagram analyses of stomatal center coordinates revealed that giant pavement cells (≥ 500 µm(2 tend to be arranged along Voronoi boundaries suggesting that they could function as a scaffold of the epidermis. In addition, we propose that pavement cells have a role in spacing and positioning of the stomata in the growing leaf and that they do so by growing within the limits of a set of 'geometrical rules'.

  14. Recent advances in biological effect and molecular mechanism of arabidopsis thaliana irradiated by ion beams

    International Nuclear Information System (INIS)

    Wu Dali; Hou Suiwen; Li Wenjian

    2008-01-01

    Newly research progresses were summarized in effect of ion beams on seed surface, biological effect, growth, development, gravitropism and so on. Furthermore, mutation molecular mechanism of Arabidopsis thaliana was discussed, for example, alteration of DNA bases, DNA damage, chromosomal recombination, characteristics of mutant transmissibility, etc. Meanwhile, the achievements of transfer- ring extraneous gene to Arabidopsis thaliana by ion beams were reviewed in the paper. At last, the future prospective are also discussed here in mutation molecular mechanism and the potential application of biological effect of heavy ion beams. (authors)

  15. RAPD analysis of Arabidopsis thaliana transferred with total DNA of cabbage by ion beam

    International Nuclear Information System (INIS)

    Bian Po; Yu Zengliang; Qin Guangyong; Huo Yuping; Wang Yan

    2003-01-01

    Two mutants were found among the Arabidopsis thaliana transferred with total DNA of cabbage. Variation of genome of T6 and its offspring were analyzed by RAPD-PCR with 40 random primers. The result from S168 primer was different from the CK, indicating that variation of genome can be made by total DNA transferring by use of ion beam, and this variation is hereditary. It is found that S 168-1850 is included within the gene of ABC transporter by aligning with genome of Arabidopsis thaliana in TAIT

  16. Comparative differential gene expression analysis of nucleus-encoded proteins for Rafflesia cantleyi against Arabidopsis thaliana

    Science.gov (United States)

    Ng, Siuk-Mun; Lee, Xin-Wei; Wan, Kiew-Lian; Firdaus-Raih, Mohd

    2015-09-01

    Regulation of functional nucleus-encoded proteins targeting the plastidial functions was comparatively studied for a plant parasite, Rafflesia cantleyi versus a photosynthetic plant, Arabidopsis thaliana. This study involved two species of different feeding modes and different developmental stages. A total of 30 nucleus-encoded proteins were found to be differentially-regulated during two stages in the parasite; whereas 17 nucleus-encoded proteins were differentially-expressed during two developmental stages in Arabidopsis thaliana. One notable finding observed for the two plants was the identification of genes involved in the regulation of photosynthesis-related processes where these processes, as expected, seem to be present only in the autotroph.

  17. Comparative radioresistance of chronically irradiated populations of Arabidopsis thaliana (L.) Heynh

    International Nuclear Information System (INIS)

    Dineva, S.B.; Abramov, V.I.; Shevchenko, V.A.

    1994-01-01

    The radioresistance of seeds of populations of Arabidopsis thaliana (L.) Heynh. growing for 5 years in the regions with different levels of radioactive contamination within 30 km zone of Chernobyl NPP was studied. The analysis of comparative radiosensitivity by root test was performed. It has been shown that plants from arabidopsis population growing under chronic irradiation did not gain an increased radioresistance. The data obtained shown that they are more radiosensitive

  18. Natural variation of root exudates in Arabidopsis thaliana-linking metabolomic and genomic data

    OpenAIRE

    Susann Mönchgesang; Nadine Strehmel; Stephan Schmidt; Lore Westphal; Franziska Taruttis; Erik Müller; Siska Herklotz; Steffen Neumann; Dierk Scheel

    2016-01-01

    Many metabolomics studies focus on aboveground parts of the plant, while metabolism within roots and the chemical composition of the rhizosphere, as influenced by exudation, are not deeply investigated. In this study, we analysed exudate metabolic patterns of Arabidopsis thaliana and their variation in genetically diverse accessions. For this project, we used the 19 parental accessions of the Arabidopsis MAGIC collection. Plants were grown in a hydroponic system, their exudates were harvested...

  19. The ABC transporter BcatrB from Botrytis cinerea exports camalexin and is a virulence factor on Arabidopsis thaliana

    OpenAIRE

    Stefanato, Francesca L.; Abou-Mansour, Eliane; Buchala, Antony; Kretschmer, Matthias; Mosbach, Andreas; Hahn, Matthias; Bochet, Christian G.; Métraux, Jean-Pierre; Schoonbeek, Henk-jan

    2009-01-01

    Arabidopsis thaliana is known to produce the phytoalexin camalexin in response to abiotic and biotic stress. Here we studied the mechanisms of tolerance to camalexin in the fungus Botrytis cinerea, a necrotrophic pathogen of A. thaliana. Exposure of B. cinerea to camalexin induces expression of BcatrB, an ABC transporter that functions in the efflux of fungitoxic compounds. B. cinerea inoculated on wild-type A. thaliana plants yields smaller lesions than on camalexin-deficient A. thaliana mut...

  20. Metabolite profiling of Arabidopsis thaliana (L.) plants transformed with an antisense chalcone synthase gene

    DEFF Research Database (Denmark)

    Le Gall, G.; Metzdorff, Stine Broeng; Pedersen, Jan W.

    2005-01-01

    A metabolite profiling study has been carried out on Arabidopsis thaliana (L.) Heynh. ecotype Wassilewskija and a series of transgenic lines of the ecotype transformed with a CHS (chalcone synthase) antisense construct. Compound identifications by LC/MS and H-1 NMR are discussed. The glucosinolate...

  1. Characterization of the MADS domain transcription factor family in Arabidopsis thaliana

    NARCIS (Netherlands)

    Folter, Stefan de

    2006-01-01

    Gene regulation at the level of transcription is crucial for almost all biological processes in a cell or organism. Transcription factors are sequence-specific DNA-binding proteins that are capable of activating and/or repressing transcription. The genome of Arabidopsis thaliana, for instance,

  2. Coronatine-Insensitive 1 (COI1) Mediates Transcriptional Responses of Arabidopsis thaliana to External Potassium Supply

    NARCIS (Netherlands)

    Armengaud, Patrick; Breitling, Rainer; Amtmann, Anna

    The ability to adjust growth and development to the availability of mineral nutrients in the soil is an essential life skill of plants but the underlying signaling pathways are poorly understood. In Arabidopsis thaliana, shortage of potassium (K) induces a number of genes related to the phytohormone

  3. Effect of antenna-depletion in photosystem II on excitation energy transfer in Arabidopsis thaliana

    NARCIS (Netherlands)

    Van Oort, Bart; Alberts, Marieke; De Bianchi, Silvia; Dall'Osto, Luca; Bassi, Roberto; Trinkunas, Gediminas; Croce, Roberta; van Amerongen, Herbert

    2010-01-01

    The role of individual photosynthetic antenna complexes of Photosystem II (PSII) both in membrane organization and excitation energy transfer have been investigated. Thylakoid membranes from wild-type Arabidopsis thaliana, and three mutants lacking light-harvesting complexes CP24, CP26, or CP29,

  4. Natural variation in flowering time among populations of the annual crucifer Arabidopsis thaliana

    NARCIS (Netherlands)

    Hammad, I.; Van Tienderen, P.H.

    1997-01-01

    Genetic variation in flowering time was studied in four natural populations of Arabidopsis thaliana, using greenhouse experiments. Two populations from ruderal sites flowered early, two others from river dykes late. However, the late flowering plants flowered almost as early as the others after cold

  5. Variation in seed dormancy quantitative trait loci in Arabidopsis thaliana originating from one site

    NARCIS (Netherlands)

    Silady, R.A.; Effgen, S.; Koornneef, M.; Reymond, M.

    2011-01-01

    A Quantitative Trait Locus (QTL) analysis was performed using two novel Recombinant Inbred Line (RIL) populations, derived from the progeny between two Arabidopsis thaliana genotypes collected at the same site in Kyoto (Japan) crossed with the reference laboratory strain Landsberg erecta (Ler). We

  6. Vacuolar and cytosolic cytokinin dehydrogenases of Arabidopsis thaliana: heterologous expression, purification and properties

    Czech Academy of Sciences Publication Activity Database

    Kowalska, M.; Galuszka, Petr; Frébortová, Jitka; Šebela, M.; Béres, Tibor; Hluska, T.; Šmehilová, M.; Bilyeu, K. D.; Frébort, Ivo

    2010-01-01

    Roč. 71, č. 17 (2010), s. 1970-1978 ISSN 0031-9422 R&D Projects: GA ČR GA301/08/1649 Institutional research plan: CEZ:AV0Z50380511 Keywords : Arabidopsis thaliana * Pichia pastoris expression system * Electron acceptor Subject RIV: CE - Biochemistry Impact factor: 3.150, year: 2010

  7. Electron transfer reactivity of the Arabidopsis thaliana sulfhydryl oxidase AtErv1

    DEFF Research Database (Denmark)

    Farver, Ole; Vitu, Elvira; Wherland, Scot

    2009-01-01

    The redox reactivity of the three disulfide bridges and the flavin present in each protomer of the wild-type Arabidopsis thaliana mitochondrial sulfhydryl oxidase (AtErv1) homodimer has been investigated. Pulse radiolytically produced CO2- radical ions were found to reduce the disulfide bridges...

  8. Pleiotropic effects of flowering time genes in the annual crucifer Arabidopsis thaliana (Brassicaceae)

    NARCIS (Netherlands)

    Van Tienderen, P.H.; Hammad, I.; Zwaal, F.C.

    1996-01-01

    Variation in flowering time of Arabidopsis thaliana was studied in an experiment with mutant lines. The pleiotropic effects of flowering time genes on morphology and reproductive yield were assessed under three levels of nutrient supply. At all nutrient levels flowering time and number of rosette

  9. Isolation and characterization of an auxin-inducible glutathione S-transferase gene of Arabidopsis thaliana

    NARCIS (Netherlands)

    Kop, D.A.M. van der; Schuyer, M.; Scheres, B.J.G.; Zaal, B.J. van der; Hooykaas, P.J.J.

    1996-01-01

    Genes homologous to the auxin-inducible Nt103 glutathione S-transferase (GST) gene of tobacco, were isolated from a genomic library of Arabidopsis thaliana. We isolated a λ clone containing an auxin-inducible gene, At103-1a, and part of a constitutively expressed gene, At103-1b. The coding regions

  10. Alleviation of Copper Toxicity in Arabidopsis Thaliana and Zinnia Elegans by Silicon Addition

    Science.gov (United States)

    While the role of silicon in plants has been studied for over 150 years, and this element can mitigate the effects of certain heavy metals, its role in Cu metabolism is unclear. Therefore, the role of Si in plant response to Cu stress was investigated in Arabidopsis thaliana L. (Heyn) and Zinnia el...

  11. NBS1 plays a synergistic role with telomerase in the maintenance of telomeres in Arabidopsis thaliana

    Czech Academy of Sciences Publication Activity Database

    Najdekrová, Lucie; Široký, Jiří

    2012-01-01

    Roč. 12, č. 167 (2012), s. 1-12 ISSN 1471-2229 R&D Projects: GA ČR GBP501/12/G090 Keywords : telomere * Arabidopsis thaliana * chromosomes Subject RIV: BO - Biophysics Impact factor: 4.354, year: 2012

  12. A composite transcriptional signature differentiates responses towards closely related herbicides in Arabidopsis thaliana and brassica napus

    Science.gov (United States)

    In this study, genome-wide expression profiling based on Affymetrix ATH1 arrays was used to identify discriminating responses of Arabidopsis thaliana to five herbicides, which contain active ingredients targeting two different branches of amino acid biosynthesis. One herbicide co...

  13. The genetics of some planthormones and photoreceptors in Arabidopsis thaliana (L.) Heynh.

    NARCIS (Netherlands)

    Koornneef, M.

    1982-01-01

    This thesis describes the isolation and characterization in Arabidopsis thaliana (L.) Heynh. of induced mutants, deficient for gibberellins (GA's), abscisic acid (ABA) and photoreceptors.

    These compounds are known to regulate various facets of plant growth and

  14. A previously undescribed jasmonate compound in flowering Arabidopsis thaliana - The identification of cis-(+)-OPDA-Ile

    Czech Academy of Sciences Publication Activity Database

    Floková, K.; Feussner, K.; Herrfurth, C.; Miersch, O.; Mik, V.; Tarkowská, Danuše; Strnad, Miroslav; Feussner, I.; Wasternack, Claus; Novák, Ondřej

    2016-01-01

    Roč. 122, FEB (2016), s. 230-237 ISSN 0031-9422 R&D Projects: GA MŠk(CZ) LO1204; GA MŠk LK21306 Institutional support: RVO:61389030 Keywords : Arabidopsis thaliana (Brassicaceae) * Jasmonates * Cis-(+)-12-oxo-phytodienoyl-L-isoleucine Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.205, year: 2016

  15. Impact of elevated CO2 on growth and development of Arabidopsis thaliana L

    NARCIS (Netherlands)

    van der Kooij, T.A W; De Kok, L.J.

    1996-01-01

    After germination, Arabidopsis thaliana L (cv. Landsberg) was grown at 350 mu l l(-1) (control) or 700 mu l l(-1) (elevated) CO2. Total shoot biomass at the end of the vegetative growth period was increased by 56% due to a short transient stimulation of the relative growth rate by elevated CO2 at

  16. Differentially expressed genes associated with dormancy or germination of Arabidopsis thaliana seeds

    NARCIS (Netherlands)

    Toorop, P.E.; Barroco, R.M.; Engler, G.; Groot, S.P.C.; Hilhorst, H.W.M.

    2005-01-01

    Differential display analysis using dormant and non-dormant Arabidopsis thaliana (L.) Heynh seeds resulted in a set of genes that were associated with either dormancy or germination. Expression of the germination-associated genes AtRPL36B and AtRPL27B, encoding two ribosomal proteins, was

  17. GWA Mapping of Anthocyanin Accumulation Reveals Balancing Selection of MYB90 in Arabidopsis thaliana

    NARCIS (Netherlands)

    Bac-Molenaar, J.A.; Dijk-Fradin, van E.F.; Rienstra, J.A.; Vreugdenhil, D.; Keurentjes, J.J.B.

    2015-01-01

    Induction of anthocyanin accumulation by osmotic stress was assessed in 360 accessions of Arabidopsis thaliana. A wide range of natural variation, with phenotypes ranging from green to completely red/purple rosettes, was observed. A genome wide association (GWA) mapping approach revealed that

  18. Optimized Whole-Mount In Situ Immunolocalization for Arabidopsis thaliana Root Meristems and Lateral Root Primordia.

    Science.gov (United States)

    Karampelias, Michael; Tejos, Ricardo; Friml, Jiří; Vanneste, Steffen

    2018-01-01

    Immunolocalization is a valuable tool for cell biology research that allows to rapidly determine the localization and expression levels of endogenous proteins. In plants, whole-mount in situ immunolocalization remains a challenging method, especially in tissues protected by waxy layers and complex cell wall carbohydrates. Here, we present a robust method for whole-mount in situ immunolocalization in primary root meristems and lateral root primordia in Arabidopsis thaliana. For good epitope preservation, fixation is done in an alkaline paraformaldehyde/glutaraldehyde mixture. This fixative is suitable for detecting a wide range of proteins, including integral transmembrane proteins and proteins peripherally attached to the plasma membrane. From initiation until emergence from the primary root, lateral root primordia are surrounded by several layers of differentiated tissues with a complex cell wall composition that interferes with the efficient penetration of all buffers. Therefore, immunolocalization in early lateral root primordia requires a modified method, including a strong solvent treatment for removal of hydrophobic barriers and a specific cocktail of cell wall-degrading enzymes. The presented method allows for easy, reliable, and high-quality in situ detection of the subcellular localization of endogenous proteins in primary and lateral root meristems without the need of time-consuming crosses or making translational fusions to fluorescent proteins.

  19. Phytotoxicity of chiral herbicide bromacil: Enantioselectivity of photosynthesis in Arabidopsis thaliana

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Zunwei; Zou, Yuqin; Wang, Jia [MOE Key Laboratory of Environmental Remediation & Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058 (China); Li, Meichao [Research Center of Analysis and Measurement, Zhejiang University of Technology, Hangzhou 310032 (China); Wen, Yuezhong, E-mail: wenyuezhong@zju.edu.cn [MOE Key Laboratory of Environmental Remediation & Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058 (China)

    2016-04-01

    With the wide application of chiral herbicides and the frequent detection of photosystem II (PSII) herbicides, it is of great importance to assess the direct effects of PSII herbicides on photosynthesis in an enantiomeric level. In the present study, the enantioselective phytotoxicity of bromacil (BRO), typical photosynthesis inhibition herbicide, on Arabidopsis thaliana was investigated. The results showed that S-BRO exhibited a greater inhibition of electron transmission in photosystem I (PSI) of A. thaliana than R-BRO by inhibiting the transcription of fnr 1. S-BRO also changed the chlorophyll fluorescence parameters Y (II), Y (NO), and Y (NPQ) to a greater extent than R-Bro. Transcription of genes psbO2, Lhcb3 and Lhcb6 was down-regulated in an enantioselective rhythm and S-BRO caused more serious influence, indicating that S-BRO did worse damage to the photosystem II (PSII) of A. thaliana than R-BRO. This study suggested that S-BRO disturbed the photosynthesis of plants to a larger extent than R-BRO and provided a new sight to evaluate the phytotoxicity of chiral herbicides. - Highlights: • It is necessary to assess the direct effects of PSII herbicides on photosynthesis. • Phytotoxicity of bromacil is investigated in an enantiomeric level. • Bromacil disturbed enantioselectively the photosystem II of Arabidopsis thaliana. • S-bromacil caused severer damage to photosynthesis of Arabidopsis than R-bromacil. • Photosynthesis should be considered for phytotoxicity assessment of herbicides.

  20. Phytotoxicity of chiral herbicide bromacil: Enantioselectivity of photosynthesis in Arabidopsis thaliana

    International Nuclear Information System (INIS)

    Chen, Zunwei; Zou, Yuqin; Wang, Jia; Li, Meichao; Wen, Yuezhong

    2016-01-01

    With the wide application of chiral herbicides and the frequent detection of photosystem II (PSII) herbicides, it is of great importance to assess the direct effects of PSII herbicides on photosynthesis in an enantiomeric level. In the present study, the enantioselective phytotoxicity of bromacil (BRO), typical photosynthesis inhibition herbicide, on Arabidopsis thaliana was investigated. The results showed that S-BRO exhibited a greater inhibition of electron transmission in photosystem I (PSI) of A. thaliana than R-BRO by inhibiting the transcription of fnr 1. S-BRO also changed the chlorophyll fluorescence parameters Y (II), Y (NO), and Y (NPQ) to a greater extent than R-Bro. Transcription of genes psbO2, Lhcb3 and Lhcb6 was down-regulated in an enantioselective rhythm and S-BRO caused more serious influence, indicating that S-BRO did worse damage to the photosystem II (PSII) of A. thaliana than R-BRO. This study suggested that S-BRO disturbed the photosynthesis of plants to a larger extent than R-BRO and provided a new sight to evaluate the phytotoxicity of chiral herbicides. - Highlights: • It is necessary to assess the direct effects of PSII herbicides on photosynthesis. • Phytotoxicity of bromacil is investigated in an enantiomeric level. • Bromacil disturbed enantioselectively the photosystem II of Arabidopsis thaliana. • S-bromacil caused severer damage to photosynthesis of Arabidopsis than R-bromacil. • Photosynthesis should be considered for phytotoxicity assessment of herbicides.

  1. Cloning and sequencing of cDNAs specifying a novel class of phosphoribosyl diphosphate synthase in Arabidopsis thaliana

    DEFF Research Database (Denmark)

    Krath, Britta N.; Eriksen, Tina A.; Poulsen, Tim S.

    1999-01-01

    cDNAs specifying four active phosphoribosyl diphosphate synthase isozymes were isolated from an Arabidopsis thaliana cDNA library. In contrast to other phosphoribosyl diphosphate synthases the activity of two of the A. thaliana isozymes are independent of Pi. Amino acid sequence comparison...

  2. Establishment of an Indirect Genetic Transformation Method for Arabidopsis thaliana ecotype Bangladesh

    Directory of Open Access Journals (Sweden)

    Bulbul AHMED

    2011-11-01

    Full Text Available Arabidopsis thaliana is a small flowering plant belonging to the Brassicaceae family, which is adopted as a model plant for genetic research. Agrobacterium tumifaciensmediated transformation method for A. thaliana ecotype Bangladesh was established. Leaf discs of A. thaliana were incubated with A. tumefaciens strain LBA4404 containing chimeric nos. nptII. nos and intron-GUS genes. Following inoculation and co-cultivation, leaf discs were cultured on selection medium containing 50 mg/l kanamycin + 50 mg/l cefotaxime + 1.5 mg/l NAA and kanamycin resistant shoots were induced from the leaf discs after two weeks. Shoot regeneration was achieved after transferring the tissues onto fresh medium of the same combination. Finally, the shoots were rooted on MS medium containing 50 mg/l kanamycin. Incorporation and expression of the transgenes were confirmed by PCR analysis. Using this protocol, transgenic A. thaliana plants can be obtained and indicates that genomic transformation in higher plants is possible through insertion of desired gene. Although Agrobacterium mediated genetic transformation is established for A. thaliana, this study was the conducted to transform A. thaliana ecotype Bangladesh.

  3. Purification, crystallization and preliminary crystallographic analysis of deoxyuridine triphosphate nucleotidohydrolase from Arabidopsis thaliana

    International Nuclear Information System (INIS)

    Bajaj, Mamta; Moriyama, Hideaki

    2007-01-01

    The first crystallization of deoxyuridine triphosphate nucleotidohydrolase from plant, Arabidopsis thaliana, has been performed. An additive, taurine, was effective in producing the single crystal. The deoxyuridine triphosphate nucleotidohydrolase gene from Arabidopsis thaliana was expressed and the gene product was purified. Crystallization was performed by the hanging-drop vapour-diffusion method at 298 K using 2 M ammonium sulfate as the precipitant. X-ray diffraction data were collected to 2.2 Å resolution using Cu Kα radiation. The crystal belongs to the orthorhombic space group P2 1 2 1 2 1 , with unit-cell parameters a = 69.90, b = 70.86 Å, c = 75.55 Å. Assuming the presence of a trimer in the asymmetric unit, the solvent content was 30%, with a V M of 1.8 Å 3 Da −1

  4. Purification, crystallization and preliminary crystallographic analysis of deoxyuridine triphosphate nucleotidohydrolase from Arabidopsis thaliana

    Energy Technology Data Exchange (ETDEWEB)

    Bajaj, Mamta [School of Biological Sciences, University of Nebraska-Lincoln, Manter Hall, Lincoln, Nebraska 68588-0304 (United States); Moriyama, Hideaki, E-mail: hmoriyama2@unl.edu [Department of Chemistry, e-Toxicology and Biotechnology, University of Nebraska-Lincoln, Hamilton Hall, Lincoln, Nebraska 68588-0304 (United States); School of Biological Sciences, University of Nebraska-Lincoln, Manter Hall, Lincoln, Nebraska 68588-0304 (United States)

    2007-05-01

    The first crystallization of deoxyuridine triphosphate nucleotidohydrolase from plant, Arabidopsis thaliana, has been performed. An additive, taurine, was effective in producing the single crystal. The deoxyuridine triphosphate nucleotidohydrolase gene from Arabidopsis thaliana was expressed and the gene product was purified. Crystallization was performed by the hanging-drop vapour-diffusion method at 298 K using 2 M ammonium sulfate as the precipitant. X-ray diffraction data were collected to 2.2 Å resolution using Cu Kα radiation. The crystal belongs to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 69.90, b = 70.86 Å, c = 75.55 Å. Assuming the presence of a trimer in the asymmetric unit, the solvent content was 30%, with a V{sub M} of 1.8 Å{sup 3} Da{sup −1}.

  5. Toxicity and transfer of CuO Nanoparticles on Arabidopsis thaliana

    Science.gov (United States)

    Zhao, Shilin; Dai, Yanhui; Xu, Lina

    2018-02-01

    CuO engineered nanoparticles (ENPs) are widely used in commercial applications. With increasing CuO ENPs production, CuO ENPs are likely to present in the environment and cause a potential threaten to ecosystem. In this work, Arabidopsis thaliana (Bay-0) was chosen to take the toxic experiment after exposed to CuO ENPs (0, 20, and 50 mg/L) and Cu2+ (0.15 mg/L). And the copper content of shoots at 50 mg/L CuO ENPs was about 20 times of control, indicating that CuO ENPs could be absorbed into Arabidopsis thaliana seedlings and transfered from root to shoot in a certain way.

  6. Phosphate Uptake and Allocation – A Closer Look at Arabidopsis thaliana L. and Oryza sativa L.

    Science.gov (United States)

    Młodzińska, Ewa; Zboińska, Magdalena

    2016-01-01

    This year marks the 20th anniversary of the discovery and characterization of the two Arabidopsis PHT1 genes encoding the phosphate transporter in Arabidopsis thaliana. So far, multiple inorganic phosphate (Pi) transporters have been described, and the molecular basis of Pi acquisition by plants has been well-characterized. These genes are involved in Pi acquisition, allocation, and/or signal transduction. This review summarizes how Pi is taken up by the roots and further distributed within two plants: A. thaliana and Oryza sativa L. by plasma membrane phosphate transporters PHT1 and PHO1 as well as by intracellular transporters: PHO1, PHT2, PHT3, PHT4, PHT5 (VPT1), SPX-MFS and phosphate translocators family. We also describe the role of the PHT1 transporters in mycorrhizal roots of rice as an adaptive strategy to cope with limited phosphate availability in soil. PMID:27574525

  7. Strictly NO3- Nutrition Alleviates Iron Deficiency Chlorosis in Arabidopsis thaliana Plants

    Directory of Open Access Journals (Sweden)

    Najoua Msilini

    2014-03-01

    Full Text Available The effects of NO3- nutrition on iron deficiency responses were investigated in Arabidopsis thaliana. Plants were grown with or without 5 µM Fe, and with NO3- alone or a mixture of NO3- and NH4+. The results indicated that, NO3- nutrition induced higher dry matter production, regardless the Fe concentration. Fe deficiency reduced growth activity, photosynthetic pigment concentration and Fe content of plants, whatever the N forms. This decrease was more pronounced in plants grown with mixed N source; those plants presented the highest EL and MDA and anthocyanin contents compared to plants grown under Fe sufficient conditions. In iron free-solutions, with NO3- as the sole nitrogen source, enhanced FC-R activity in the roots was observed. However, in the presence of NH4+, plants displayed some decrease in in FC-R and PEPC activities. The presence of NH4+ modified typical Fe stress responses in Arabidopsis thaliana plants.

  8. Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana.

    Science.gov (United States)

    Wang, Xiu-Jie; Gaasterland, Terry; Chua, Nam-Hai

    2005-01-01

    Natural antisense transcripts (NAT) are a class of endogenous coding or non-protein-coding RNAs with sequence complementarity to other transcripts. Several lines of evidence have shown that cis- and trans-NATs may participate in a broad range of gene regulatory events. Genome-wide identification of cis-NATs in human, mouse and rice has revealed their widespread occurrence in eukaryotes. However, little is known about cis-NATs in the model plant Arabidopsis thaliana. We developed a new computational method to predict and identify cis-encoded NATs in Arabidopsis and found 1,340 potential NAT pairs. The expression of both sense and antisense transcripts of 957 NAT pairs was confirmed using Arabidopsis full-length cDNAs and public massively parallel signature sequencing (MPSS) data. Three known or putative Arabidopsis imprinted genes have cis-antisense transcripts. Sequences and the genomic arrangement of two Arabidopsis NAT pairs are conserved in rice. We combined information from full-length cDNAs and Arabidopsis genome annotation in our NAT prediction work and reported cis-NAT pairs that could not otherwise be identified by using one of the two datasets only. Analysis of MPSS data suggested that for most Arabidopsis cis-NAT pairs, there is predominant expression of one of the two transcripts in a tissue-specific manner.

  9. A novel role for methyl cysteinate, a cysteine derivative, in cesium accumulation in Arabidopsis thaliana

    DEFF Research Database (Denmark)

    Adams, Eri; Miyazaki, Takae; Hayaishi-Satoh, Aya

    2017-01-01

    Phytoaccumulation is a technique to extract metals from soil utilising ability of plants. Cesium is a valuable metal while radioactive isotopes of cesium can be hazardous. In order to establish a more efficient phytoaccumulation system, small molecules which promote plants to accumulate cesium were...... investigated. Through chemical library screening, 14 chemicals were isolated as 'cesium accumulators' in Arabidopsis thaliana. Of those, methyl cysteinate, a derivative of cysteine, was found to function within the plant to accumulate externally supplemented cesium. Moreover, metabolite profiling demonstrated...

  10. Chlorophyll fluorescence emission can screen cold tolerance of cold acclimated Arabidopsis thaliana accessions

    Czech Academy of Sciences Publication Activity Database

    Mishra, Anamika; Heyer, A. G.; Mishra, Kumud

    2014-01-01

    Roč. 10, č. 38 (2014) ISSN 1746-4811 R&D Projects: GA MŠk EE2.3.20.0246; GA MŠk 7E12047 Institutional support: RVO:67179843 Keywords : high-throughput screening * chlorophyll a fluorescence transients * cold tolerance * cold acclimation * whole plant * Arabidopsis thaliana Subject RIV: EH - Ecology, Behaviour Impact factor: 3.102, year: 2014

  11. Kontrolle der Expression des UNUSUAL FLORAL ORGANS (UFO) Gens in Arabidopsis thaliana

    OpenAIRE

    Hobe, Martin

    2004-01-01

    Die vorliegende Arbeit befaßt sich mit der Kontrolle des Expressionsmusters des UNUSUAL FLORAL ORGANS (UFO) Gens von Arabidopsis thaliana. UFO wird im Sproß- und Blütenmeristemen aller Entwicklungsstadien der Pflanze exprimiert. In Blütenmeristemen agiert UFO als Kofaktor von LEAFY (LFY) bei der Aktivierung der Organidentitätsgene des zweiten und dritten Wirtels. UFO stellt also einen generellen Faktor der Musterbildung in Meristemen dar. Um regulatorische Gene, die die Expression von UFO bee...

  12. Isoflavonoids are present in Arabidopsis thaliana despite the absence of any homologue to known isoflavonoid synthases

    Czech Academy of Sciences Publication Activity Database

    Lapčík, O.; Honys, David; Koblovská, R.; Macková, Z.; Vítková, M.; Klejdus, B.

    2006-01-01

    Roč. 44, 2-3 (2006), s. 106-114 ISSN 0981-9428 R&D Projects: GA ČR GA525/03/0352; GA AV ČR KJB6038409 Institutional research plan: CEZ:AV0Z50380511 Keywords : Arabidopsis thaliana * Brassicaceae * HPLC-MS Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.847, year: 2006

  13. Mass spectrometry-based metabolomic fingerprinting for screening cold tolerance in Arabidopsis thaliana accessions

    Czech Academy of Sciences Publication Activity Database

    Václavík, L.; Mishra, Anamika; Mishra, Kumud; Hajslova, J.

    2013-01-01

    Roč. 405, č. 8 (2013), s. 2671-2683 ISSN 1618-2642 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0073; GA MŠk OC08055 Institutional support: RVO:67179843 Keywords : cold tolerance * Arabidopsis thaliana * metabolomic fingerprinting * LC-MS * DART-MS * chemometric analysis Subject RIV: EH - Ecology, Behaviour Impact factor: 3.578, year: 2013

  14. Metabolism of ibuprofen in higher plants: A model Arabidopsis thaliana cell suspension culture system

    Czech Academy of Sciences Publication Activity Database

    Maršík, Petr; Šíša, Miroslav; Lacina, O.; Moťková, Kateřina; Langhansová, Lenka; Rezek, Jan; Vaněk, Tomáš

    2017-01-01

    Roč. 220, JAN (2017), s. 383-392 ISSN 0269-7491 R&D Projects: GA ČR(CZ) GA14-22593S Grant - others:European Regional Development Fund(XE) CZ.2.16/3.1.00/24014 Institutional support: RVO:61389030 Keywords : Arabidopsis thaliana * Ibuprofen * Metabolism * Plant cells * Sequestration Subject RIV: CE - Biochemistry OBOR OECD: Plant sciences, botany Impact factor: 5.099, year: 2016

  15. Dissecting a Hidden Gene Duplication: The Arabidopsis thaliana SEC10 Locus

    Czech Academy of Sciences Publication Activity Database

    Vukašinović, Nemanja; Cvrčková, F.; Eliáš, M.; Cole, R.; Fowler, J.E.; Žárský, Viktor; Synek, Lukáš

    2014-01-01

    Roč. 9, č. 4 (2014) E-ISSN 1932-6203 R&D Projects: GA ČR GPP501/11/P853; GA ČR(CZ) GAP305/11/1629 Grant - others:GA MŠk ME10033 Institutional support: RVO:61389030 Keywords : WHOLE-GENOME * ARABIDOPSIS -THALIANA * RECENT SEGMENTAL DUPLICATIONS Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.234, year: 2014

  16. Genomic and Physiological Characterization of the Mutant time for coffee within the Arabidopsis thaliana Circadian Clock

    OpenAIRE

    Sánchez Villarreal, Alfredo

    2010-01-01

    ircadian clocks are internal timekeepers that provide organisms with a sense of time. These oscillators, which are entrained by external stimuli, predict the daily day/night transitions and have a periodicity of about 24 hours. The Arabidopsis thaliana circadian clock is composed of interconnected transcriptional-translational feedback loops. The morning expressed elements CCA1 and LHY, which are clock controlled and light inducible, repress the transcription of the evening element TOC1. At d...

  17. PRC2 Represses Hormone-Induced Somatic Embryogenesis in Vegetative Tissue of Arabidopsis thaliana

    Czech Academy of Sciences Publication Activity Database

    Mozgová, Iva; Munoz-Viana, R.; Hennig, L.

    2017-01-01

    Roč. 13, č. 1 (2017), s. 1-27, č. článku e1006562. ISSN 1553-7404 R&D Projects: GA ČR(CZ) GJ16-08423Y; GA MŠk(CZ) LO1416 Institutional support: RVO:61388971 Keywords : PRC2 * SE formation * Arabidopsis thaliana Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 6.100, year: 2016

  18. ML3: a novel regulator of herbivory-induced responses in Arabidopsis thaliana

    Czech Academy of Sciences Publication Activity Database

    Fridborg, I.; Johansson, A.; Lagensjo, J.; Leelarasamee, N.; Floková, Kristýna; Tarkowská, Danuše; Meijer, J.; Bejai, S.

    2013-01-01

    Roč. 64, č. 4 (2013), s. 935-948 ISSN 0022-0957 R&D Projects: GA AV ČR KAN200380801 Grant - others:GA MŠk(CZ) ED0007/01/01 Program:ED Institutional research plan: CEZ:AV0Z50380511 Keywords : Arabidopsis thaliana * herbivory * jasmonic acid Subject RIV: EC - Immunology Impact factor: 5.794, year: 2013

  19. Round-shape gold nanoparticles: effect of particle size and concentration on Arabidopsis thaliana root growth

    Czech Academy of Sciences Publication Activity Database

    Siegel, J.; Záruba, K.; Švorčík, V.; Kroumanová, Kristýna; Burketová, Lenka; Martinec, Jan

    2018-01-01

    Roč. 13, APR 10 (2018), č. článku 95. ISSN 1556-276X R&D Projects: GA ČR GA17-10907S; GA ČR(CZ) GBP108/12/G108 Institutional support: RVO:61389030 Keywords : Arabidopsis thaliana * Concentration * Gold nanoparticles * Root growth * Size Subject RIV: JJ - Other Materials OBOR OECD: Plant sciences, botany Impact factor: 2.833, year: 2016

  20. The Genomic and Morphological Effects of Bisphenol A on Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Derek Frejd

    Full Text Available The environmental toxin bisphenol A (BPA is a known mammalian hormone disrupter but its effects on plants have not been well established. The effect of BPA on gene expression in Arabidopsis thaliana was determined using microarray analysis and quantitative gene PCR. Many hormone responsive genes showed changes in expression after BPA treatment. BPA disrupted flowering by a mechanism that may involve disruption of auxin signaling. The results presented here indicate that BPA is a plant hormone disrupter.

  1. Effects of trehalose on gene expression in "Arabidopsis thaliana" seedlings : a genome-wide analysis

    OpenAIRE

    Brodmann, David

    2006-01-01

    Trehalose (α-D-glucopyranosyl-[1,1]-α-D-glucopyranoside), a non reducing disaccharide consisting of two glucose units is present in a large variety of organisms such as bacteria, fungi and invertebrate animals where it may serve as a storage compound or stress protectant. Trehalose also accumulates in a few desiccation-tolerant ‘resurrection plants’ and may have similar functions there. However, in almost all higher plants, including the model plant Arabidopsis thaliana, trehal...

  2. The genetics of some planthormones and photoreceptors in Arabidopsis thaliana (L.) Heynh.

    OpenAIRE

    Koornneef, M.

    1982-01-01

    This thesis describes the isolation and characterization in Arabidopsis thaliana (L.) Heynh. of induced mutants, deficient for gibberellins (GA's), abscisic acid (ABA) and photoreceptors.

    These compounds are known to regulate various facets of plant growth and differentiation, so mutants lacking one of these substances are expected to be affected in several aspects of their physiology. It is shown in this thesis that the earliest expression of these mutants occur...

  3. Cloning of taxadiene synthase gene into Arabidopsis thaliana ...

    African Journals Online (AJOL)

    USER

    2010-03-22

    Mar 22, 2010 ... construct for further uses in transformation of Agro- bacterium and Arabidopsis. Cloning was confirmed by. PCR reaction and the result showed that all of the selective colonies have an 800 bp band in gel electrophoresis. For transformation of Agro-bacterium, a natural method entitled Triparental mating was ...

  4. Proteomic analysis of the Arabidopsis thaliana-Botrytis cinerea ...

    African Journals Online (AJOL)

    A two-dimensional liquid chromatography (2D LC) system, ProteomeLab PF 2D, was employed to study the defence proteome of Arabidopsis following infection with the necrotrophic fungal pathogen, Botrytis cinerea. This system demonstrated differential protein expression in control and treated samples in some fractions.

  5. Phytoremediation potential of Arabidopsis thaliana, expressing ectopically a vacuolar proton pump, for the industrial waste phosphogypsum.

    Science.gov (United States)

    Khoudi, Habib; Maatar, Yafa; Brini, Faïçal; Fourati, Amine; Ammar, Najoua; Masmoudi, Khaled

    2013-01-01

    Phosphogypsum (PG) is a by-product of the phosphorus-fertiliser industry and represents an environmental concern since it contains pollutants such as cadmium (Cd). We have recently shown that the overexpression of a proton pump gene (TaVP1) in transgenic tobacco (Nicotiana tabacum) led to an enhanced Cd tolerance and accumulation. The aim of this study was to evaluate the potential of transgenic Arabidopsis thaliana plants harbouring the TaVP1 gene to phytoremediate phosphogypsum. A pot experiment was carried out under greenhouse conditions. Transgenic A. thaliana plants harbouring the TaVP1 gene were grown on various substrates containing phosphogypsum (0, 25, 50 and 100 %) for 40 days. At the end of the growth period, we examined the growth (germination, root length, fresh weight) and physiological parameters (chlorophyll and protein contents, catalase activity and proteolysis) as well as the cadmium, Mg, Ca, and P contents of the A. thaliana plants. In order to evaluate Cd tolerance of the A. thaliana lines harbouring the TaVP1 gene, an in vitro experiment was also carried out. One week-old seedlings were transferred to Murashige and Skoog agar plates containing various concentrations of cadmium; the germination, total leaf area and root length were determined. The growth and physiological parameters of all A. thaliana plants were significantly altered by PG. The germination capacity, root growth and biomass production of wild-type (WT) plants were more severely inhibited by PG compared with the TaVP1 transgenic A. thaliana lines. In addition, TaVP1 transgenic A. thaliana plants maintained a higher antioxidant capacity than the WT. Interestingly, elemental analysis of leaf material derived from plants grown on PG revealed that the transgenic A. thaliana line accumulated up to ten times more Cd than WT. Despite its higher Cd content, the transgenic A. thaliana line performed better than the WT counterpart. In vitro evaluation of Cd tolerance showed that TaVP1

  6. Comparison of Flowering Time Genes in Brassica Rapa, B. Napus and Arabidopsis Thaliana

    Science.gov (United States)

    Osborn, T. C.; Kole, C.; Parkin, IAP.; Sharpe, A. G.; Kuiper, M.; Lydiate, D. J.; Trick, M.

    1997-01-01

    The major difference between annual and biennial cultivars of oilseed Brassica napus and B. rapa is conferred by genes controlling vernalization-responsive flowering time. These genes were compared between the species by aligning the map positions of flowering time quantitative trait loci (QTLs) detected in a segregating population of each species. The results suggest that two major QTLs identified in B. rapa correspond to two major QTLs identified in B. napus. Since B. rapa is one of the hypothesized diploid parents of the amphidiploid B. napus, the vernalization requirement of B. napus probably originated from B. rapa. Brassica genes also were compared to flowering time genes in Arabidopsis thaliana by mapping RFLP loci with the same probes in both B. napus and Arabidopsis. The region containing one pair of Brassica QTLs was collinear with the top of chromosome 5 in A. thaliana where flowering time genes FLC, FY and CO are located. The region containing the second pair of QTLs showed fractured collinearity with several regions of the Arabidopsis genome, including the top of chromosome 4 where FRI is located. Thus, these Brassica genes may correspond to two genes (FLC and FRI) that regulate flowering time in the latest flowering ecotypes of Arabidopsis. PMID:9215913

  7. MULTIPLEX POLYMERASE CHAIN REACTION FOR GENOTYPING OF Arabidopsis thaliana ECOTYPES USING SSLP MARKERS

    Directory of Open Access Journals (Sweden)

    Zimina O. V.

    2014-08-01

    Full Text Available The goal of the work was, using the database «The Arabidopsis Information Resource» TAIR, to select 12 SSLP-markers distributed along the Arabidopsis chromosomes and chromosome arms, to optimize the conditions of amplification of each fragment and for simultaneous amplification of several fragments. For identification of A. thaliana ecotypes and their hybrid, the SSLP sequences were used. These DNA markers are highly polymorphic in Arabidopsis and easy to use. Using this database, the primers were selected for 12 SSLP-markers distributed along all chromosomes and their arms. A. thaliana ecotypes Columbia and Landsberg erecta were used. The experiments revealed that two-stage PCR using two annealing temperatures of primers in each cycle allows efficient amplification of all the fragments considered. The conditions for carrying out two multiplex PCR, each of which allows the two fragments were amplified and a single multiplex PCR allowing three markers for amplification were defined. The developed system of DNA markers can be used to study the behavior and inheritance of each chromosome of maternal and paternal genomes of Arabidopsis hybrids and enables quick and efficient genetic analysis.

  8. Composition and function of P bodies in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Luis David Maldonado-Bonilla

    2014-05-01

    Full Text Available mRNA accumulation is tightly regulated by diverse molecular pathways. The identification and characterization of enzymes and regulatory proteins involved in controlling the fate of mRNA offers the possibility to broaden our understanding of posttranscriptional gene regulation. Processing bodies (P bodies, PB are cytoplasmic protein complexes involved in degradation and translational arrest of mRNA. Composition and dynamics of these subcellular structures have been studied in animal systems, yeasts and in the model plant Arabidopsis. Their assembly implies the aggregation of specific factors related to decapping, deadenylation and exoribonucleases that operate synchronously to regulate certain mRNA targets during development and adaptation to stress. Although the general function of PB along with the flow of genetic information is understood, several questions still remain open. This review summarizes data on the composition, potential molecular roles, and biological significance of PB and potentially related proteins in Arabidopsis.

  9. 1001 Proteomes: a functional proteomics portal for the analysis of Arabidopsis thaliana accessions.

    Science.gov (United States)

    Joshi, Hiren J; Christiansen, Katy M; Fitz, Joffrey; Cao, Jun; Lipzen, Anna; Martin, Joel; Smith-Moritz, A Michelle; Pennacchio, Len A; Schackwitz, Wendy S; Weigel, Detlef; Heazlewood, Joshua L

    2012-05-15

    The sequencing of over a thousand natural strains of the model plant Arabidopsis thaliana is producing unparalleled information at the genetic level for plant researchers. To enable the rapid exploitation of these data for functional proteomics studies, we have created a resource for the visualization of protein information and proteomic datasets for sequenced natural strains of A. thaliana. The 1001 Proteomes portal can be used to visualize amino acid substitutions or non-synonymous single-nucleotide polymorphisms in individual proteins of A. thaliana based on the reference genome Col-0. We have used the available processed sequence information to analyze the conservation of known residues subject to protein phosphorylation among these natural strains. The substitution of amino acids in A. thaliana natural strains is heavily constrained and is likely a result of the conservation of functional attributes within proteins. At a practical level, we demonstrate that this information can be used to clarify ambiguously defined phosphorylation sites from phosphoproteomic studies. Protein sets of available natural variants are available for download to enable proteomic studies on these accessions. Together this information can be used to uncover the possible roles of specific amino acids in determining the structure and function of proteins in the model plant A. thaliana. An online portal to enable the community to exploit these data can be accessed at http://1001proteomes.masc-proteomics.org/

  10. Zinc triggers signaling mechanisms and defense responses promoting resistance to Alternaria brassicicola in Arabidopsis thaliana.

    Science.gov (United States)

    Martos, Soledad; Gallego, Berta; Cabot, Catalina; Llugany, Mercè; Barceló, Juan; Poschenrieder, Charlotte

    2016-08-01

    According to the elemental defense hypothesis the accumulation of trace elements by plants may substitute for organic defenses, while the joint effects hypothesis proposes that trace elements and organic defenses can have additive or synergistic effects against pathogens or herbivores. To evaluate these hypotheses the response of the pathosystem Alternaria brassicicola-Arabidopsis thaliana to control (2μM) and surplus (12μM) Zn was evaluated using the camalexin deficient mutant pad3-1 and mtp1-1, a mutant with impaired Zn vacuolar storage, along with the corresponding wildtypes. In vitro, a 50% inhibition of fungal growth was achieved by 440μM Zn. A. thaliana leaves could accumulate equivalent concentrations without harm. In fact, surplus Zn enhanced the resistance of A. thaliana to fungal attack in Columbia (Col-0), Wassilewskija (WS), and mtp1-1. However, surplus Zn was unable to protect pad3-1 demonstrating that Zn cannot substitute for camalexin, the main organic defense in A. thaliana. High, non phytotoxic leaf Zn concentrations enhanced the resistance to A. brassicicola of A. thaliana genotypes able to produce camalexin. This was mainly due to Zn-induced enhancement of the JA/ETH signaling pathway leading to enhanced PAD3 expression. These results support the joint effects hypothesis and highlight the importance of adequate Zn supply for reinforced pathogen resistance. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  11. Gravity-regulated gene expression in Arabidopsis thaliana

    Science.gov (United States)

    Sederoff, Heike; Brown, Christopher S.; Heber, Steffen; Kajla, Jyoti D.; Kumar, Sandeep; Lomax, Terri L.; Wheeler, Benjamin; Yalamanchili, Roopa

    Plant growth and development is regulated by changes in environmental signals. Plants sense environmental changes and respond to them by modifying gene expression programs to ad-just cell growth, differentiation, and metabolism. Functional expression of genes comprises many different processes including transcription, translation, post-transcriptional and post-translational modifications, as well as the degradation of RNA and proteins. Recently, it was discovered that small RNAs (sRNA, 18-24 nucleotides long), which are heritable and systemic, are key elements in regulating gene expression in response to biotic and abiotic changes. Sev-eral different classes of sRNAs have been identified that are part of a non-cell autonomous and phloem-mobile network of regulators affecting transcript stability, translational kinetics, and DNA methylation patterns responsible for heritable transcriptional silencing (epigenetics). Our research has focused on gene expression changes in response to gravistimulation of Arabidopsis roots. Using high-throughput technologies including microarrays and 454 sequencing, we iden-tified rapid changes in transcript abundance of genes as well as differential expression of small RNA in Arabidopsis root apices after minutes of reorientation. Some of the differentially regu-lated transcripts are encoded by genes that are important for the bending response. Functional mutants of those genes respond faster to reorientation than the respective wild type plants, indicating that these proteins are repressors of differential cell elongation. We compared the gravity responsive sRNAs to the changes in transcript abundances of their putative targets and identified several potential miRNA: target pairs. Currently, we are using mutant and transgenic Arabidopsis plants to characterize the function of those miRNAs and their putative targets in gravitropic and phototropic responses in Arabidopsis.

  12. Does Arabidopsis thaliana DREAM of cell cycle control?

    OpenAIRE

    Fischer, Martin; DeCaprio, James A

    2015-01-01

    Strict temporal control of cell cycle gene expression is essential for all eukaryotes including animals and plants. DREAM complexes have been identified in worm, fly, and mammals, linking several distinct transcription factors to coordinate gene expression throughout the cell cycle. In this issue of The EMBO Journal, Kobayashi et al (2015) identify distinct activator and repressor complexes for genes expressed during the G2 and M phases in Arabidopsis that can be temporarily separated during ...

  13. Arbuscular mycorrhizal fungi reduce growth and infect roots of the non-host plant Arabidopsis thaliana.

    Science.gov (United States)

    Veiga, Rita S L; Faccio, Antonella; Genre, Andrea; Pieterse, Corné M J; Bonfante, Paola; van der Heijden, Marcel G A

    2013-11-01

    The arbuscular mycorrhizal (AM) symbiosis is widespread throughout the plant kingdom and important for plant nutrition and ecosystem functioning. Nonetheless, most terrestrial ecosystems also contain a considerable number of non-mycorrhizal plants. The interaction of such non-host plants with AM fungi (AMF) is still poorly understood. Here, in three complementary experiments, we investigated whether the non-mycorrhizal plant Arabidopsis thaliana, the model organism for plant molecular biology and genetics, interacts with AMF. We grew A. thaliana alone or together with a mycorrhizal host species (either Trifolium pratense or Lolium multiflorum) in the presence or absence of the AMF Rhizophagus irregularis. Plants were grown in a dual-compartment system with a hyphal mesh separating roots of A. thaliana from roots of the host species, avoiding direct root competition. The host plants in the system ensured the presence of an active AM fungal network. AM fungal networks caused growth depressions in A. thaliana of more than 50% which were not observed in the absence of host plants. Microscopy analyses revealed that R. irregularis supported by a host plant was capable of infecting A. thaliana root tissues (up to 43% of root length colonized), but no arbuscules were observed. The results reveal high susceptibility of A. thaliana to R. irregularis, suggesting that A. thaliana is a suitable model plant to study non-host/AMF interactions and the biological basis of AM incompatibility. © 2013 John Wiley & Sons Ltd.

  14. Dissecting a hidden gene duplication: the Arabidopsis thaliana SEC10 locus.

    Directory of Open Access Journals (Sweden)

    Nemanja Vukašinović

    Full Text Available Repetitive sequences present a challenge for genome sequence assembly, and highly similar segmental duplications may disappear from assembled genome sequences. Having found a surprising lack of observable phenotypic deviations and non-Mendelian segregation in Arabidopsis thaliana mutants in SEC10, a gene encoding a core subunit of the exocyst tethering complex, we examined whether this could be explained by a hidden gene duplication. Re-sequencing and manual assembly of the Arabidopsis thaliana SEC10 (At5g12370 locus revealed that this locus, comprising a single gene in the reference genome assembly, indeed contains two paralogous genes in tandem, SEC10a and SEC10b, and that a sequence segment of 7 kb in length is missing from the reference genome sequence. Differences between the two paralogs are concentrated in non-coding regions, while the predicted protein sequences exhibit 99% identity, differing only by substitution of five amino acid residues and an indel of four residues. Both SEC10 genes are expressed, although varying transcript levels suggest differential regulation. Homozygous T-DNA insertion mutants in either paralog exhibit a wild-type phenotype, consistent with proposed extensive functional redundancy of the two genes. By these observations we demonstrate that recently duplicated genes may remain hidden even in well-characterized genomes, such as that of A. thaliana. Moreover, we show that the use of the existing A. thaliana reference genome sequence as a guide for sequence assembly of new Arabidopsis accessions or related species has at least in some cases led to error propagation.

  15. Glucosinolates are produced in trichomes of Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Henning eFrerigmann

    2012-10-01

    Full Text Available Glucosinolates are important plant secondary metabolites in plant resistance to herbivors, bacteria and fungi, which have been shown to be accumulating in different organs and tissue types at varying concentrations. There are more than 200 glucosinolate species found in order Brassicales and presence of these compounds is well documented on organ-specific but not on cell-specific level. We used UPLC/ESI-QTOF-MS to measure the presence of glucosinolates and qRT-PCR to analyse the expression of glucosinolate biosynthetic and regulatory genes in isolated A. thaliana trichomes. Trichomes of A. thaliana are shown to synthesize chemoprotective aliphatic and indolic glucosinolates, which are known for their biological activities against fungi, bacterial pathogens or herbivores. UPLC/ESI-QTOF-MS analysis of various indolic glucosinolate mutants reveal increased or decreased levels of indolic glucosinolates in trichomes of gain- and loss-of-function mutants correspondingly. Using pMYB51/HIG1-uidA and pMYB28/PMG1/HAG1-uidA reporter plants we demonstrate that production of these important compounds is activated in trichomes of leaves or inflorescences in response to wounding. Since trichoimes represent the first interface in plant-environment interactions, the possible role of glucosinolate containing trichomes in plant defense or signaling is discussed.

  16. Mode of action of the Arabidopsis thaliana phytoalexin camalexin and its role in Arabidopsis-pathogen interactions.

    Science.gov (United States)

    Rogers, E E; Glazebrook, J; Ausubel, F M

    1996-11-01

    The virulent Arabidopsis thaliana pathogen Pseudomonas syringae pv. maculicola strain ES4326 (Psm ES4326) and other gram-negative bacteria are sensitive to camalexin (3-thiazol-2'-yl-indole), the Arabidopsis phytoalexin. Furthermore, Psm ES4326 is unable to degrade camalexin or to become tolerant to it. Apparently, Psm ES4326 is a successful pathogen even though it elicits synthesis of a host phytoalexin to which it is sensitive. Assays of membrane integrity revealed that, like other phytoalexins, camalexin disrupts bacterial membranes, suggesting that camalexin toxicity is a consequence of membrane disruption. A screen for camalexin-resistant mutants of Psm ES4326 yielded only partially resistant mutants, which displayed partial resistance in both killing and membrane integrity assays. These mutants were also resistant to low concentrations of tetracycline and nalidixic acid, suggesting that they were affected in components of the outer membrane. The mutants were not distinguishable from Psm ES4326 in virulence assays. Camalexin was toxic to Arabidopsis cells growing in tissue culture. However, comparison of the extent of cell death associated with disease symptoms in infected leaves of wild-type Arabidopsis and a camalexin-deficient mutant suggested that camalexin does not contribute significantly to cell death in infected tissue.

  17. Increased Ac excision (iae): Arabidopsis thaliana mutations affecting Ac transposition

    International Nuclear Information System (INIS)

    Jarvis, P.; Belzile, F.; Page, T.; Dean, C.

    1997-01-01

    The maize transposable element Ac is highly active in the heterologous hosts tobacco and tomato, but shows very much reduced levels of activity in Arabidopsis. A mutagenesis experiment was undertaken with the aim of identifying Arabidopsis host factors responsible for the observed low levels of Ac activity. Seed from a line carrying a single copy of the Ac element inserted into the streptomycin phosphotransferase (SPT) reporter fusion, and which displayed typically low levels of Ac activity, were mutagenized using gamma rays. Nineteen mutants displaying high levels of somatic Ac activity, as judged by their highly variegated phenotypes, were isolated after screening the M2 generation on streptomycin-containing medium. The mutations fall into two complementation groups, iae1 and iae2, are unlinked to the SPT::Ac locus and segregate in a Mendelian fashion. The iae1 mutation is recessive and the iae2 mutation is semi-dominant. The iae1 and iae2 mutants show 550- and 70-fold increases, respectively, in the average number of Ac excision sectors per cotyledon. The IAE1 locus maps to chromosome 2, whereas the SPT::Ac reporter maps to chromosome 3. A molecular study of Ac activity in the iae1 mutant confirmed the very high levels of Ac excision predicted using the phenotypic assay, but revealed only low levels of Ac re-insertion. Analyses of germinal transposition in the iae1 mutant demonstrated an average germinal excision frequency of 3% and a frequency of independent Ac re-insertions following germinal excision of 22%. The iae mutants represents a possible means of improving the efficiency of Ac/Ds transposon tagging systems in Arabidopsis, and will enable the dissection of host involvement in Ac transposition and the mechanisms employed for controlling transposable element activity

  18. Does Arabidopsis thaliana DREAM of cell cycle control?

    Science.gov (United States)

    Fischer, Martin; DeCaprio, James A

    2015-08-04

    Strict temporal control of cell cycle gene expression is essential for all eukaryotes including animals and plants. DREAM complexes have been identified in worm, fly, and mammals, linking several distinct transcription factors to coordinate gene expression throughout the cell cycle. In this issue of The EMBO Journal, Kobayashi et al (2015) identify distinct activator and repressor complexes for genes expressed during the G2 and M phases in Arabidopsis that can be temporarily separated during proliferating and post‐mitotic stages of development. The complexes incorporate specific activator and repressor MYB and E2F transcription factors and indicate the possibility of the existence of multiple DREAM complexes in plants.

  19. STN1 protects chromosome ends in Arabidopsis thaliana.

    Science.gov (United States)

    Song, Xiangyu; Leehy, Katherine; Warrington, Ross T; Lamb, Jonathan C; Surovtseva, Yulia V; Shippen, Dorothy E

    2008-12-16

    Telomeres shield the natural ends of chromosomes from nucleolytic attack, recognition as double-strand breaks, and inappropriate processing by DNA repair machinery. The trimeric Stn1/Ten1/Cdc13 complex is critical for chromosome end protection in Saccharomyces cerevisiae, while vertebrate telomeres are protected by shelterin, a complex of six proteins that does not include STN1 or TEN1. Recent studies demonstrate that Stn1 and Ten1 orthologs in Schizosaccharomyces pombe contribute to telomere integrity in a complex that is distinct from the shelterin components, Pot1 and Tpp1. Thus, chromosome-end protection may be mediated by distinct subcomplexes of telomere proteins. Here we report the identification of a STN1 gene in Arabidopsis that is essential for chromosome-end protection. AtSTN1 encodes an 18-kDa protein bearing a single oligonucleotide/oligosaccharide binding fold with significant sequence similarity to the yeast Stn1 proteins. Plants null for AtSTN1 display an immediate onset of growth and developmental defects and reduced fertility. These outward phenotypes are accompanied by catastrophic loss of telomeric and subtelomeric DNA, high levels of end-to-end chromosome fusions, increased G-overhang signals, and elevated telomere recombination. Thus, AtSTN1 is a crucial component of the protective telomere cap in Arabidopsis, and likely in other multicellular eukaryotes.

  20. [Expression of Arabidopsis thaliana thioesterase gene in Pichia pastoris].

    Science.gov (United States)

    Hao, Zhaocheng; Wang, Tengfei; Li, Zhongkui; Hao, Zikai; Dai, Kun; Wang, Ruiming

    2015-01-01

    Thioesterase catalyzes the hydrolysis of acyl-ACP and saturated fatty acyl chain. It plays a key role in the accumulation of medium chain fatty acids in vivo. In this study, to construct an engineering strain to produce MCFAs, the Arabidopsis acyl-ACP thioesterase gene AtFatA was amplified by PCR from cDNA of arabidopsis and double digested by EcoR I/Xba I, then linked to the plasmid digested with same enzymes to get the recombinant plasmid pPICZaA-AtFatA. We transformed the gene into Pichia pastoris GS115 by electroporation and screened positive colonies by YPD medium with Zeocin. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) results showed that the recombinant enzyme had a molecular of 45 kDa band which was consistent with the predicted molecular mass and we constructed the expression system of gene AtFatA in fungus for the first time. Under shake-flask conditions, Gas Chromatograph-Mass Spectrometer-computer results indicated that recombinant strain produced 51% more extracellular free MCFAs than the wild and its yield reached 28.7% of all extracellular fatty acids. This figure is 10% higher than the control group. The result provides a new way to produce MCFAs.

  1. Identification of imprinted genes subject to parent-of-origin specific expression in Arabidopsis thaliana seeds

    LENUS (Irish Health Repository)

    McKeown, Peter C

    2011-08-12

    Abstract Background Epigenetic regulation of gene dosage by genomic imprinting of some autosomal genes facilitates normal reproductive development in both mammals and flowering plants. While many imprinted genes have been identified and intensively studied in mammals, smaller numbers have been characterized in flowering plants, mostly in Arabidopsis thaliana. Identification of additional imprinted loci in flowering plants by genome-wide screening for parent-of-origin specific uniparental expression in seed tissues will facilitate our understanding of the origins and functions of imprinted genes in flowering plants. Results cDNA-AFLP can detect allele-specific expression that is parent-of-origin dependent for expressed genes in which restriction site polymorphisms exist in the transcripts derived from each allele. Using a genome-wide cDNA-AFLP screen surveying allele-specific expression of 4500 transcript-derived fragments, we report the identification of 52 maternally expressed genes (MEGs) displaying parent-of-origin dependent expression patterns in Arabidopsis siliques containing F1 hybrid seeds (3, 4 and 5 days after pollination). We identified these MEGs by developing a bioinformatics tool (GenFrag) which can directly determine the identities of transcript-derived fragments from (i) their size and (ii) which selective nucleotides were added to the primers used to generate them. Hence, GenFrag facilitates increased throughput for genome-wide cDNA-AFLP fragment analyses. The 52 MEGs we identified were further filtered for high expression levels in the endosperm relative to the seed coat to identify the candidate genes most likely representing novel imprinted genes expressed in the endosperm of Arabidopsis thaliana. Expression in seed tissues of the three top-ranked candidate genes, ATCDC48, PDE120 and MS5-like, was confirmed by Laser-Capture Microdissection and qRT-PCR analysis. Maternal-specific expression of these genes in Arabidopsis thaliana F1 seeds was

  2. Azospirillum brasilense ameliorates the response of Arabidopsis thaliana to drought mainly via enhancement of ABA levels.

    Science.gov (United States)

    Cohen, Ana C; Bottini, Rubén; Pontin, Mariela; Berli, Federico J; Moreno, Daniela; Boccanlandro, Hernán; Travaglia, Claudia N; Piccoli, Patricia N

    2015-01-01

    Production of phytohormones is one of the main mechanisms to explain the beneficial effects of plant growth-promoting rhizobacteria (PGPR) such as Azospirillum sp. The PGPRs induce plant growth and development, and reduce stress susceptibility. However, little is known regarding the stress-related phytohormone abscisic acid (ABA) produced by bacteria. We investigated the effects of Azospirillum brasilense Sp 245 strain on Arabidopsis thaliana Col-0 and aba2-1 mutant plants, evaluating the morphophysiological and biochemical responses when watered and in drought. We used an in vitro-grown system to study changes in the root volume and architecture after inoculation with Azospirillum in Arabidopsis wild-type Col-0 and on the mutant aba2-1, during early growth. To examine Arabidopsis development and reproductive success as affected by the bacteria, ABA and drought, a pot experiment using Arabidopsis Col-0 plants was also carried out. Azospirillum brasilense augmented plant biomass, altered root architecture by increasing lateral roots number, stimulated photosynthetic and photoprotective pigments and retarded water loss in correlation with incremented ABA levels. As well, inoculation improved plants seed yield, plants survival, proline levels and relative leaf water content; it also decreased stomatal conductance, malondialdehyde and relative soil water content in plants submitted to drought. Arabidopsis inoculation with A. brasilense improved plants performance, especially in drought. © 2014 Scandinavian Plant Physiology Society.

  3. Characterization and enzymatic properties of protein kinase ACR4 from Arabidopsis thaliana.

    Science.gov (United States)

    Zhao, Yu; Liu, Xuehe; Xu, Ziyan; Yang, Hui; Li, Jixi

    2017-07-22

    Serine/threonine-protein kinase-like protein ARABIDOPSIS CRINKLY4 (ACR4), a transmembrane protein of Arabidopsis thaliana, plays important roles in cell division and differentiation. Although accumulating studies shed light on the function of ACR4, the structure and catalytic mechanism of ACR4 remain to be elucidated. Here, we report the purification and enzymatic properties of the intracellular kinase domain (residues 464-799) of ACR4 (ACR4 IKD ). Through Ni-affinity chromatography and gel filter chromatography methods, we successfully obtain high-purity ACR4 IKD protein from Escherichia coli. Dynamic light scattering and gel-filtration methods reveal that ACR4 IKD distributes with high homogeneity and exists as a monomer in solution. In addition, the ACR4 IKD protein has typical kinase activity with myelin basic protein (MBP) as the substrate. Our study may lay the foundation for structure determination of ACR4 IKD and further functional research, for example, screening significant substrates of ACR4 in Arabidopsis thaliana. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. Molecular evolutionary analysis of the Alfin-like protein family in Arabidopsis lyrata, Arabidopsis thaliana, and Thellungiella halophila.

    Directory of Open Access Journals (Sweden)

    Yu Song

    Full Text Available In previous studies, the Alfin1 gene, a transcription factor, enhanced salt tolerance in alfalfa, primarily through altering gene expression levels in the root. Here, we examined the molecular evolution of the Alfin-like (AL proteins in two Arabidopsis species (A. lyrata and A. thaliana and a salt-tolerant close relative Thellungiella halophila. These AL-like proteins could be divided into four groups and the two known DUF3594 and PHD-finger domains had co-evolved within each group of genes, irrespective of species, due to gene duplication events in the common ancestor of all three species while gene loss was observed only in T. halophila. To detect whether natural selection acted in the evolution of AL genes, we calculated synonymous substitution ratios (dn/ds and codon usage statistics, finding positive selection operated on four branches and significant differences in biased codon usage in the AL family between T. halophila and A. lyrata or A. thaliana. Distinctively, only the AL7 branch was under positive selection on the PHD-finger domain and the three members on the branch showed the smallest difference when codon bias was evaluated among the seven clusters. Functional analysis based on transgenic overexpression lines and T-DNA insertion mutants indicated that salt-stress-induced AtAL7 could play a negative role in salt tolerance of A. thaliana, suggesting that adaptive evolution occurred in the members of AL gene family.

  5. Molecular evolutionary analysis of the Alfin-like protein family in Arabidopsis lyrata, Arabidopsis thaliana, and Thellungiella halophila.

    Science.gov (United States)

    Song, Yu; Gao, Jie; Yang, Fengxi; Kua, Chai-Shian; Liu, Jingxin; Cannon, Charles H

    2013-01-01

    In previous studies, the Alfin1 gene, a transcription factor, enhanced salt tolerance in alfalfa, primarily through altering gene expression levels in the root. Here, we examined the molecular evolution of the Alfin-like (AL) proteins in two Arabidopsis species (A. lyrata and A. thaliana) and a salt-tolerant close relative Thellungiella halophila. These AL-like proteins could be divided into four groups and the two known DUF3594 and PHD-finger domains had co-evolved within each group of genes, irrespective of species, due to gene duplication events in the common ancestor of all three species while gene loss was observed only in T. halophila. To detect whether natural selection acted in the evolution of AL genes, we calculated synonymous substitution ratios (dn/ds) and codon usage statistics, finding positive selection operated on four branches and significant differences in biased codon usage in the AL family between T. halophila and A. lyrata or A. thaliana. Distinctively, only the AL7 branch was under positive selection on the PHD-finger domain and the three members on the branch showed the smallest difference when codon bias was evaluated among the seven clusters. Functional analysis based on transgenic overexpression lines and T-DNA insertion mutants indicated that salt-stress-induced AtAL7 could play a negative role in salt tolerance of A. thaliana, suggesting that adaptive evolution occurred in the members of AL gene family.

  6. Conservation of Arabidopsis thaliana circadian clock genes in Chrysanthemum lavandulifolium.

    Science.gov (United States)

    Fu, Jianxin; Yang, Liwen; Dai, Silan

    2014-07-01

    In Arabidopsis, circadian clock genes play important roles in photoperiod pathway by regulating the daytime expression of CONSTANS (CO), but related reports for chrysanthemum are notably limited. In this study, we isolated eleven circadian clock genes, which lie in the three interconnected negative and positive feedback loops in a wild diploid chrysanthemum, Chrysanthemum lavandulifolium. With the exception of ClELF3, ClPRR1 and ClPRR73, most of the circadian clock genes are expressed more highly in leaves than in other tested tissues. The diurnal rhythms of these circadian clock genes are similar to those of their homologs in Arabidopsis. ClELF3 and ClZTL are constitutively expressed at all time points in both assessed photoperiods. The expression succession from morning to night of the PSEUDO RESPONSE REGULATOR (PRR) gene family occurs in the order ClPRR73/ClPRR37, ClPRR5, and then ClPRR1. ClLHY is expressed during the dawn period, and ClGIs is expressed during the dusk period. The peak expression levels of ClFKF1 and ClGIs are synchronous in the inductive photoperiod. However, in the non-inductive night break (NB) condition or non-24 h photoperiod, the peak expression level of ClFKF1 is significantly changed, indicating that ClFKF1 itself or the synchronous expression of ClFKF1 and ClGIs might be essential to initiate the flowering of C. lavandulifolium. This study provides the first extensive evaluation of circadian clock genes, and it presents a useful foundation for dissecting the functions of circadian clock genes in C. lavandulifolium. Copyright © 2014. Published by Elsevier Masson SAS.

  7. Enhancement of Thiamin Content in Arabidopsis thaliana by Metabolic Engineering.

    Science.gov (United States)

    Dong, Wei; Stockwell, Virginia O; Goyer, Aymeric

    2015-12-01

    Thiamin is an essential nutrient in the human diet. Severe thiamin deficiency leads to beriberi, a lethal disease which is common in developing countries. Thiamin biofortification of staple food crops is a possible strategy to alleviate thiamin deficiency-related diseases. In plants, thiamin plays a role in the response to abiotic and biotic stresses, and data from the literature suggest that boosting thiamin content could increase resistance to stresses. Here, we tested an engineering strategy to increase thiamin content in Arabidopsis. Thiamin is composed of a thiazole ring linked to a pyrimidine ring by a methylene bridge. THI1 and THIC are the first committed steps in the synthesis of the thiazole and pyrimidine moieties, respectively. Arabidopsis plants were transformed with a vector containing the THI1-coding sequence under the control of a constitutive promoter. Total thiamin leaf content in THI1 plants was up approximately 2-fold compared with the wild type. THI1-overexpressing lines were then crossed with pre-existing THIC-overexpressing lines. Resulting THI1 × THIC plants accumulated up to 3.4- and 2.6-fold more total thiamin than wild-type plants in leaf and seeds, respectively. After inoculation with Pseudomonas syringae, THI1 × THIC plants had lower populations than the wild-type control. However, THI1 × THIC plants subjected to various abiotic stresses did not show any visible or biochemical changes compared with the wild type. We discuss the impact of engineering thiamin biosynthesis on the nutritional value of plants and their resistance to biotic and abiotic stresses. © The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  8. Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencing.

    Science.gov (United States)

    Meyers, Blake C; Vu, Tam H; Tej, Shivakundan Singh; Ghazal, Hassan; Matvienko, Marta; Agrawal, Vikas; Ning, Jianchang; Haudenschild, Christian D

    2004-08-01

    Large-scale sequencing of short mRNA-derived tags can establish the qualitative and quantitative characteristics of a complex transcriptome. We sequenced 12,304,362 tags from five diverse libraries of Arabidopsis thaliana using massively parallel signature sequencing (MPSS). A total of 48,572 distinct signatures, each representing a different transcript, were expressed at significant levels. These signatures were compared to the annotation of the A. thaliana genomic sequence; in the five libraries, this comparison yielded between 17,353 and 18,361 genes with sense expression, and between 5,487 and 8,729 genes with antisense expression. An additional 6,691 MPSS signatures mapped to unannotated regions of the genome. Expression was demonstrated for 1,168 genes for which expression data were previously unknown. Alternative polyadenylation was observed for more than 25% of A. thaliana genes transcribed in these libraries. The MPSS expression data suggest that the A. thaliana transcriptome is complex and contains many as-yet uncharacterized variants of normal coding transcripts.

  9. In Arabidopsis thaliana codon volatility scores reflect GC3 composition rather than selective pressure

    Directory of Open Access Journals (Sweden)

    O'Connell Mary J

    2012-07-01

    Full Text Available Abstract Background Synonymous codon usage bias has typically been correlated with, and attributed to translational efficiency. However, there are other pressures on genomic sequence composition that can affect codon usage patterns such as mutational biases. This study provides an analysis of the codon usage patterns in Arabidopsis thaliana in relation to gene expression levels, codon volatility, mutational biases and selective pressures. Results We have performed synonymous codon usage and codon volatility analyses for all genes in the A. thaliana genome. In contrast to reports for species from other kingdoms, we find that neither codon usage nor volatility are correlated with selection pressure (as measured by dN/dS, nor with gene expression levels on a genome wide level. Our results show that codon volatility and usage are not synonymous, rather that they are correlated with the abundance of G and C at the third codon position (GC3. Conclusions Our results indicate that while the A. thaliana genome shows evidence for synonymous codon usage bias, this is not related to the expression levels of its constituent genes. Neither codon volatility nor codon usage are correlated with expression levels or selective pressures but, because they are directly related to the composition of G and C at the third codon position, they are the result of mutational bias. Therefore, in A. thaliana codon volatility and usage do not result from selection for translation efficiency or protein functional shift as measured by positive selection.

  10. Molecular and biochemical characterization of the Fe(III) chelate reductase gene family in Arabidopsis thaliana.

    Science.gov (United States)

    Wu, Huilan; Li, Lihua; Du, Juan; Yuan, Youxi; Cheng, Xudong; Ling, Hong-Qing

    2005-09-01

    Iron chelate reductase is required for iron acquisition from soil and for metabolism in plants. In the genome of Arabidopsis thaliana there are eight genes classified into the iron chelate reductase gene family (AtFROs) based on sequence homology with AtFRO2 (a ferric chelate reductase in Arabidopsis). They are localized on chromosome 1 (three AtFROs) and chromosome 5 (five AtFROs) of Arabidopsis and show a high level of amino acid sequence similarity to each other. An assay for ferric chelate reductase activity revealed that AtFRO2, AtFRO3, AtFRO4, AtFRO5, AtFRO7 and AtFRO8 conferred significantly increased iron reduction activity compared with the control when expressed in yeast cells, indicating that the six AtFROs encode iron chelate reductases functioning in iron homeostasis in Arabidopsis. AtFRO2 displayed the highest iron reduction activity among the AtFROs investigated, further demonstrating that AtFRO2 is a major iron reductase gene in Arabidopsis. AtFRO2 and AtFRO3 were mainly expressed in roots of Arabidopsis, AtFRO5 and AtFRO6 in shoots and flowers, and AtFRO7 in cotyledons and trichomes, whereas the transcription of AtFRO8 was specific for leaf veins. Considering the tissue-specific expression profiles of AtFRO genes, we suggest that AtFRO2 and AtFRO3 are two Fe(III) chelate reductases mainly functioning in iron acquisition and metabolism in Arabidopsis roots, while AtFRO5, AtFRO6, AtFRO7 and AtFRO8 are required for iron homeostasis in different tissues of shoots.

  11. A Shortest-Path-Based Method for the Analysis and Prediction of Fruit-Related Genes in Arabidopsis thaliana.

    Science.gov (United States)

    Zhu, Liucun; Zhang, Yu-Hang; Su, Fangchu; Chen, Lei; Huang, Tao; Cai, Yu-Dong

    2016-01-01

    Biologically, fruits are defined as seed-bearing reproductive structures in angiosperms that develop from the ovary. The fertilization, development and maturation of fruits are crucial for plant reproduction and are precisely regulated by intrinsic genetic regulatory factors. In this study, we used Arabidopsis thaliana as a model organism and attempted to identify novel genes related to fruit-associated biological processes. Specifically, using validated genes, we applied a shortest-path-based method to identify several novel genes in a large network constructed using the protein-protein interactions observed in Arabidopsis thaliana. The described analyses indicate that several of the discovered genes are associated with fruit fertilization, development and maturation in Arabidopsis thaliana.

  12. Crystallization and preliminary X-ray analysis of tubulin-folding cofactor A from Arabidopsis thaliana

    International Nuclear Information System (INIS)

    Lu, Lu; Nan, Jie; Mi, Wei; Wei, Chun-Hong; Li, Lan-Fen; Li, Yi

    2010-01-01

    Tubulin-folding cofactor A from A. thaliana has been crystallized and preliminarily analyzed using X-ray diffraction. Tubulin-folding cofactor A (TFC A) is a molecular post-chaperonin that is involved in the β-tubulin-folding pathway. It has been identified in many organisms including yeasts, humans and plants. In this work, Arabidopsis thaliana TFC A was expressed in Escherichia coli and purified to homogeneity. After thrombin cleavage, a well diffracting crystal was obtained by the sitting-drop vapour-diffusion method at 289 K. The crystal diffracted to 1.6 Å resolution using synchrotron radiation and belonged to space group I4 1 , with unit-cell parameters a = 55.0, b = 55.0, c = 67.4 Å

  13. A family portrait: structural comparison of the Whirly proteins from Arabidopsis thaliana and Solanum tuberosum.

    Science.gov (United States)

    Cappadocia, Laurent; Parent, Jean-Sébastien; Sygusch, Jurgen; Brisson, Normand

    2013-11-01

    DNA double-strand breaks are highly detrimental genomic lesions that routinely arise in genomes. To protect the integrity of their genetic information, all organisms have evolved specialized DNA-repair mechanisms. Whirly proteins modulate DNA repair in plant chloroplasts and mitochondria by binding single-stranded DNA in a non-sequence-specific manner. Although most of the results showing the involvement of the Whirly proteins in DNA repair have been obtained in Arabidopsis thaliana, only the crystal structures of the potato Whirly proteins WHY1 and WHY2 have been reported to date. The present report of the crystal structures of the three Whirly proteins from A. thaliana (WHY1, WHY2 and WHY3) reveals that these structurally similar proteins assemble into tetramers. Furthermore, structural alignment with a potato WHY2-DNA complex reveals that the residues in these proteins are properly oriented to bind single-stranded DNA in a non-sequence-specific manner.

  14. Allelopathic Effects of Plant-Derived Aerosol Smoke on Seed Germination of Arabidopsis thaliana (L.) Heynh

    International Nuclear Information System (INIS)

    Pennacchio, M.; Jefferson, L.V.; Havens, K.

    2007-01-01

    The role that plant-derived smoke plays in promoting seed germination is well documented, but little is known about its ability to inhibit seed germination. To better understand this phenomenon, we tested the effects of eight aerosol smoke treatments on the Columbia-3 ecotype of non dormant Arabidopsis thaliana (L.) Heynh. seeds. Our results revealed that aerosol smoke significantly inhibits germination when seeds were exposed to prolonged periods of aerosol smoke. Short durations of smoke treatments significantly promoted the rate of germination of A. thaliana seed. We briefly discuss this dual regulation of smoke and its possible impact on conservation and restoration practices. We also propose that plant-derived smoke may be another vehicle by which allelo chemicals can be introduced into the environment.

  15. Differential regulation of an auxin-producing nitrilase gene family in Arabidopsis thaliana.

    Science.gov (United States)

    Bartel, B; Fink, G R

    1994-01-01

    Nitrilases (nitrile aminohydrolase, EC 3.5.5.1) convert nitriles to carboxylic acids. We report the cloning, characterization, and expression patterns of four Arabidopsis thaliana nitrilase genes (NIT1-4), one of which was previously described [Bartling, D., Seedorf, M., Mithöfer, A. & Weiler, E. W. (1992) Eur. J. Biochem. 205, 417-424]. The nitrilase genes encode very similar proteins that hydrolyze indole-3-acetonitrile to the phytohormone indole-3-acetic acid in vitro, and three of the four genes are tandemly arranged on chromosome III. Northern analysis using gene-specific probes and analysis of transgenic plants containing promoter-reporter gene fusions indicate that the four genes are differentially regulated. NIT2 expression is specifically induced around lesions caused by bacterial pathogen infiltration. The sites of nitrilase expression may represent sites of auxin biosynthesis in A. thaliana. Images PMID:8022831

  16. Yeast Methylotrophy and Autophagy in a Methanol-Oscillating Environment on Growing Arabidopsis thaliana Leaves

    Science.gov (United States)

    Kawaguchi, Kosuke; Yurimoto, Hiroya; Oku, Masahide; Sakai, Yasuyoshi

    2011-01-01

    The yeast Candida boidinii capable of growth on methanol proliferates and survives on the leaves of Arabidopsis thaliana. The local methanol concentration at the phyllosphere of growing A. thaliana exhibited daily periodicity, and yeast cells responded by altering both the expression of methanol-inducible genes and peroxisome proliferation. Even under these dynamically changing environmental conditions, yeast cells proliferated 3 to 4 times in 11 days. Among the C1-metabolic enzymes, enzymes in the methanol assimilation pathway, but not formaldehyde dissimilation or anti-oxidizing enzymes, were necessary for yeast proliferation at the phyllosphere. Furthermore, both peroxisome assembly and pexophagy, a selective autophagy pathway that degrades peroxisomes, were necessary for phyllospheric proliferation. Thus, the present study sheds light on the life cycle and physiology of yeast in the natural environment at both the molecular and cellular levels. PMID:21966472

  17. Quantitative proteome changes in Arabidopsis thaliana suspension-cultured cells in response to plant natriuretic peptides

    KAUST Repository

    Turek, Ilona

    2015-06-30

    Proteome changes in the Arabidopsis thaliana suspension cells in response to the A. thaliana plant natriuretic peptide (PNP), AtPNP-A (At2g18660) were assessed using quantitative proteomics employing tandem mass tag (TMT) labeling and tandem mass spectrometry (LC–MS/MS). In this study, we characterized temporal responses of suspension-cultured cells to 1 nM and 10 pM AtPNP-A at 0, 10 and 30 min post-treatment. Both concentrations we found to yield a distinct differential proteome signature. The data shown in this article are associated with the article “Plant natriuretic peptides induce a specific set of proteins diagnostic for an adaptive response to abiotic stress” by Turek et al. (Front. Plant Sci. 5 (2014) 661) and have been deposited to the ProteomeXchange with identifier PXD001386.

  18. Efeito das xiloglucanas de sementes e derivados no crescimento de Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Adriana Tourinho Salamoni

    2008-01-01

    Full Text Available Studies on xyloglucan (XG extracted from Hymenaea courbaril L. (jatoba seeds showed that this biopolymer has biological activity that enhanced wheat coleoptiles growth. In apple tree micropropagation, the culture medium containing XG combined with agar induced a higher multiplication rate, rooting rate and root length than medium solidified with agar only. The purpose of this study was to determine the effect of XG from jatobá seeds extracted from jatoba seeds collected in Sinope/MT (XGS and Cuiabá/MT (XGC, and from XGC hydrolysed with a cellulase (XGCH, as well from Tamarindus indica seeds (XGT collected in Bahia/BA, on the growth of in vitro cultured Arabidopsis thaliana plantlets. In the first experiment, XGCH (0.25, 25 and 250 nM or XGC (0.5, 50 and 500 nM were added to a liquid half-strength MS medium. In the second experiment, XGs from several origins were compared: XGC (500 nM, XGS (1200 nM and XGT (800 nM, using culture medium solidified with 6 g.L-1agar. Arabidopsis thaliana L. seeds germinated in Petri plates for 4 to 5 days were transferred to culture media containing the different concentrations of XGs and cultured in a growing room. When the plantlets were cultured in a liquid medium, their growth was very slow in the presence of XGC and XGCH at the highest concentration tested, and it was faster at the lowest concentration. In the semi-solid culture medium, XGs also reduced growth. It was concluded that XGs can play a biological role in Arabidopsis thaliana (L. Heynh. plantlets, stimulating or inhibiting the root system growth and the lateral root formation. These opposite effects varied according to the plant specie that furnished the seeds containing XG, as well as the place where the seeds were collected, to the XG form used (hydrolyzed or not and to its concentration in the culture media.

  19. Reconstruction and analysis of nutrient-induced phosphorylation networks in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Guangyou eDuan

    2013-12-01

    Full Text Available Elucidating the dynamics of molecular processes in living organisms in response to external perturbations is a central goal in modern systems biology. We investigated the dynamics of protein phosphorylation events in Arabidopsis thaliana exposed to changing nutrient conditions. Phosphopeptide expression levels were detected at five consecutive time points over a time interval of 30 minutes after nutrient resupply following prior starvation. The three tested inorganic, ionic nutrients NH4+, NO3-, PO43- elicited similar phosphosignaling responses that were distinguishable from those invoked by the sugars mannitol, sucrose. When embedded in the protein-protein interaction network of Arabidopsis thaliana, phosphoproteins were found to exhibit a higher degree compared to average proteins. Based on the time-series data, we reconstructed a network of regulatory interactions mediated by phosphorylation. The performance of different network inference methods was evaluated by the observed likelihood of physical interactions within and across different subcellular compartments and based on gene ontology semantic similarity. The dynamic phosphorylation network was then reconstructed using a Pearson correlation method with added directionality based on partial variance differences. The topology of the inferred integrated network corresponds to an information dissemination architecture, in which the phosphorylation signal is passed on to an increasing number of phosphoproteins stratified into an initiation, processing, and effector layer. Specific phosphorylation peptide motifs associated with the distinct layers were identified indicating the action of layer-specific kinases. Despite the limited temporal resolution, combined with information on subcellular location, the available time-series data proved useful for reconstructing the dynamics of the molecular signaling cascade in response to nutrient stress conditions in the plant Arabidopsis thaliana.

  20. Constructing gene regulatory networks for long term photosynthetic light acclimation in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Chen Bor-Sen

    2011-08-01

    Full Text Available Abstract Background Photosynthetic light acclimation is an important process that allows plants to optimize the efficiency of photosynthesis, which is the core technology for green energy. However, currently little is known about the molecular mechanisms behind the regulation of the photosynthetic light acclimation response. In this study, a systematic method is proposed to investigate this mechanism by constructing gene regulatory networks from microarray data of Arabidopsis thaliana. Methods The potential TF-gene regulatory pairs of photosynthetic light acclimation have been obtained by data mining of literature and databases. Following the identification of these potential TF-gene pairs, they have been refined using Pearson's correlation, allowing the construction of a rough gene regulatory network. This rough gene regulatory network is then pruned using time series microarray data of Arabidopsis thaliana via the maximum likelihood system identification method and Akaike's system order detection method to approach the real gene regulatory network of photosynthetic light acclimation. Results By comparing the gene regulatory networks under the PSI-to-PSII light shift and the PSII-to-PSI light shift, it is possible to identify important transcription factors for the different light shift conditions. Furthermore, the robustness of the gene network, in particular the hubs and weak linkage points, are also discussed under the different light conditions to gain further insight into the mechanisms of photosynthesis. Conclusions This study investigates the molecular mechanisms of photosynthetic light acclimation for Arabidopsis thaliana from the physiological level. This has been achieved through the construction of gene regulatory networks from the limited data sources and literature via an efficient computation method. If more experimental data for whole-genome ChIP-chip data and microarray data with multiple sampling points becomes available in the

  1. Novel features of radiation-induced bystander signaling in Arabidopsis thaliana demonstrated using root micro-grafting

    OpenAIRE

    Wang, Ting; Li, Fanghua; Xu, Wei; Bian, Po; Wu, Yuejin; Wu, Lijun

    2012-01-01

    Radiation-induced bystander effects (RIBE) have been well demonstrated in whole organisms, as well as in single-cell culture models in vitro and multi-cellular tissues models in vitro, however, the underlying mechanisms remain unclear, including the temporal and spatial course of bystander signaling. The RIBE in vivo has been shown to exist in the model plant Arabidopsis thaliana (A. thaliana). Importantly, the unique plant grafting provides a delicate approach for studying the temporal and s...

  2. Increased level of hemoglobin 1 enhances survival of hypoxic stress and promotes early growth in Arabidopsis thaliana

    OpenAIRE

    Hunt, P. W.; Klok, E. J.; Trevaskis, B.; Watts, R. A.; Ellis, M. H.; Peacock, W. J.; Dennis, E. S.

    2002-01-01

    Overexpression of a class 1 Hb (GLB1) protects Arabidopsis thaliana plants from the effects of severe hypoxia. Overexpression of the bifunctional symbiotic Hb (GLB1S) from Parasponia andersonii in A. thaliana also increases survival after hypoxia. Plants overexpressing the Hb 1 protein, mutated to have a low oxygen affinity, are as susceptible to hypoxia as WT plants, suggesting that the protection against hypoxia depends on the ability of the Hb to bind ligands, such as oxygen, with high aff...

  3. Dynamic subnuclear relocalisation of WRKY40 in response to Abscisic acid in Arabidopsis thaliana

    OpenAIRE

    Geilen, Katja; B?hmer, Maik

    2015-01-01

    WRKY18, WRKY40 and WRKY60 are members of the WRKY transcription factor family and function as transcriptional regulators in ABA signal transduction in Arabidopsis thaliana. Here we show that WRKY18 and WRKY40, but not WRKY60, co-localise with PIF3, PIF4 and PHYB to Phytochrome B-containing nuclear bodies (PNBs). Localisation to the PNBs is phosphorylation-dependent and is inhibited by the general Ser/Thr-kinase inhibitor Staurosporine. Upon ABA treatment, WRKY40 relocalises from PNBs to the n...

  4. Growth enhancement and gene expression of Arabidopsis thaliana irradiated with active oxygen species

    Science.gov (United States)

    Watanabe, Satoshi; Ono, Reoto; Hayashi, Nobuya; Shiratani, Masaharu; Tashiro, Kosuke; Kuhara, Satoru; Inoue, Asami; Yasuda, Kaori; Hagiwara, Hiroko

    2016-07-01

    The characteristics of plant growth enhancement effect and the mechanism of the enhancement induced by plasma irradiation are investigated using various active species in plasma. Active oxygen species in oxygen plasma are effective for growth enhancement of plants. DNA microarray analysis of Arabidopsis thaliana indicates that the genes coding proteins that counter oxidative stresses by eliminating active oxygen species are expressed at significantly high levels. The size of plant cells increases owing to oxygen plasma irradiation. The increases in gene expression levels and cell size suggest that the increase in the expression level of the expansin protein is essential for plant growth enhancement phenomena.

  5. Differential regulation of an auxin-producing nitrilase gene family in Arabidopsis thaliana.

    OpenAIRE

    Bartel, B; Fink, G R

    1994-01-01

    Nitrilases (nitrile aminohydrolase, EC 3.5.5.1) convert nitriles to carboxylic acids. We report the cloning, characterization, and expression patterns of four Arabidopsis thaliana nitrilase genes (NIT1-4), one of which was previously described [Bartling, D., Seedorf, M., Mithöfer, A. & Weiler, E. W. (1992) Eur. J. Biochem. 205, 417-424]. The nitrilase genes encode very similar proteins that hydrolyze indole-3-acetonitrile to the phytohormone indole-3-acetic acid in vitro, and three of the fou...

  6. Biochemical and genetic characterization of three molybdenum cofactor hydroxylases in Arabidopsis thaliana

    DEFF Research Database (Denmark)

    Hoff, Tine; Frandsen, Gitte Inselmann; Rocher, Anne

    1998-01-01

    Aldehyde oxidases and xanthine dehydrogenases/oxidases belong to the molybdenum cofactor dependent hydroxylase class of enzymes. Zymograms show that Arabidopsis thaliana has at least three different aldehyde oxidases and one xanthine oxidase. Three different cDNA clones encoding putative aldehyde...... oxidases (AtAO1, 2, 3) were isolated. An aldehyde oxidase is the last step in abscisic acid (ABA) biosynthesis. AtAO1 is mainly expressed in seeds and roots which might reflect that it is involved in ABA biosynthesis....

  7. ADN ribosomique 5S chez Arabidopsis thaliana : dynamique chromatinienne et ARN polymérase IV

    OpenAIRE

    Douet , Julien

    2008-01-01

    In Arabidopsis thaliana, 5S rRNA genes are found clustered at pericentromeric heterochromatin of chromosomes 3, 4 and 5. 5S rRNA genes transcription is epigenetically regulated through the formation of specific chromatin structure. In order to determine the events that lead to the establishment of such structures, a study during the first steps of post-germinative plant development was done. Unexpectedly, we observed a decondensation followed by a rapid "re"condensation of 5S rDNA chromatin. ...

  8. Blue and Green Light-Induced Phototropism in Arabidopsis thaliana and Lactuca sativa L. Seedlings 1

    Science.gov (United States)

    Steinitz, Benjamin; Ren, Zhangling; Poff, Kenneth L.

    1985-01-01

    Exposure time-response curves for blue and green light-induced phototropic bending in hypocotyls of Arabidopsis thaliana (L.) Heynh. and Lactuca sativa L. seedlings are presented. These seedlings show significant phototropic sensitivity up to 540 to 550 nanometers. Since wave-lengths longer than 560 nanometers do not induce phototropic bending, it is suggested that the response to 510 to 550 nanometers light is mediated by the specific blue light photoreceptor of phototropism. We advise care in the use of green `safelights' for studies of phototropism. PMID:16664021

  9. UV- and gamma-radiation sensitive mutants of Arabidopsis thaliana

    International Nuclear Information System (INIS)

    Jiang, C.Z.; Yen, C.N.; Cronin, K.; Mitchell, D.; Britt, A.B.

    1997-01-01

    Arabidopsis seedlings repair UV-induced DNA damage via light-dependent and -independent pathways. The mechanism of the ''dark repair'' pathway is still unknown. To determine the number of genes required for dark repair and to investigate the substrate-specificity of this process we isolated mutants with enhanced sensitivity to UV radiation in the absence of photoreactivating light. Seven independently derived UV sensitive mutants were isolated from an EMS-mutagenized population. These fell into six complementation groups, two of which (UVR1 and UVH1) have previously been defined. Four of these mutants are defective in the dark repair of UV-induced pyrimidine [6-4] pyrimidinone dimers. These four mutant lines are sensitive to the growth-inhibitory effects of gamma radiation, suggesting that this repair pathway is also involved in the repair of some type of gamma-induced DNA damage product. The requirement for the coordinate action of several different gene products for effective repair of pyrimidine dimers, as well as the nonspecific nature of the repair activity, is consistent with nucleotide excision repair mechanisms previously described in Saccharomyces cerevisiae and nonplant higher eukaryotes and inconsistent with substrate-specific base excision repair mechanisms found in some bacteria, bacteriophage, and fungi. (author)

  10. Arabidopsis thaliana subcellular responses to compatible Erysiphe cichoracearum infections.

    Science.gov (United States)

    Koh, Serry; André, Aurélie; Edwards, Herb; Ehrhardt, David; Somerville, Shauna

    2005-11-01

    Subcellular events of Erysiphe cichoracearum infections of epidermal cells were visualized in living tissues of Arabidopsis plants carrying various green fluorescent protein (GFP)-tagged organelles via laser scanning confocal microscopy. Early in the infection sequence, cytoplasm and organelles moved towards penetration sites and accumulated near penetration pegs. Peroxisomes appeared to accumulate preferentially relative to the cytoplasm at penetration sites. Another early event, which preceded haustorium formation, was the aggregation of some GFP-tagged plasma membrane marker proteins into rings around penetration sites, which extended across cell-wall boundaries into neighboring cells. This feature localized to sites where papillae were deposited. The extrahaustorial membrane (EHM) encases the fungal feeding structure, the haustorium, separating it from the host cytoplasm. Eight plasma membrane markers were excluded from the EHM and remained in a collar-like formation around the haustorial neck. These observations support the suggestions that the EHM is a unique, specialized membrane and is different from the plasma membrane. Our results suggested two possibilities for the origin of the EHM: invagination of the plasma membrane coupled with membrane differentiation; or de novo synthesis of the EHM by targeted vesicle trafficking.

  11. Arogenate Dehydratase Isoforms Differentially Regulate Anthocyanin Biosynthesis in Arabidopsis thaliana.

    Science.gov (United States)

    Chen, Qingbo; Man, Cong; Li, Danning; Tan, Huijuan; Xie, Ye; Huang, Jirong

    2016-12-05

    Anthocyanins, a group of L-phenylalanine (Phe)-derived flavonoids, have been demonstrated to play important roles in plant stress resistance and interactions between plants and insects. Although the anthocyanin biosynthetic pathway and its regulatory mechanisms have been extensively studied, it remains unclear whether the level of Phe supply affects anthocyanin biosynthesis. Here, we investigated the roles of arogenate dehydratases (ADTs), the key enzymes that catalyze the conversion of arogenate into Phe, in sucrose-induced anthocyanin biosynthesis in Arabidopsis. Genetic analysis showed that all six ADT isoforms function redundantly in anthocyanin biosynthesis but have differential contributions. ADT2 contributes the most to anthocyanin accumulation, followed by ADT1 and ADT3, and ADT4-ADT6. We found that anthocyanin content is positively correlated with the levels of Phe and sucrose-induced ADT transcripts in seedlings. Consistently, addition of Phe to the medium could dramatically increase anthocyanin content in the wild-type plants and rescue the phenotype of the adt1 adt3 double mutant regarding the anthocyanin accumulation. Moreover, transgenic plants overexpressing ADT4, which appears to be less sensitive to Phe than overexpression of ADT2, hyperaccumulate Phe and produce elevated level of anthocyanins. Taken together, our results suggest that the level of Phe is an important regulatory factor for sustaining anthocyanin biosynthesis. Copyright © 2016 The Author. Published by Elsevier Inc. All rights reserved.

  12. Arabidopsis thaliana - Myzus persicae interaction: shaping the understanding of plant defense against phloem-feeding aphids

    Directory of Open Access Journals (Sweden)

    Joe eLouis

    2013-07-01

    Full Text Available The phloem provides a unique niche for several organisms. Aphids are a large group of Hemipteran insects that utilize stylets present in their mouthparts to pierce sieve elements and drink large volumes of phloem sap. In addition, many aphids also vector viral diseases. Myzus persicae, commonly known as the green peach aphid (GPA, is an important pest of a large variety of plants that includes Arabidopsis thaliana. This review summarizes recent studies that have exploited the compatible interaction between Arabidopsis and GPA to understand the molecular and physiological mechanisms utilized by plants to control aphid infestation, as well as genes and mechanisms that contribute to susceptibility. In addition, recent efforts to identify aphid-delivered elicitors of plant defenses and novel aphid salivary components that facilitate infestation are also discussed.

  13. Specific Arabidopsis thaliana malic enzyme isoforms can provide anaplerotic pyruvate carboxylation function in Saccharomyces cerevisiae.

    Science.gov (United States)

    Badia, Mariana Beatriz; Mans, Robert; Lis, Alicia V; Tronconi, Marcos Ariel; Arias, Cintia Lucía; Maurino, Verónica Graciela; Andreo, Carlos Santiago; Drincovich, María Fabiana; van Maris, Antonius J A; Gerrard Wheeler, Mariel Claudia

    2017-02-01

    NAD(P)-malic enzyme (NAD(P)-ME) catalyzes the reversible oxidative decarboxylation of malate to pyruvate, CO 2 , and NAD(P)H and is present as a multigene family in Arabidopsis thaliana. The carboxylation reaction catalyzed by purified recombinant Arabidopsis NADP-ME proteins is faster than those reported for other animal or plant isoforms. In contrast, no carboxylation activity could be detected in vitro for the NAD-dependent counterparts. In order to further investigate their putative carboxylating role in vivo, Arabidopsis NAD(P)-ME isoforms, as well as the NADP-ME2del2 (with a decreased ability to carboxylate pyruvate) and NADP-ME2R115A (lacking fumarate activation) versions, were functionally expressed in the cytosol of pyruvate carboxylase-negative (Pyc - ) Saccharomyces cerevisiae strains. The heterologous expression of NADP-ME1, NADP-ME2 (and its mutant proteins), and NADP-ME3 restored the growth of Pyc - S. cerevisiae on glucose, and this capacity was dependent on the availability of CO 2 . On the other hand, NADP-ME4, NAD-ME1, and NAD-ME2 could not rescue the Pyc - strains from C 4 auxotrophy. NADP-ME carboxylation activity could be measured in leaf crude extracts of knockout and overexpressing Arabidopsis lines with modified levels of NADP-ME, where this activity was correlated with the amount of NADP-ME2 transcript. These results indicate that specific A. thaliana NADP-ME isoforms are able to play an anaplerotic role in vivo and provide a basis for the study on the carboxylating activity of NADP-ME, which may contribute to the synthesis of C 4 compounds and redox shuttling in plant cells. © 2017 Federation of European Biochemical Societies.

  14. Analysis and visualization of Arabidopsis thaliana GWAS using web 2.0 technologies.

    Science.gov (United States)

    Huang, Yu S; Horton, Matthew; Vilhjálmsson, Bjarni J; Seren, Umit; Meng, Dazhe; Meyer, Christopher; Ali Amer, Muhammad; Borevitz, Justin O; Bergelson, Joy; Nordborg, Magnus

    2011-01-01

    With large-scale genomic data becoming the norm in biological studies, the storing, integrating, viewing and searching of such data have become a major challenge. In this article, we describe the development of an Arabidopsis thaliana database that hosts the geographic information and genetic polymorphism data for over 6000 accessions and genome-wide association study (GWAS) results for 107 phenotypes representing the largest collection of Arabidopsis polymorphism data and GWAS results to date. Taking advantage of a series of the latest web 2.0 technologies, such as Ajax (Asynchronous JavaScript and XML), GWT (Google-Web-Toolkit), MVC (Model-View-Controller) web framework and Object Relationship Mapper, we have created a web-based application (web app) for the database, that offers an integrated and dynamic view of geographic information, genetic polymorphism and GWAS results. Essential search functionalities are incorporated into the web app to aid reverse genetics research. The database and its web app have proven to be a valuable resource to the Arabidopsis community. The whole framework serves as an example of how biological data, especially GWAS, can be presented and accessed through the web. In the end, we illustrate the potential to gain new insights through the web app by two examples, showcasing how it can be used to facilitate forward and reverse genetics research. Database URL: http://arabidopsis.usc.edu/

  15. DEWAX Transcription Factor Is Involved in Resistance to Botrytis cinerea in Arabidopsis thaliana and Camelina sativa

    Directory of Open Access Journals (Sweden)

    Seulgi Ju

    2017-07-01

    Full Text Available The cuticle of land plants is the first physical barrier to protect their aerial parts from biotic and abiotic stresses. DEWAX, an AP2/ERF-type transcription factor, negatively regulates cuticular wax biosynthesis. In this study, we investigated the resistance to Botrytis cinerea in Arabidopsis thaliana and Camelina sativa overexpressing DEWAX and in Arabidopsis dewax mutant. Compared to wild type (WT leaves, Arabidopsis DEWAX OX and dewax leaves were more and less permeable to toluidine blue dye, respectively. The ROS levels increased in DEWAX OX leaves, but decreased in dewax relative to WT leaves. Compared to WT, DEWAX OX was more resistant, while dewax was more sensitive to B. cinerea; however, defense responses to Pseudomonas syringae pv. tomato DC3000:GFP were inversely modulated. Microarray and RT-PCR analyses indicated that the expression of defense-related genes was upregulated in DEWAX OX, but downregulated in dewax relative to WT. Transactivation assay showed that DEWAX upregulated the expression of PDF1.2a, IGMT1, and PRX37. Chromatin immunoprecipitation assay revealed that DEWAX directly interacts with the GCC-box motifs of PDF1.2a promoter. In addition, ectopic expression of DEWAX increased the tolerance to B. cinerea in C. sativa. Taken together, we suggest that increased ROS accumulation and DEWAX-mediated upregulation of defense-related genes are closely associated with enhanced resistance to B. cinerea in Arabidopsis and C. sativa.

  16. Biochemical and structural properties of cyanases from Arabidopsis thaliana and Oryza sativa.

    Directory of Open Access Journals (Sweden)

    Dan Qian

    Full Text Available Cyanate is toxic to all organisms. Cyanase converts cyanate to CO₂ and NH₃ in a bicarbonate-dependent reaction. The biophysical functions and biochemical characteristics of plant cyanases are poorly studied, although it has been investigated in a variety of proteobacteria, cyanobacteria and fungi. In this study, we characterised plant cyanases from Arabidopsis thaliana and Oryza sativa (AtCYN and OsCYN. Prokaryotic-expressed AtCYN and OsCYN both showed cyanase activity in vitro. Temperature had a similar influence on the activity of both cyanases, but pH had a differential impact on AtCYN and OsCYN activity. Homology modelling provided models of monomers of AtCYN and OsCYN, and a coimmunoprecipitation assay and gel filtration indicated that AtCYN and OsCYN formed homodecamers. The analysis of single-residue mutants of AtCYN indicated that the conserved catalytic residues also contributed to the stability of the homodecamer. KCNO treatment inhibited Arabidopsis germination and early seedling growth. Plants containing AtCYN or OsCYN exhibited resistance to KCNO stress, which demonstrated that one role of cyanases in plants is detoxification. Transcription level of AtCYN was higher in the flower than in other organs of Arabidopsis. AtCYN transcription was not significantly affected by KCNO treatment in Arabidopsis, but was induced by salt stress. This research broadens our knowledge on plant detoxification of cyanate via cyanase.

  17. Genetic basis for dosage sensitivity in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Isabelle M Henry

    2007-04-01

    Full Text Available Aneuploidy, the relative excess or deficiency of specific chromosome types, results in gene dosage imbalance. Plants can produce viable and fertile aneuploid individuals, while most animal aneuploids are inviable or developmentally abnormal. The swarms of aneuploid progeny produced by Arabidopsis triploids constitute an excellent model to investigate the mechanisms governing dosage sensitivity and aneuploid syndromes. Indeed, genotype alters the frequency of aneuploid types within these swarms. Recombinant inbred lines that were derived from a triploid hybrid segregated into diploid and tetraploid individuals. In these recombinant inbred lines, a single locus, which we call SENSITIVE TO DOSAGE IMBALANCE (SDI, exhibited segregation distortion in the tetraploid subpopulation only. Recent progress in quantitative genotyping now allows molecular karyotyping and genetic analysis of aneuploid populations. In this study, we investigated the causes of the ploidy-specific distortion at SDI. Allele frequency was distorted in the aneuploid swarms produced by the triploid hybrid. We developed a simple quantitative measure for aneuploidy lethality and using this measure demonstrated that distortion was greatest in the aneuploids facing the strongest viability selection. When triploids were crossed to euploids, the progeny, which lack severe aneuploids, exhibited no distortion at SDI. Genetic characterization of SDI in the aneuploid swarm identified a mechanism governing aneuploid survival, perhaps by buffering the effects of dosage imbalance. As such, SDI could increase the likelihood of retaining genomic rearrangements such as segmental duplications. Additionally, in species where triploids are fertile, aneuploid survival would facilitate gene flow between diploid and tetraploid populations via a triploid bridge and prevent polyploid speciation. Our results demonstrate that positional cloning of loci affecting traits in populations containing ploidy and

  18. Transcriptomic responses to aluminum stress in roots of Arabidopsis thaliana.

    Science.gov (United States)

    Kumari, Manjeet; Taylor, Gregory J; Deyholos, Michael K

    2008-04-01

    To help characterize the cellular mechanisms underlying the toxicity of Al to plants, we present the first large-scale, transcriptomic analysis of root responses to Al, using a microarray representing approximately 93% of the predicted genes in the genome of Arabidopsis. More transcripts were responsive to Al (25 microM) during long (48 h, 1,114 genes), as compared to short (6 h, 401 genes) exposures, which contrasts with previous microarray analyses of plant responses to other types of abiotic stress. Exposure to Al triggered changes in the transcript levels for several genes related to oxidative stress pathway, membrane transporters, cell wall, energy, and polysaccharide metabolism. Interestingly, lack of abundance of transcripts encoding TCA cycle enzymes, except for malate dehydrogenase, suggested that synthesis of organic anions in response to Al may not be transcriptionally regulated. Al exposures induced differential abundance of transcripts for several ribosomal proteins, peptidases and protein phosphatases mostly after 48 h. We also detected increased abundance of transcripts for several membrane receptor kinases and non-membrane calcium response kinases, which could play a role in transmission of Al-stress signals. Among Al responsive transcription factors, the most predominant families identified were AP2/EREBP, MYB and bHLH. Further, we studied the kinetics of Al stress responses for class III peroxidases using Q-RT-PCR. Our results indicated that Al triggered dynamic changes in transcript abundance of various peroxidases within 1 h. The results of this screen contribute to the identification of candidate genes for the generation of Al-tolerant transgenic plants.

  19. Spatio-Temporal Expression Patterns of Arabidopsis thaliana and Medicago truncatula Defensin-Like Genes

    Science.gov (United States)

    Nallu, Sumitha; Wang, Lin; Botanga, Christopher J.; Gomez, S. Karen; Costa, Liliana M.; Harrison, Maria J.; Samac, Deborah A.; Glazebrook, Jane; Katagiri, Fumiaki; Gutierrez-Marcos, Jose F.; VandenBosch, Kathryn A.

    2013-01-01

    Plant genomes contain several hundred defensin-like (DEFL) genes that encode short cysteine-rich proteins resembling defensins, which are well known antimicrobial polypeptides. Little is known about the expression patterns or functions of many DEFLs because most were discovered recently and hence are not well represented on standard microarrays. We designed a custom Affymetrix chip consisting of probe sets for 317 and 684 DEFLs from Arabidopsis thaliana and Medicago truncatula, respectively for cataloging DEFL expression in a variety of plant organs at different developmental stages and during symbiotic and pathogenic associations. The microarray analysis provided evidence for the transcription of 71% and 90% of the DEFLs identified in Arabidopsis and Medicago, respectively, including many of the recently annotated DEFL genes that previously lacked expression information. Both model plants contain a subset of DEFLs specifically expressed in seeds or fruits. A few DEFLs, including some plant defensins, were significantly up-regulated in Arabidopsis leaves inoculated with Alternaria brassicicola or Pseudomonas syringae pathogens. Among these, some were dependent on jasmonic acid signaling or were associated with specific types of immune responses. There were notable differences in DEFL gene expression patterns between Arabidopsis and Medicago, as the majority of Arabidopsis DEFLs were expressed in inflorescences, while only a few exhibited root-enhanced expression. By contrast, Medicago DEFLs were most prominently expressed in nitrogen-fixing root nodules. Thus, our data document salient differences in DEFL temporal and spatial expression between Arabidopsis and Medicago, suggesting distinct signaling routes and distinct roles for these proteins in the two plant species. PMID:23527067

  20. Spatio-temporal expression patterns of Arabidopsis thaliana and Medicago truncatula defensin-like genes.

    Directory of Open Access Journals (Sweden)

    Mesfin Tesfaye

    Full Text Available Plant genomes contain several hundred defensin-like (DEFL genes that encode short cysteine-rich proteins resembling defensins, which are well known antimicrobial polypeptides. Little is known about the expression patterns or functions of many DEFLs because most were discovered recently and hence are not well represented on standard microarrays. We designed a custom Affymetrix chip consisting of probe sets for 317 and 684 DEFLs from Arabidopsis thaliana and Medicago truncatula, respectively for cataloging DEFL expression in a variety of plant organs at different developmental stages and during symbiotic and pathogenic associations. The microarray analysis provided evidence for the transcription of 71% and 90% of the DEFLs identified in Arabidopsis and Medicago, respectively, including many of the recently annotated DEFL genes that previously lacked expression information. Both model plants contain a subset of DEFLs specifically expressed in seeds or fruits. A few DEFLs, including some plant defensins, were significantly up-regulated in Arabidopsis leaves inoculated with Alternaria brassicicola or Pseudomonas syringae pathogens. Among these, some were dependent on jasmonic acid signaling or were associated with specific types of immune responses. There were notable differences in DEFL gene expression patterns between Arabidopsis and Medicago, as the majority of Arabidopsis DEFLs were expressed in inflorescences, while only a few exhibited root-enhanced expression. By contrast, Medicago DEFLs were most prominently expressed in nitrogen-fixing root nodules. Thus, our data document salient differences in DEFL temporal and spatial expression between Arabidopsis and Medicago, suggesting distinct signaling routes and distinct roles for these proteins in the two plant species.

  1. Floral and insect-induced volatile formation in Arabidopsis lyrata ssp. petraea, a perennial, outcrossing relative of A. thaliana

    OpenAIRE

    Abel, Christian; Clauss, Maria; Schaub, Andrea; Gershenzon, Jonathan; Tholl, Dorothea

    2009-01-01

    Volatile organic compounds have been reported to serve some important roles in plant communication with other organisms, but little is known about the biological functions of most of these substances. To gain insight into this problem, we have compared differences in floral and vegetative volatiles between two closely related plant species with different life histories. The self-pollinating annual, Arabidopsis thaliana, and its relative, the outcrossing perennial, Arabidopsis lyrata, have mar...

  2. In Silico Evaluation of Predicted Regulatory Interactions in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Tranchina Daniel

    2009-12-01

    Full Text Available Abstract Background Prediction of transcriptional regulatory mechanisms in Arabidopsis has become increasingly critical with the explosion of genomic data now available for both gene expression and gene sequence composition. We have shown in previous work 1, that a combination of correlation measurements and cis-regulatory element (CRE detection methods are effective in predicting targets for candidate transcription factors for specific case studies which were validated. However, to date there has been no quantitative assessment as to which correlation measures or CRE detection methods used alone or in combination are most effective in predicting TF→target relationships on a genome-wide scale. Results We tested several widely used methods, based on correlation (Pearson and Spearman Rank correlation and cis-regulatory element (CRE detection (≥1 CRE or CRE over-representation, to determine which of these methods individually or in combination is the most effective by various measures for making regulatory predictions. To predict the regulatory targets of a transcription factor (TF of interest, we applied these methods to microarray expression data for genes that were regulated over treatment and control conditions in wild type (WT plants. Because the chosen data sets included identical experimental conditions used on TF over-expressor or T-DNA knockout plants, we were able to test the TF→target predictions made using microarray data from WT plants, with microarray data from mutant/transgenic plants. For each method, or combination of methods, we computed sensitivity, specificity, positive and negative predictive value and the F-measure of balance between sensitivity and positive predictive value (precision. This analysis revealed that the ≥1 CRE and Spearman correlation (used alone or in combination were the most balanced CRE detection and correlation methods, respectively with regard to their power to accurately predict regulatory

  3. Genome-wide comparative analysis of the IQD gene families in Arabidopsis thaliana and Oryza sativa

    Science.gov (United States)

    Abel, Steffen; Savchenko, Tatyana; Levy, Maggie

    2005-01-01

    Background Calcium signaling plays a prominent role in plants for coordinating a wide range of developmental processes and responses to environmental cues. Stimulus-specific generation of intracellular calcium transients, decoding of calcium signatures, and transformation of the signal into cellular responses are integral modules of the transduction process. Several hundred proteins with functions in calcium signaling circuits have been identified, and the number of downstream targets of calcium sensors is expected to increase. We previously identified a novel, calmodulin-binding nuclear protein, IQD1, which stimulates glucosinolate accumulation and plant defense in Arabidopsis thaliana. Here, we present a comparative genome-wide analysis of a new class of putative calmodulin target proteins in Arabidopsis and rice. Results We identified and analyzed 33 and 29 IQD1-like genes in Arabidopsis thaliana and Oryza sativa, respectively. The encoded IQD proteins contain a plant-specific domain of 67 conserved amino acid residues, referred to as the IQ67 domain, which is characterized by a unique and repetitive arrangement of three different calmodulin recruitment motifs, known as the IQ, 1-5-10, and 1-8-14 motifs. We demonstrated calmodulin binding for IQD20, the smallest IQD protein in Arabidopsis, which consists of a C-terminal IQ67 domain and a short N-terminal extension. A striking feature of IQD proteins is the high isoelectric point (~10.3) and frequency of serine residues (~11%). We compared the Arabidopsis and rice IQD gene families in terms of gene structure, chromosome location, predicted protein properties and motifs, phylogenetic relationships, and evolutionary history. The existence of an IQD-like gene in bryophytes suggests that IQD proteins are an ancient family of calmodulin-binding proteins and arose during the early evolution of land plants. Conclusion Comparative phylogenetic analyses indicate that the major IQD gene lineages originated before the

  4. Differential expression and regulation of iron-regulated metal transporters in Arabidopsis halleri and Arabidopsis thaliana--the role in zinc tolerance.

    Science.gov (United States)

    Shanmugam, Varanavasiappan; Lo, Jing-Chi; Wu, Chia-Lin; Wang, Shan-Li; Lai, Chong-Cheong; Connolly, Erin L; Huang, Jing-Ling; Yeh, Kuo-Chen

    2011-04-01

    To avoid zinc (Zn) toxicity, plants have developed a Zn homeostasis mechanism to cope with Zn excess in the surrounding soil. In this report, we uncovered the difference of a cross-homeostasis system between iron (Fe) and Zn in dealing with Zn excess in the Zn hyperaccumulator Arabidopsis halleri ssp. gemmifera and nonhyperaccumulator Arabidopsis thaliana. Arabidopsis halleri shows low expression of the Fe acquisition and deficiency response-related genes IRT1 and IRT2 compared with A. thaliana. In A. thaliana, lowering the expression of IRT1 and IRT2 through the addition of excess Fe to the medium increases Zn tolerance. Excess Zn induces significant Fe deficiency in A. thaliana and reduces Fe accumulation in shoots. By contrast, the accumulation of Fe in shoots of A. halleri was stable under various Zn treatments. Root ferric chelate reductase (FRO) activity and expression of FIT are low in A. halleri compared with A. thaliana. Overexpressing a ZIP family member IRT3 in irt1-1, rescues the Fe-deficient phenotype. A fine-tuned Fe homeostasis mechanism in A. halleri maintains optimum Fe level by Zn-regulated ZIP transporters and prevents high Zn uptake through Fe-regulated metal transporters, and in part be responsible for Zn tolerance. © 2011 The Authors. New Phytologist © 2011 New Phytologist Trust.

  5. Sensitivity of two ecotypes of Arabidopsis Thaliana (Cvi and Te) towards UV-B irradiation

    International Nuclear Information System (INIS)

    Velichkova, M.; Stanoeva, D.; Popova, A.

    2013-01-01

    he susceptibility of Arabidopsis thaliana towards the detrimental effect of UV-B irradiation was investigated using two ecotypes, Cvi and Te. The effect of UV-B treatment on primary photosynthetic reactions - energy interaction between the main pigment-protein complexes and oxygen evolution, was evaluated at low (4 0 C) and at room (22 0 C) temperature. UV-B-induced alterations of investigated photosynthetic reactions are better expressed at 22 0 C than at 4 0 C for Cvi. For Te ecotype the energy interaction was suppressed to higher extent at 22 0 C, while oxygen evolving activity was affected similarly at both temperatures. At low and room temperature, the energy interaction in the complex PSII-core antenna is affected stronger by UV-B treatment than the energy distribution between both photosystems, as revealed by fluorescence ratios of 77 K spectra. The results presented indicate that the Arabidopsis thaliana ecotype Cvi (Cape Verde Islands) is less affected by UV-B irradiation in respect to the investigated primary photosynthetic reactions than the ecotype Te (Finland)

  6. Natural genetic variation in Arabidopsis thaliana defense metabolism genes modulates field fitness

    Science.gov (United States)

    Kerwin, Rachel; Feusier, Julie; Corwin, Jason; Rubin, Matthew; Lin, Catherine; Muok, Alise; Larson, Brandon; Li, Baohua; Joseph, Bindu; Francisco, Marta; Copeland, Daniel; Weinig, Cynthia; Kliebenstein, Daniel J

    2015-01-01

    Natural populations persist in complex environments, where biotic stressors, such as pathogen and insect communities, fluctuate temporally and spatially. These shifting biotic pressures generate heterogeneous selective forces that can maintain standing natural variation within a species. To directly test if genes containing causal variation for the Arabidopsis thaliana defensive compounds, glucosinolates (GSL) control field fitness and are therefore subject to natural selection, we conducted a multi-year field trial using lines that vary in only specific causal genes. Interestingly, we found that variation in these naturally polymorphic GSL genes affected fitness in each of our environments but the pattern fluctuated such that highly fit genotypes in one trial displayed lower fitness in another and that no GSL genotype or genotypes consistently out-performed the others. This was true both across locations and within the same location across years. These results indicate that environmental heterogeneity may contribute to the maintenance of GSL variation observed within Arabidopsis thaliana. DOI: http://dx.doi.org/10.7554/eLife.05604.001 PMID:25867014

  7. An ANN-GA model based promoter prediction in Arabidopsis thaliana using tilling microarray data.

    Science.gov (United States)

    Mishra, Hrishikesh; Singh, Nitya; Misra, Krishna; Lahiri, Tapobrata

    2011-01-01

    Identification of promoter region is an important part of gene annotation. Identification of promoters in eukaryotes is important as promoters modulate various metabolic functions and cellular stress responses. In this work, a novel approach utilizing intensity values of tilling microarray data for a model eukaryotic plant Arabidopsis thaliana, was used to specify promoter region from non-promoter region. A feed-forward back propagation neural network model supported by genetic algorithm was employed to predict the class of data with a window size of 41. A dataset comprising of 2992 data vectors representing both promoter and non-promoter regions, chosen randomly from probe intensity vectors for whole genome of Arabidopsis thaliana generated through tilling microarray technique was used. The classifier model shows prediction accuracy of 69.73% and 65.36% on training and validation sets, respectively. Further, a concept of distance based class membership was used to validate reliability of classifier, which showed promising results. The study shows the usability of micro-array probe intensities to predict the promoter regions in eukaryotic genomes.

  8. Natural variation of root exudates in Arabidopsis thaliana-linking metabolomic and genomic data.

    Science.gov (United States)

    Mönchgesang, Susann; Strehmel, Nadine; Schmidt, Stephan; Westphal, Lore; Taruttis, Franziska; Müller, Erik; Herklotz, Siska; Neumann, Steffen; Scheel, Dierk

    2016-07-01

    Many metabolomics studies focus on aboveground parts of the plant, while metabolism within roots and the chemical composition of the rhizosphere, as influenced by exudation, are not deeply investigated. In this study, we analysed exudate metabolic patterns of Arabidopsis thaliana and their variation in genetically diverse accessions. For this project, we used the 19 parental accessions of the Arabidopsis MAGIC collection. Plants were grown in a hydroponic system, their exudates were harvested before bolting and subjected to UPLC/ESI-QTOF-MS analysis. Metabolite profiles were analysed together with the genome sequence information. Our study uncovered distinct metabolite profiles for root exudates of the 19 accessions. Hierarchical clustering revealed similarities in the exudate metabolite profiles, which were partly reflected by the genetic distances. An association of metabolite absence with nonsense mutations was detected for the biosynthetic pathways of an indolic glucosinolate hydrolysis product, a hydroxycinnamic acid amine and a flavonoid triglycoside. Consequently, a direct link between metabolic phenotype and genotype was detected without using segregating populations. Moreover, genomics can help to identify biosynthetic enzymes in metabolomics experiments. Our study elucidates the chemical composition of the rhizosphere and its natural variation in A. thaliana, which is important for the attraction and shaping of microbial communities.

  9. DNA fingerprinting and new tools for fine-scale discrimination of Arabidopsis thaliana accessions.

    Science.gov (United States)

    Simon, Matthieu; Simon, Adeline; Martins, Fréderic; Botran, Lucy; Tisné, Sébastien; Granier, Fabienne; Loudet, Olivier; Camilleri, Christine

    2012-03-01

    One of the main strengths of Arabidopsis thaliana as a model species is the impressive number of public resources available to the scientific community. Exploring species genetic diversity--and therefore adaptation--relies on collections of individuals from natural populations taken from diverse environments. Nevertheless, due to a few mislabeling events or genotype mixtures, some variants available in stock centers have been misidentified, causing inconsistencies and limiting the potential of genetic analyses. To improve the identification of natural accessions, we genotyped 1311 seed stocks from our Versailles Arabidopsis Stock Center and from other collections to determine their molecular profiles at 341 single nucleotide polymorphism markers. These profiles were used to compare genotypes at both the intra- and inter-accession levels. We confirmed previously described inconsistencies and revealed new ones, and suggest likely identities for accessions whose lineage had been lost. We also developed two new tools: a minimal fingerprint computation to quickly verify the identity of an accession, and an optimized marker set to assist in the identification of unknown or mixed accessions. These tools are available on a dedicated web interface called ANATool (https://www.versailles.inra.fr/ijpb/crb/anatool) that provides a simple and efficient means to verify or determine the identity of A. thaliana accessions in any laboratory, without the need for any specific or expensive technology. © 2011 The Authors. The Plant Journal © 2011 Blackwell Publishing Ltd.

  10. ERECTA Regulates Cell Elongation by Activating Auxin Biosynthesis in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Xiaoya Qu

    2017-09-01

    Full Text Available The ERECTA family genes, ERECTA (ER, ERECTA-LIKE1 (ERL1, and ERECTA-LIKE2 (ERL2, encode leucine-rich repeat receptor-like kinases in Arabidopsis thaliana. Knocking out these three genes can cause severe phenotypes, which indicates that they play significant roles in plant growth and development. However, the molecular mechanism within remains unclear. Here we show that the short hypocotyl phenotypes of er erl1 erl2 mutants are mainly due to the defects of cell elongation rather than the cell division. In contrast, in the ERECTA overexpression transgenic plants, the hypocotyl length is increased with elongated cells. Moreover, we show that the er erl1 erl2 triple mutant contains a low level of auxin, and the expression levels of the key auxin biosynthesis genes are significantly reduced. Consistent with this observation, increasing exogenous or endogenous auxin levels could partially rescue the cell elongation defects of the er erl1 erl2 triple mutant. Therefore, our results provide a molecular basis for auxin mediated ERECTA control of the hypocotyl length in Arabidopsis thaliana.

  11. Functional interactome of Aquaporin 1 sub-family reveals new physiological functions in Arabidopsis Thaliana

    Directory of Open Access Journals (Sweden)

    Mohamed Ragab Abdel Gawwad

    2013-09-01

    Full Text Available Aquaporins are channel proteins found in plasma membranes and intercellular membranes of different cellular compartments, facilitate the water flux, solutes and gases across the cellular plasma membranes. The present study highlights the sub-family plasma membrane intrinsic protein (PIP predicting the 3-D structure and analyzing the functional interactome of it homologs. PIP1 homologs integrate with many proteins with different plant physiological roles in Arabidopsis thaliana including; PIP1A and PIP1B: facilitate the transport of water, diffusion of amino acids and/or peptides from the vacuolar compartment to the cytoplasm, play a role in the control of cell turgor and cell expansion and involved in root water uptake respectively. In addition we found that PIP1B plays a defensive role against Pseudomonas syringae infection through the interaction with the plasma membrane Rps2 protein. Another substantial function of PIP1C via the interaction with PIP2E is the response to nematode infection. Generally, PIP1 sub-family interactome controlling many physiological processes in plant cell like; osmoregulation in plants under high osmotic stress such as under a high salt, response to nematode, facilitate the transport of water across cell membrane and regulation of floral initiation in Arabidopsis thaliana.

  12. Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Natacha Bodenhausen

    Full Text Available Diverse communities of bacteria inhabit plant leaves and roots and those bacteria play a crucial role for plant health and growth. Arabidopsis thaliana is an important model to study plant pathogen interactions, but little is known about its associated bacterial community under natural conditions. We used 454 pyrosequencing to characterize the bacterial communities associated with the roots and the leaves of wild A. thaliana collected at 4 sites; we further compared communities on the outside of the plants with communities in the endophytic compartments. We found that the most heavily sequenced bacteria in A. thaliana associated community are related to culturable species. Proteobacteria, Actinobacteria, and Bacteroidetes are the most abundant phyla in both leaf and root samples. At the genus level, sequences of Massilia and Flavobacterium are prevalent in both samples. Organ (leaf vs root and habitat (epiphytes vs endophytes structure the community. In the roots, richness is higher in the epiphytic communities compared to the endophytic compartment (P = 0.024, while the reverse is true for the leaves (P = 0.032. Interestingly, leaf and root endophytic compartments do not differ in richness, diversity and evenness, while they differ in community composition (P = 0.001. The results show that although the communities associated with leaves and roots share many bacterial species, the associated communities differ in structure.

  13. The AraGWAS Catalog: a curated and standardized Arabidopsis thaliana GWAS catalog.

    Science.gov (United States)

    Togninalli, Matteo; Seren, Ümit; Meng, Dazhe; Fitz, Joffrey; Nordborg, Magnus; Weigel, Detlef; Borgwardt, Karsten; Korte, Arthur; Grimm, Dominik G

    2018-01-04

    The abundance of high-quality genotype and phenotype data for the model organism Arabidopsis thaliana enables scientists to study the genetic architecture of many complex traits at an unprecedented level of detail using genome-wide association studies (GWAS). GWAS have been a great success in A. thaliana and many SNP-trait associations have been published. With the AraGWAS Catalog (https://aragwas.1001genomes.org) we provide a publicly available, manually curated and standardized GWAS catalog for all publicly available phenotypes from the central A. thaliana phenotype repository, AraPheno. All GWAS have been recomputed on the latest imputed genotype release of the 1001 Genomes Consortium using a standardized GWAS pipeline to ensure comparability between results. The catalog includes currently 167 phenotypes and more than 222 000 SNP-trait associations with P Catalog can be accessed via a modern web-interface and provides various features to easily access, download and visualize the results and summary statistics across GWAS. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  14. Allyl Isothiocyanate Inhibits Actin-Dependent Intracellular Transport in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Bjørnar Sporsheim

    2015-12-01

    Full Text Available Volatile allyl isothiocyanate (AITC derives from the biodegradation of the glucosinolate sinigrin and has been associated with growth inhibition in several plants, including the model plant Arabidopsis thaliana. However, the underlying cellular mechanisms of this feature remain scarcely investigated in plants. In this study, we present evidence of an AITC-induced inhibition of actin-dependent intracellular transport in A. thaliana. A transgenic line of A. thaliana expressing yellow fluorescent protein (YFP-tagged actin filaments was used to show attenuation of actin filament movement by AITC. This appeared gradually in a time- and dose-dependent manner and resulted in actin filaments appearing close to static. Further, we employed four transgenic lines with YFP-fusion proteins labeling the Golgi apparatus, endoplasmic reticulum (ER, vacuoles and peroxisomes to demonstrate an AITC-induced inhibition of actin-dependent intracellular transport of or, in these structures, consistent with the decline in actin filament movement. Furthermore, the morphologies of actin filaments, ER and vacuoles appeared aberrant following AITC-exposure. However, AITC-treated seedlings of all transgenic lines tested displayed morphologies and intracellular movements similar to that of the corresponding untreated and control-treated plants, following overnight incubation in an AITC-absent environment, indicating that AITC-induced decline in actin-related movements is a reversible process. These findings provide novel insights into the cellular events in plant cells following exposure to AITC, which may further expose clues to the physiological significance of the glucosinolate-myrosinase system.

  15. The AraGWAS Catalog: a curated and standardized Arabidopsis thaliana GWAS catalog

    Science.gov (United States)

    Togninalli, Matteo; Seren, Ümit; Meng, Dazhe; Fitz, Joffrey; Nordborg, Magnus; Weigel, Detlef

    2018-01-01

    Abstract The abundance of high-quality genotype and phenotype data for the model organism Arabidopsis thaliana enables scientists to study the genetic architecture of many complex traits at an unprecedented level of detail using genome-wide association studies (GWAS). GWAS have been a great success in A. thaliana and many SNP-trait associations have been published. With the AraGWAS Catalog (https://aragwas.1001genomes.org) we provide a publicly available, manually curated and standardized GWAS catalog for all publicly available phenotypes from the central A. thaliana phenotype repository, AraPheno. All GWAS have been recomputed on the latest imputed genotype release of the 1001 Genomes Consortium using a standardized GWAS pipeline to ensure comparability between results. The catalog includes currently 167 phenotypes and more than 222 000 SNP-trait associations with P < 10−4, of which 3887 are significantly associated using permutation-based thresholds. The AraGWAS Catalog can be accessed via a modern web-interface and provides various features to easily access, download and visualize the results and summary statistics across GWAS. PMID:29059333

  16. Human Norovirus and Its Surrogates Induce Plant Immune Response in Arabidopsis thaliana and Lactuca sativa.

    Science.gov (United States)

    Markland, Sarah M; Bais, Harsh; Kniel, Kalmia E

    2017-08-01

    Human norovirus is the leading cause of foodborne illness worldwide with the majority of outbreaks linked to fresh produce and leafy greens. It is essential that we thoroughly understand the type of relationship and interactions that take place between plants and human norovirus to better utilize control strategies to reduce transmission of norovirus in the field onto plants harvested for human consumption. In this study the expression of gene markers for the salicylic acid (SA) and jasmonic acid (JA) plant defense pathways was measured and compared in romaine lettuce (Lactuca sativa) and Arabidopsis thaliana Col-0 plants that were inoculated with Murine Norovirus-1, Tulane Virus, human norovirus GII.4, or Hank's Balanced Salt Solution (control). Genes involving both the SA and JA pathways were expressed in both romaine lettuce and A. thaliana for all three viruses, as well as controls. Studies, including gene expression of SA- and JA-deficient A. thaliana mutant lines, suggest that the JA pathway is more likely involved in the plant immune response to human norovirus. This research provides the first pieces of information regarding how foodborne viruses interact with plants in the preharvest environment.

  17. Translocation of Bacillus thuringiensis in Phaseolus vulgaris tissues and vertical transmission in Arabidopsis thaliana.

    Science.gov (United States)

    García-Suárez, R; Verduzco-Rosas, L A; Del Rincón-Castro, M C; Délano-Frier, J P; Ibarra, J E

    2017-04-01

    To demonstrate the ability of Bacillus thuringiensis to penetrate as spore-crystal complex to the internal tissues of bean plants, and keep its insecticidal activity. To test the vertical transmission of the spore-crystal complex in Arabidopsis thaliana. The experimental strain was transformed with the pMUTIN-gfp plasmid which labelled the spores of B. thuringiensis HD-73 with the GFP protein. Once the rhizosphere of the bean plants was inoculated with the labelled strain, the bacterium was recovered from leaves, stems, and petioles. Furthermore, toxicity of treated plants was significantly higher than control plants when bio-assayed on cabbage looper larvae. The labelled strain was recovered from the dead insects. When the rhizosphere of A. thaliana plants was inoculated with the labelled strain, mature seeds from these plants were surface-sterilized and grown under in vitro conditions. The labelled strain was recovered from the seedlings. We showed that B. thuringiensis subsp. kurstaki (HD-73) in the rhizosphere can translocate to upper tissues of bean plants, and keep its insecticidal activity. Transmission of the labelled B. thuringiensis strain passed to the next generation of A. thaliana. The role of B. thuringiensis as a potential facultative endophyte bacterium and the possible biotechnological repercussions are discussed. © 2017 The Society for Applied Microbiology.

  18. Carpeloidy in flower evolution and diversification: a comparative study in Carica papaya and Arabidopsis thaliana.

    Science.gov (United States)

    Ronse De Craene, Louis; Tréhin, Christophe; Morel, Patrice; Negrutiu, Ioan

    2011-06-01

    Bisexual flowers of Carica papaya range from highly regular flowers to morphs with various fusions of stamens to the ovary. Arabidopsis thaliana sup1 mutants have carpels replaced by chimeric carpel-stamen structures. Comparative analysis of stamen to carpel conversions in the two different plant systems was used to understand the stage and origin of carpeloidy when derived from stamen tissues, and consequently to understand how carpeloidy contributes to innovations in flower evolution. Floral development of bisexual flowers of Carica was studied by scanning electron microscopy and was compared with teratological sup mutants of A. thaliana. In Carica development of bisexual flowers was similar to wild (unisexual) forms up to locule initiation. Feminization ranges from fusion of stamen tissue to the gynoecium to complete carpeloidy of antepetalous stamens. In A. thaliana, partial stamen feminization occurs exclusively at the flower apex, with normal stamens forming at the periphery. Such transformations take place relatively late in development, indicating strong developmental plasticity of most stamen tissues. These results are compared with evo-devo theories on flower bisexuality, as derived from unisexual ancestors. The Arabidopsis data highlight possible early evolutionary events in the acquisition of bisexuality by a patchy transformation of stamen parts into female parts linked to a flower axis-position effect. The Carica results highlight tissue-fusion mechanisms in angiosperms leading to carpeloidy once bisexual flowers have evolved. We show two different developmental routes leading to stamen to carpel conversions by late re-specification. The process may be a fundamental aspect of flower development that is hidden in most instances by developmental homeostasis.

  19. Characterization of two Arabidopsis thaliana myb-like proteins showing affinity to telomeric DNA sequence.

    Science.gov (United States)

    Schrumpfová, Petra; Kuchar, Milan; Miková, Gabriela; Skrísovská, Lenka; Kubicárová, Tatiana; Fajkus, Jirí

    2004-04-01

    Telomere-binding proteins participate in forming a functional nucleoprotein structure at chromosome ends. Using a genomic approach, two Arabidopsis thaliana genes coding for candidate Myb-like telomere binding proteins were cloned and expressed in E. coli. Both proteins, termed AtTBP2 (accession Nos. T46051 (protein database) and GI:638639 (nucleotide database); 295 amino acids, 32 kDa, pI 9.53) and AtTBP3 (BAB08466, GI:9757879; 299 amino acids, 33 kDa, pI 9.88), contain a single Myb-like DNA-binding domain at the N-terminus, and a histone H1/H5-like DNA-binding domain in the middle of the protein sequence. Both proteins are expressed in various A. thaliana tissues. Using the two-hybrid system interaction between the proteins AtTBP2 and AtTBP3 and self interactions of each of the proteins were detected. Gel-retardation assays revealed that each of the two proteins is able to bind the G-rich strand and double-stranded DNA of plant telomeric sequence with an affinity proportional to a number of telomeric repeats. Substrates bearing a non-telomeric DNA sequence positioned between two telomeric repeats were bound with an efficiency depending on the length of interrupting sequence. The ability to bind variant telomere sequences decreased with sequence divergence from the A. thaliana telomeric DNA. None of the proteins alone or their mixture affects telomerase activity in vitro. Correspondingly, no interaction was observed between any of two proteins and the Arabidopsis telomerase reverse transcriptase catalytic subunit TERT (accession No. AF172097) using two-hybrid assay.

  20. The flowering repressor SVP underlies a novel Arabidopsis thaliana QTL interacting with the genetic background.

    Science.gov (United States)

    Méndez-Vigo, Belén; Martínez-Zapater, José M; Alonso-Blanco, Carlos

    2013-01-01

    The timing of flowering initiation is a fundamental trait for the adaptation of annual plants to different environments. Large amounts of intraspecific quantitative variation have been described for it among natural accessions of many species, but the molecular and evolutionary mechanisms underlying this genetic variation are mainly being determined in the model plant Arabidopsis thaliana. To find novel A. thaliana flowering QTL, we developed introgression lines from the Japanese accession Fuk, which was selected based on the substantial transgression observed in an F(2) population with the reference strain Ler. Analysis of an early flowering line carrying a single Fuk introgression identified Flowering Arabidopsis QTL1 (FAQ1). We fine-mapped FAQ1 in an 11 kb genomic region containing the MADS transcription factor gene SHORT VEGETATIVE PHASE (SVP). Complementation of the early flowering phenotype of FAQ1-Fuk with a SVP-Ler transgen demonstrated that FAQ1 is SVP. We further proved by directed mutagenesis and transgenesis that a single amino acid substitution in SVP causes the loss-of-function and early flowering of Fuk allele. Analysis of a worldwide collection of accessions detected FAQ1/SVP-Fuk allele only in Asia, with the highest frequency appearing in Japan, where we could also detect a potential ancestral genotype of FAQ1/SVP-Fuk. In addition, we evaluated allelic and epistatic interactions of SVP natural alleles by analysing more than one hundred transgenic lines carrying Ler or Fuk SVP alleles in five genetic backgrounds. Quantitative analyses of these lines showed that FAQ1/SVP effects vary from large to small depending on the genetic background. These results support that the flowering repressor SVP has been recently selected in A. thaliana as a target for early flowering, and evidence the relevance of genetic interactions for the intraspecific evolution of FAQ1/SVP and flowering time.

  1. The flowering repressor SVP underlies a novel Arabidopsis thaliana QTL interacting with the genetic background.

    Directory of Open Access Journals (Sweden)

    Belén Méndez-Vigo

    Full Text Available The timing of flowering initiation is a fundamental trait for the adaptation of annual plants to different environments. Large amounts of intraspecific quantitative variation have been described for it among natural accessions of many species, but the molecular and evolutionary mechanisms underlying this genetic variation are mainly being determined in the model plant Arabidopsis thaliana. To find novel A. thaliana flowering QTL, we developed introgression lines from the Japanese accession Fuk, which was selected based on the substantial transgression observed in an F(2 population with the reference strain Ler. Analysis of an early flowering line carrying a single Fuk introgression identified Flowering Arabidopsis QTL1 (FAQ1. We fine-mapped FAQ1 in an 11 kb genomic region containing the MADS transcription factor gene SHORT VEGETATIVE PHASE (SVP. Complementation of the early flowering phenotype of FAQ1-Fuk with a SVP-Ler transgen demonstrated that FAQ1 is SVP. We further proved by directed mutagenesis and transgenesis that a single amino acid substitution in SVP causes the loss-of-function and early flowering of Fuk allele. Analysis of a worldwide collection of accessions detected FAQ1/SVP-Fuk allele only in Asia, with the highest frequency appearing in Japan, where we could also detect a potential ancestral genotype of FAQ1/SVP-Fuk. In addition, we evaluated allelic and epistatic interactions of SVP natural alleles by analysing more than one hundred transgenic lines carrying Ler or Fuk SVP alleles in five genetic backgrounds. Quantitative analyses of these lines showed that FAQ1/SVP effects vary from large to small depending on the genetic background. These results support that the flowering repressor SVP has been recently selected in A. thaliana as a target for early flowering, and evidence the relevance of genetic interactions for the intraspecific evolution of FAQ1/SVP and flowering time.

  2. Genotype-environment interactions affect flower and fruit herbivory and plant chemistry of Arabidopsis thaliana in a transplant experiment

    NARCIS (Netherlands)

    Mosleh Arany, A.; de Jong, T.; Kim, H.K.; Van Dam, N.M.; Choi, Y.L.; van Mil, H.G.J.; Verpoorte, R.; van der Meijden, E.

    2009-01-01

    Large differences exist in flower and fruit herbivory between dune and inland populations of plants of Arabidopsis thaliana (Brassicaceae). Two specialist weevils Ceutorhynchus atomus and C. contractus (Curculionidae) and their larvae are responsible for this pattern in herbivory. We test, by means

  3. Analysis of the chromatin domain organisation around the plastocyanin gene reveals an MAR-specific sequence element in Arabidopsis thaliana

    NARCIS (Netherlands)

    van Drunen, C. M.; Oosterling, R. W.; Keultjes, G. M.; Weisbeek, P. J.; van Driel, R.; Smeekens, S. C.

    1997-01-01

    The Arabidopsis thaliana genome is currently being sequenced, eventually leading towards the unravelling of all potential genes. We wanted to gain more insight into the way this genome might be organized at the ultrastructural level. To this extent we identified matrix attachment regions demarking

  4. Epistasis × environment interactions among Arabidopsis thaliana glucosinolate genes impact complex traits and fitness in the field

    DEFF Research Database (Denmark)

    Kerwin, Rachel E.; Feusier, Julie; Muok, Alise

    2017-01-01

    (GSL) defense chemistry, leaf damage, and relative fitness using mutant lines of Arabidopsis thaliana varying at pairs of causal aliphatic GSL defense genes to test the impact of epistatic and epistasis × environment interactions on adaptive trait variation. We found that aliphatic GSL accumulation...

  5. Probing cytokinin homeostasis in Arabidopsis thaliana by constitutively overexpressing two forms of the maize cytokinin oxidase/dehydrogenase 1 gene

    Czech Academy of Sciences Publication Activity Database

    Kopečný, D.; Tarkowski, Petr; Majira, M.; Bouchez-Mahiout, I.; Nogué, F.; Laurière, M.; Sandberg, G.; Laloue, M.; Houba-Hérin, N.

    2006-01-01

    Roč. 171, č. 1 (2006), s. 114-122 ISSN 0168-9452 Institutional research plan: CEZ:AV0Z50380511 Keywords : Arabidopsis thaliana * Cytokinin oxidase/dehydrogenase * Homeostasis Subject RIV: CE - Biochemistry Impact factor: 1.631, year: 2006

  6. Structure and development of somatic embryos formed in Arabidopsis thaliana pt mutant callus cultures derived from seedlings

    NARCIS (Netherlands)

    Recklinghausen, von I.R.; Iwanowska, A.; Kieft, H.; Mordhorst, A.P.; Schel, J.H.N.; Lammeren, van A.A.M.

    2000-01-01

    Seeds of the Arabidopsis thaliana mutant primordia timing (pt) were germinated in 2,4-dichlorophenoxyacetic acid- containing liquid medium. The seedlings formed somatic embryos and nonembryogenic and embryogenic callus in vitro in a time period of approximately two to three weeks. Embryogenesis and

  7. Effect of abscisic acid on stomatal opening in isolated epidermal strips of abi mutants of Arabidopsis thaliana

    NARCIS (Netherlands)

    Roelfsema, MRG; Prins, HBA

    1995-01-01

    Abscisic acid-insensitive mutants of Arabidopsis thaliana L. var. Landsberg erecta were selected for their decreased sensitivity to ABA during germination. Two of these mutants, abi-1 and abi-2, display a wilty phenotype as adult plants, indicating disturbed water relations. Experiments were

  8. Root hair defective4 encodes a phosphatidylinositol-4-phosphate phosphatase required for proper root hair development in Arabidopsis thaliana

    NARCIS (Netherlands)

    Thole, J.M.; Vermeer, J.E.M.; Zhang, Y.; Gadella, Th.W.J.; Nielsen, E.

    2008-01-01

    Polarized expansion of root hair cells in Arabidopsis thaliana is improperly controlled in root hair-defective rhd4-1 mutant plants, resulting in root hairs that are shorter and randomly form bulges along their length. Using time-lapse fluorescence microscopy in rhd4-1 root hairs, we analyzed

  9. ARABIDOPSIS THALIANA HOMEOBOX25 uncovers a role for Gibberellins in seed longevity.

    Science.gov (United States)

    Bueso, Eduardo; Muñoz-Bertomeu, Jesús; Campos, Francisco; Brunaud, Veronique; Martínez, Liliam; Sayas, Enric; Ballester, Patricia; Yenush, Lynne; Serrano, Ramón

    2014-02-01

    Seed longevity is crucial for agriculture and plant genetic diversity, but it is limited by cellular damage during storage. Seeds are protected against aging by cellular defenses and by structures such as the seed coat. We have screened an activation-tagging mutant collection of Arabidopsis (Arabidopsis thaliana) and selected four dominant mutants with improved seed longevity (isl1-1D to isl4-1D) under both natural and accelerated aging conditions. In the isl1-1D mutant, characterized in this work, overexpression of the transcription factor ARABIDOPSIS THALIANA HOMEOBOX25 (ATHB25; At5g65410) increases the expression of GIBBERELLIC ACID3-OXIDASE2, encoding a gibberellin (GA) biosynthetic enzyme, and the levels of GA1 and GA4 are higher (3.2- and 1.4-fold, respectively) in the mutant than in the wild type. The morphological and seed longevity phenotypes of the athb25-1D mutant were recapitulated in transgenic plants with moderate (4- to 6-fold) overexpression of ATHB25. Simultaneous knockdown of ATHB25, ATHB22, and ATHB31 expression decreases seed longevity, as does loss of ATHB25 and ATHB22 function in a double mutant line. Seeds from wild-type plants treated with GA and from a quintuple DELLA mutant (with constitutive GA signaling) are more tolerant to aging, providing additional evidence for a role of GA in seed longevity. A correlation was observed in several genotypes between seed longevity and mucilage formation at the seed surface, suggesting that GA may act by reinforcing the seed coat. This mechanism was supported by the observation of a maternal effect in reciprocal crosses between the wild type and the athb25-1D mutant.

  10. ARABIDOPSIS THALIANA HOMEOBOX25 Uncovers a Role for Gibberellins in Seed Longevity1[C][W

    Science.gov (United States)

    Bueso, Eduardo; Muñoz-Bertomeu, Jesús; Campos, Francisco; Brunaud, Veronique; Martínez, Liliam; Sayas, Enric; Ballester, Patricia; Yenush, Lynne; Serrano, Ramón

    2014-01-01

    Seed longevity is crucial for agriculture and plant genetic diversity, but it is limited by cellular damage during storage. Seeds are protected against aging by cellular defenses and by structures such as the seed coat. We have screened an activation-tagging mutant collection of Arabidopsis (Arabidopsis thaliana) and selected four dominant mutants with improved seed longevity (isl1-1D to isl4-1D) under both natural and accelerated aging conditions. In the isl1-1D mutant, characterized in this work, overexpression of the transcription factor ARABIDOPSIS THALIANA HOMEOBOX25 (ATHB25; At5g65410) increases the expression of GIBBERELLIC ACID3-OXIDASE2, encoding a gibberellin (GA) biosynthetic enzyme, and the levels of GA1 and GA4 are higher (3.2- and 1.4-fold, respectively) in the mutant than in the wild type. The morphological and seed longevity phenotypes of the athb25-1D mutant were recapitulated in transgenic plants with moderate (4- to 6-fold) overexpression of ATHB25. Simultaneous knockdown of ATHB25, ATHB22, and ATHB31 expression decreases seed longevity, as does loss of ATHB25 and ATHB22 function in a double mutant line. Seeds from wild-type plants treated with GA and from a quintuple DELLA mutant (with constitutive GA signaling) are more tolerant to aging, providing additional evidence for a role of GA in seed longevity. A correlation was observed in several genotypes between seed longevity and mucilage formation at the seed surface, suggesting that GA may act by reinforcing the seed coat. This mechanism was supported by the observation of a maternal effect in reciprocal crosses between the wild type and the athb25-1D mutant. PMID:24335333

  11. The rapidly evolving centromere-specific histone has stringent functional requirements in Arabidopsis thaliana.

    Science.gov (United States)

    Ravi, Maruthachalam; Kwong, Pak N; Menorca, Ron M G; Valencia, Joel T; Ramahi, Joseph S; Stewart, Jodi L; Tran, Robert K; Sundaresan, Venkatesan; Comai, Luca; Chan, Simon W-L

    2010-10-01

    Centromeres control chromosome inheritance in eukaryotes, yet their DNA structure and primary sequence are hypervariable. Most animals and plants have megabases of tandem repeats at their centromeres, unlike yeast with unique centromere sequences. Centromere function requires the centromere-specific histone CENH3 (CENP-A in human), which replaces histone H3 in centromeric nucleosomes. CENH3 evolves rapidly, particularly in its N-terminal tail domain. A portion of the CENH3 histone-fold domain, the CENP-A targeting domain (CATD), has been previously shown to confer kinetochore localization and centromere function when swapped into human H3. Furthermore, CENP-A in human cells can be functionally replaced by CENH3 from distantly related organisms including Saccharomyces cerevisiae. We have used cenh3-1 (a null mutant in Arabidopsis thaliana) to replace endogenous CENH3 with GFP-tagged variants. A H3.3 tail domain-CENH3 histone-fold domain chimera rescued viability of cenh3-1, but CENH3's lacking a tail domain were nonfunctional. In contrast to human results, H3 containing the A. thaliana CATD cannot complement cenh3-1. GFP-CENH3 from the sister species A. arenosa functionally replaces A. thaliana CENH3. GFP-CENH3 from the close relative Brassica rapa was targeted to centromeres, but did not complement cenh3-1, indicating that kinetochore localization and centromere function can be uncoupled. We conclude that CENH3 function in A. thaliana, an organism with large tandem repeat centromeres, has stringent requirements for functional complementation in mitosis.

  12. AtHKT1 drives adaptation of Arabidopsis thaliana to salinity by reducing floral sodium content.

    Science.gov (United States)

    An, Dong; Chen, Jiu-Geng; Gao, Yi-Qun; Li, Xiang; Chao, Zhen-Fei; Chen, Zi-Ru; Li, Qian-Qian; Han, Mei-Ling; Wang, Ya-Ling; Wang, Yong-Fei; Chao, Dai-Yin

    2017-10-01

    Arabidopsis thaliana high-affinity potassium transporter 1 (AtHKT1) limits the root-to-shoot sodium transportation and is believed to be essential for salt tolerance in A. thaliana. Nevertheless, natural accessions with 'weak allele' of AtHKT1, e.g. Tsu-1, are mainly distributed in saline areas and are more tolerant to salinity. These findings challenge the role of AtHKT1 in salt tolerance and call into question the involvement of AtHKT1 in salinity adaptation in A. thaliana. Here, we report that AtHKT1 indeed drives natural variation in the salt tolerance of A. thaliana and the coastal AtHKT1, so-called weak allele, is actually hyper-functional in reducing flowers sodium content upon salt stress. Our data showed that AtHKT1 positively contributes to saline adaptation in a linear manner. Forward and reverse genetics analysis established that the single AtHKT1 locus is responsible for the variation in the salinity adaptation between Col-0 and Tsu-1. Reciprocal grafting experiments revealed that shoot AtHKT1 determines the salt tolerance of Tsu-1, whereas root AtHKT1 primarily drives the salt tolerance of Col-0. Furthermore, evidence indicated that Tsu-1 AtHKT1 is highly expressed in stems and is more effective compared to Col-0 AtHKT1 at limiting sodium flow to the flowers. Such efficient retrieval of sodium to the reproductive organ endows Tsu-1 with stronger fertility compared to Col-0 upon salt stress, thus improving Tsu-1 adaptation to a coastal environment. To conclude, our data not only confirm the role of AtHKT1 in saline adaptation, but also sheds light on our understanding of the salt tolerance mechanisms in plants.

  13. Genome wide analysis of stress responsive WRKY transcription factors in Arabidopsis thaliana

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    Shaiq Sultan

    2016-04-01

    Full Text Available WRKY transcription factors are a class of DNA-binding proteins that bind with a specific sequence C/TTGACT/C known as W-Box found in promoters of genes which are regulated by these WRKYs. From previous studies, 43 different stress responsive WRKY transcription factors in Arabidopsis thaliana, identified and then categorized in three groups viz., abiotic, biotic and both of these stresses. A comprehensive genome wide analysis including chromosomal localization, gene structure analysis, multiple sequence alignment, phylogenetic analysis and promoter analysis of these WRKY genes was carried out in this study to determine the functional homology in Arabidopsis. This analysis led to the classification of these WRKY family members into 3 major groups and subgroups and showed evolutionary relationship among these groups on the base of their functional WRKY domain, chromosomal localization and intron/exon structure. The proposed groups of these stress responsive WRKY genes and annotation based on their position on chromosomes can also be explored to determine their functional homology in other plant species in relation to different stresses. The result of the present study provides indispensable genomic information for the stress responsive WRKY transcription factors in Arabidopsis and will pave the way to explain the precise role of various AtWRKYs in plant growth and development under stressed conditions.

  14. TORNADO1 regulates root epidermal patterning through the WEREWOLF pathway in Arabidopsis thaliana.

    Science.gov (United States)

    Kwak, Su-Hwan; Song, Sang-Kee; Lee, Myeong Min; Schiefelbein, John

    2015-01-01

    Cell fate in the root epidermis of Arabidopsis thaliana is determined in a position-dependent manner. SCRAMBLED (SCM), an atypical leucine-rich repeat receptor-like kinase, mediates this positional regulation via its effect on WEREWOLF (WER) expression, and subsequently, its downstream transcription factor, GLABRA2 (GL2), which are required for nonhair cell development. Previously, TORNADO1 (TRN1), a plant-specific protein with a leucine-rich repeat ribonuclease inhibitor-like domain, was shown to be required for proper epidermal patterning in Arabidopsis roots. In this work, we analyzed the possible involvement of TRN1 in the known root epidermal gene network. We discovered that the trn1 mutant caused the ectopic expression of WER and the randomized expression of GL2 and EGL3. This suggests that TRN1 regulates the position-dependent cell fate determination by affecting WER expression in Arabidopsis root epidermis. Additionally, the distinct phenotypes of the aerial parts of the trn1-t and scm-2 mutant suggest that TRN1 and SCM might have different functions in the development of aerial parts.

  15. Accumulation and phytotoxicity of perfluorooctanoic acid in the model plant species Arabidopsis thaliana

    International Nuclear Information System (INIS)

    Yang, Xinping; Ye, Chengchen; Liu, Yu; Zhao, Fang-Jie

    2015-01-01

    Perfluorooctanoic acid (PFOA) is widely used in the manufacture of many industrial and household products. To assess the potential environmental risk of PFOA, its accumulation, translocation and phytotoxic effects were investigated using the model plant species Arabidopsis thaliana. Exposure to 18 μM PFOA-F in agar plates did not affect plant growth, but 181–1811 μM PFOA-F inhibited root and shoot growth. PFOA was more phytotoxic on shoot growth than NaF at the equivalent F concentration, with the latter having 3.9–7.6 times higher EC50 for shoot biomass than PFOA. PFOA was efficiently translocated from roots to shoots, where it existed as intact PFOA molecules without transformation evidenced by the 19 F NMR spectra. PFOA caused a significant increase in the concentration of H 2 O 2 and malondialdehyde (MDA) in shoots, indicating that oxidative stress is a likely cause of PFOA phytotoxicity. - Highlights: • PFOA is more phytotoxic on shoot growth than NaF at the equivalent F concentration. • PFOA is readily taken up and translocated from roots to shoots. • PFOA exists as intact molecules without transformation in Arabidopsis shoots. • PFOA causes oxidative stress in Arabidopsis shoots. - Perfluorooctanoic acid causes oxidative stress and is more phytotoxic on shoot growth than inorganic fluoride at the equivalent F concentration.

  16. REDUCED CHLOROPLAST COVERAGE genes from Arabidopsis thaliana help to establish the size of the chloroplast compartment.

    Science.gov (United States)

    Larkin, Robert M; Stefano, Giovanni; Ruckle, Michael E; Stavoe, Andrea K; Sinkler, Christopher A; Brandizzi, Federica; Malmstrom, Carolyn M; Osteryoung, Katherine W

    2016-02-23

    Eukaryotic cells require mechanisms to establish the proportion of cellular volume devoted to particular organelles. These mechanisms are poorly understood. From a screen for plastid-to-nucleus signaling mutants in Arabidopsis thaliana, we cloned a mutant allele of a gene that encodes a protein of unknown function that is homologous to two other Arabidopsis genes of unknown function and to FRIENDLY, which was previously shown to promote the normal distribution of mitochondria in Arabidopsis. In contrast to FRIENDLY, these three homologs of FRIENDLY are found only in photosynthetic organisms. Based on these data, we proposed that FRIENDLY expanded into a small gene family to help regulate the energy metabolism of cells that contain both mitochondria and chloroplasts. Indeed, we found that knocking out these genes caused a number of chloroplast phenotypes, including a reduction in the proportion of cellular volume devoted to chloroplasts to 50% of wild type. Thus, we refer to these genes as REDUCED CHLOROPLAST COVERAGE (REC). The size of the chloroplast compartment was reduced most in rec1 mutants. The REC1 protein accumulated in the cytosol and the nucleus. REC1 was excluded from the nucleus when plants were treated with amitrole, which inhibits cell expansion and chloroplast function. We conclude that REC1 is an extraplastidic protein that helps to establish the size of the chloroplast compartment, and that signals derived from cell expansion or chloroplasts may regulate REC1.

  17. PATELLINS are regulators of auxin-mediated PIN1 relocation and plant development in Arabidopsis thaliana.

    Science.gov (United States)

    Tejos, Ricardo; Rodriguez-Furlán, Cecilia; Adamowski, Maciej; Sauer, Michael; Norambuena, Lorena; Friml, Jiří

    2018-01-29

    Coordinated cell polarization in developing tissues is a recurrent theme in multicellular organisms. In plants, a directional distribution of the plant hormone auxin is at the core of many developmental programs. A feedback regulation of auxin on the polarized localization of PIN auxin transporters in individual cells has been proposed as a self-organizing mechanism for coordinated tissue polarization, but the molecular mechanisms linking auxin signalling to PIN-dependent auxin transport remain unknown. We used a microarray-based approach to find regulators of the auxin-induced PIN relocation in Arabidopsis thaliana root, and identified a subset of a family of phosphatidylinositol transfer proteins (PITPs), the PATELLINs (PATLs). Here, we show that PATLs are expressed in partially overlapping cell types in different tissues going through mitosis or initiating differentiation programs. PATLs are plasma membrane-associated proteins accumulated in Arabidopsis embryos, primary roots, lateral root primordia and developing stomata. Higher order patl mutants display reduced PIN1 repolarization in response to auxin, shorter root apical meristem, and drastic defects in embryo and seedling development. This suggests that PATLs play a redundant and crucial role in polarity and patterning in Arabidopsis . © 2018. Published by The Company of Biologists Ltd.

  18. The efficiency of Arabidopsis thaliana (Brassicaceae) root hairs in phosphorus acquisition.

    Science.gov (United States)

    Bates, T R; Lynch, J P

    2000-07-01

    Arabidopsis thaliana root hairs grow longer and denser in response to low-phosphorus availability. In addition, plants with the root hair response acquire more phosphorus than mutants that have root hairs that do not respond to phosphorus limiting conditions. The purpose of this experiment was to determine the efficiency of root hairs in phosphorus acquisition at high- and low-phosphorus availability. Root hair growth, root growth, root respiration, plant phosphorus uptake, and plant phosphorus content of 3-wk-old wild-type Arabidopsis (WS) were compared to two root hair mutants (rhd6 and rhd2) under high (54 mmol/m) and low (0.4 mmol/m) phosphorus availability. A cost-benefit analysis was constructed from the measurements to determine root hair efficiency. Under high-phosphorus availability, root hairs did not have an effect on any of the parameters measured. Under low-phosphorus availability, wild-type Arabidopsis had greater total root surface area, shoot biomass, phosphorus per root length, and specific phosphorus uptake. The cost-benefit analysis shows that under low phosphorus, wild-type roots acquire more phosphorus for every unit of carbon respired or unit of phosphorus invested into the roots than the mutants. We conclude that the response of root hairs to low-phosphorus availability is an efficient strategy for phosphorus acquisition.

  19. Functional analysis of sporophytic transcripts repressed by the female gametophyte in the ovule of Arabidopsis thaliana.

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    Alma Armenta-Medina

    Full Text Available To investigate the genetic and molecular regulation that the female gametophyte could exert over neighboring sporophytic regions of the ovule, we performed a quantitative comparison of global expression in wild-type and nozzle/sporocyteless (spl ovules of Arabidopsis thaliana (Arabidopsis, using Massively Parallel Signature Sequencing (MPSS. This comparison resulted in 1517 genes showing at least 3-fold increased expression in ovules lacking a female gametophyte, including those encoding 89 transcription factors, 50 kinases, 25 proteins containing a RNA-recognition motif (RRM, and 20 WD40 repeat proteins. We confirmed that eleven of these genes are either preferentially expressed or exclusive of spl ovules lacking a female gametophyte as compared to wild-type, and showed that six are also upregulated in determinant infertile1 (dif1, a meiotic mutant affected in a REC8-like cohesin that is also devoided of female gametophytes. The sporophytic misexpression of IOREMPTE, a WD40/transducin repeat gene that is preferentially expressed in the L1 layer of spl ovules, caused the arrest of female gametogenesis after differentiation of a functional megaspore. Our results show that in Arabidopsis, the sporophytic-gametophytic cross talk includes a negative regulation of the female gametophyte over specific genes that are detrimental for its growth and development, demonstrating its potential to exert a repressive control over neighboring regions in the ovule.

  20. Functional analysis of sporophytic transcripts repressed by the female gametophyte in the ovule of Arabidopsis thaliana.

    Science.gov (United States)

    Armenta-Medina, Alma; Huanca-Mamani, Wilson; Sanchez-León, Nidia; Rodríguez-Arévalo, Isaac; Vielle-Calzada, Jean-Philippe

    2013-01-01

    To investigate the genetic and molecular regulation that the female gametophyte could exert over neighboring sporophytic regions of the ovule, we performed a quantitative comparison of global expression in wild-type and nozzle/sporocyteless (spl) ovules of Arabidopsis thaliana (Arabidopsis), using Massively Parallel Signature Sequencing (MPSS). This comparison resulted in 1517 genes showing at least 3-fold increased expression in ovules lacking a female gametophyte, including those encoding 89 transcription factors, 50 kinases, 25 proteins containing a RNA-recognition motif (RRM), and 20 WD40 repeat proteins. We confirmed that eleven of these genes are either preferentially expressed or exclusive of spl ovules lacking a female gametophyte as compared to wild-type, and showed that six are also upregulated in determinant infertile1 (dif1), a meiotic mutant affected in a REC8-like cohesin that is also devoided of female gametophytes. The sporophytic misexpression of IOREMPTE, a WD40/transducin repeat gene that is preferentially expressed in the L1 layer of spl ovules, caused the arrest of female gametogenesis after differentiation of a functional megaspore. Our results show that in Arabidopsis, the sporophytic-gametophytic cross talk includes a negative regulation of the female gametophyte over specific genes that are detrimental for its growth and development, demonstrating its potential to exert a repressive control over neighboring regions in the ovule.

  1. Defence responses of arabidopsis thaliana to infection by pseudomonas syringae are regulated by the circadian clock

    KAUST Repository

    Bhardwaj, Vaibhav

    2011-10-31

    The circadian clock allows plants to anticipate predictable daily changes in abiotic stimuli, such as light; however, whether the clock similarly allows plants to anticipate interactions with other organisms is unknown. Here we show that Arabidopsis thaliana (Arabidopsis) has circadian clock-mediated variation in resistance to the virulent bacterial pathogen Pseudomonas syringae pv. tomato DC3000 (Pst DC3000), with plants being least susceptible to infection in the subjective morning. We suggest that the increased resistance to Pst DC3000 observed in the morning in Col-0 plants results from clock-mediated modulation of pathogen associated molecular pattern (PAMP)-triggered immunity. Analysis of publicly available microarray data revealed that a large number of Arabidopsis defence-related genes showed both diurnal- and circadian-regulation, including genes involved in the perception of the PAMP flagellin which exhibit a peak in expression in the morning. Accordingly, we observed that PAMP-triggered callose deposition was significantly higher in wild-type plants inoculated with Pst DC3000 hrpA in the subjective morning than in the evening, while no such temporal difference was evident in arrhythmic plants. Our results suggest that PAMP-triggered immune responses are modulated by the circadian clock and that temporal regulation allows plants to anticipate and respond more effectively to pathogen challenges in the daytime. © 2011 Bhardwaj et al.

  2. Protein-protein interaction network and subcellular localization of the Arabidopsis thaliana ESCRT machinery

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    Lynn eRichardson

    2011-06-01

    Full Text Available The Endosomal Sorting Complex Required for Transport (ESCRT consists of several multi-protein subcomplexes which assemble sequentially at the endosomal surface and function in multivesicular body (MVB biogenesis. While ESCRT has been relatively well characterized in yeasts and mammals, comparably little is known about ESCRT in plants. Here we explored the yeast two-hybrid protein interaction network and subcellular localization of the Arabidopsis thaliana ESCRT machinery. We show that Arabidopsis ESCRT interactome possess a number of protein-protein interactions that are either conserved in yeasts and mammals or distinct to plants. We show also that most of the Arabidopsis ESCRT proteins examined at least partially localize to MVBs in plant cells when ectopically expressed on their own or co-expressed with other interacting ESCRT proteins, and some also induce abnormal MVB phenotypes, consistent with their proposed functional roles in MVB biogenesis. Overall, our results help define the plant ESCRT machinery by highlighting both conserved and unique features when compared to ESCRT in other evolutionarily diverse organisms, providing a foundation for further exploration of ESCRT in plants.

  3. A comparative study of salt tolerance parameters in 11 wild relatives of Arabidopsis thaliana.

    Science.gov (United States)

    Orsini, Francesco; D'Urzo, Matilde Paino; Inan, Gunsu; Serra, Sara; Oh, Dong-Ha; Mickelbart, Michael V; Consiglio, Federica; Li, Xia; Jeong, Jae Cheol; Yun, Dae-Jin; Bohnert, Hans J; Bressan, Ray A; Maggio, Albino

    2010-08-01

    Salinity is an abiotic stress that limits both yield and the expansion of agricultural crops to new areas. In the last 20 years our basic understanding of the mechanisms underlying plant tolerance and adaptation to saline environments has greatly improved owing to active development of advanced tools in molecular, genomics, and bioinformatics analyses. However, the full potential of investigative power has not been fully exploited, because the use of halophytes as model systems in plant salt tolerance research is largely neglected. The recent introduction of halophytic Arabidopsis-Relative Model Species (ARMS) has begun to compare and relate several unique genetic resources to the well-developed Arabidopsis model. In a search for candidates to begin to understand, through genetic analyses, the biological bases of salt tolerance, 11 wild relatives of Arabidopsis thaliana were compared: Barbarea verna, Capsella bursa-pastoris, Hirschfeldia incana, Lepidium densiflorum, Malcolmia triloba, Lepidium virginicum, Descurainia pinnata, Sisymbrium officinale, Thellungiella parvula, Thellungiella salsuginea (previously T. halophila), and Thlaspi arvense. Among these species, highly salt-tolerant (L. densiflorum and L. virginicum) and moderately salt-tolerant (M. triloba and H. incana) species were identified. Only T. parvula revealed a true halophytic habitus, comparable to the better studied Thellungiella salsuginea. Major differences in growth, water transport properties, and ion accumulation are observed and discussed to describe the distinctive traits and physiological responses that can now be studied genetically in salt stress research.

  4. Proteomic analysis of Arabidopsis thaliana (L.) Heynh responses to a generalist sucking pest (Myzus persicae Sulzer).

    Science.gov (United States)

    Truong, D-H; Bauwens, J; Delaplace, P; Mazzucchelli, G; Lognay, G; Francis, F

    2015-11-01

    Herbivorous insects can cause severe cellular changes to plant foliage following infestations, depending on feeding behaviour. Here, a proteomic study was conducted to investigate the influence of green peach aphid (Myzus persicae Sulzer) as a polyphagous pest on the defence response of Arabidopsis thaliana (L.) Heynh after aphid colony establishment on the host plant (3 days). Analysis of about 574 protein spots on 2-DE gels revealed 31 differentially expressed protein spots. Twenty out of these 31 differential proteins were selected for analysis by mass spectrometry. In 12 of the 20 analysed spots, we identified seven and nine proteins using MALDI-TOF-MS and LC-ESI-MS/MS, respectively. Of the analysed spots, 25% contain two proteins. Different metabolic pathways were modulated in Arabidopsis leaves according to aphid feeding: most corresponded to carbohydrate, amino acid and energy metabolism, photosynthesis, defence response and translation. This paper has established a survey of early alterations induced in the proteome of Arabidopsis by M. persicae aphids. It provides valuable insights into the complex responses of plants to biological stress, particularly for herbivorous insects with sucking feeding behaviour. © 2015 German Botanical Society and The Royal Botanical Society of the Netherlands.

  5. A comparative study of salt tolerance parameters in 11 wild relatives of Arabidopsis thaliana

    KAUST Repository

    Orsini, Francesco

    2010-07-01

    Salinity is an abiotic stress that limits both yield and the expansion of agricultural crops to new areas. In the last 20 years our basic understanding of the mechanisms underlying plant tolerance and adaptation to saline environments has greatly improved owing to active development of advanced tools in molecular, genomics, and bioinformatics analyses. However, the full potential of investigative power has not been fully exploited, because the use of halophytes as model systems in plant salt tolerance research is largely neglected. The recent introduction of halophytic Arabidopsis-Relative Model Species (ARMS) has begun to compare and relate several unique genetic resources to the well-developed Arabidopsis model. In a search for candidates to begin to understand, through genetic analyses, the biological bases of salt tolerance, 11 wild relatives of Arabidopsis thaliana were compared: Barbarea verna, Capsella bursa-pastoris, Hirschfeldia incana, Lepidium densiflorum, Malcolmia triloba, Lepidium virginicum, Descurainia pinnata, Sisymbrium officinale, Thellungiella parvula, Thellungiella salsuginea (previously T. halophila), and Thlaspi arvense. Among these species, highly salt-tolerant (L. densiflorum and L. virginicum) and moderately salt-tolerant (M. triloba and H. incana) species were identified. Only T. parvula revealed a true halophytic habitus, comparable to the better studied Thellungiella salsuginea. Major differences in growth, water transport properties, and ion accumulation are observed and discussed to describe the distinctive traits and physiological responses that can now be studied genetically in salt stress research. 2010 The Author.

  6. Increased root hair density by loss of WRKY6 in Arabidopsis thaliana

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    Markus G. Stetter

    2017-01-01

    Full Text Available Root hairs are unicellular elongations of certain rhizodermal cells that improve the uptake of sparingly soluble and immobile soil nutrients. Among different Arabidopsis thaliana genotypes, root hair density, length and the local acclimation to low inorganic phosphate (Pi differs considerably, when analyzed on split agar plates. Here, genome-wide association fine mapping identified significant single nucleotide polymorphisms associated with the increased root hair density in the absence of local phosphate on chromosome 1. A loss-of-functionmutant of the candidate transcription factor gene WRKY6, which is involved in the acclimation of plants to low phosphorus, had increased root hair density. This is partially explained by a reduced cortical cell diameter in wrky6-3, reducing the rhizodermal cell numbers adjacent to the cortical cells. As a consequence, rhizodermal cells in positions that are in contact with two cortical cells are found more often, leading to higher hair density. Distinct cortical cell diameters and epidermal cell lengths distinguish other Arabidopsis accessions with distinct root hair density and −Pi response from diploid Col-0, while tetraploid Col-0 had generally larger root cell sizes, which explain longer hairs. A distinct radial root morphology within Arabidopsis accessions and wrky6-3explains some, but not all, differences in the root hair acclimation to –Pi.

  7. Genome-wide comparative analysis of NBS-encoding genes between Brassica species and Arabidopsis thaliana.

    Science.gov (United States)

    Yu, Jingyin; Tehrim, Sadia; Zhang, Fengqi; Tong, Chaobo; Huang, Junyan; Cheng, Xiaohui; Dong, Caihua; Zhou, Yanqiu; Qin, Rui; Hua, Wei; Liu, Shengyi

    2014-01-03

    Plant disease resistance (R) genes with the nucleotide binding site (NBS) play an important role in offering resistance to pathogens. The availability of complete genome sequences of Brassica oleracea and Brassica rapa provides an important opportunity for researchers to identify and characterize NBS-encoding R genes in Brassica species and to compare with analogues in Arabidopsis thaliana based on a comparative genomics approach. However, little is known about the evolutionary fate of NBS-encoding genes in the Brassica lineage after split from A. thaliana. Here we present genome-wide analysis of NBS-encoding genes in B. oleracea, B. rapa and A. thaliana. Through the employment of HMM search and manual curation, we identified 157, 206 and 167 NBS-encoding genes in B. oleracea, B. rapa and A. thaliana genomes, respectively. Phylogenetic analysis among 3 species classified NBS-encoding genes into 6 subgroups. Tandem duplication and whole genome triplication (WGT) analyses revealed that after WGT of the Brassica ancestor, NBS-encoding homologous gene pairs on triplicated regions in Brassica ancestor were deleted or lost quickly, but NBS-encoding genes in Brassica species experienced species-specific gene amplification by tandem duplication after divergence of B. rapa and B. oleracea. Expression profiling of NBS-encoding orthologous gene pairs indicated the differential expression pattern of retained orthologous gene copies in B. oleracea and B. rapa. Furthermore, evolutionary analysis of CNL type NBS-encoding orthologous gene pairs among 3 species suggested that orthologous genes in B. rapa species have undergone stronger negative selection than those in B .oleracea species. But for TNL type, there are no significant differences in the orthologous gene pairs between the two species. This study is first identification and characterization of NBS-encoding genes in B. rapa and B. oleracea based on whole genome sequences. Through tandem duplication and whole genome

  8. Identification of genes involved in the ACC-mediated control of root cell elongation in Arabidopsis thaliana

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    Markakis Marios

    2012-11-01

    Full Text Available Abstract Background Along the root axis of Arabidopsis thaliana, cells pass through different developmental stages. In the apical meristem repeated cycles of division increase the numbers of cells. Upon leaving the meristem, these cells pass the transition zone where they are physiologically and mechanically prepared to undergo subsequent rapid elongation. During the process of elongation epidermal cells increase their length by 300% in a couple of hours. When elongation ceases, the cells acquire their final size, shape and functions (in the differentiation zone. Ethylene administered as its precursor 1-aminocyclopropane-1-carboxylic acid (ACC is capable of inhibiting elongation in a concentration-dependent way. Using a microarray analysis, genes and/or processes involved in this elongation arrest are identified. Results Using a CATMA-microarray analysis performed on control and 3h ACC-treated roots, 240 differentially expressed genes were identified. Quantitative Real-Time RT-PCR analysis of the 10 most up and down regulated genes combined with literature search confirmed the accurateness of the analysis. This revealed that inhibition of cell elongation is, at least partly, caused by restricting the events that under normal growth conditions initiate elongation and by increasing the processes that normally stop cellular elongation at the end of the elongation/onset of differentiation zone. Conclusions ACC interferes with cell elongation in the Arabidopsis thaliana roots by inhibiting cells from entering the elongation process and by immediately stimulating the formation of cross-links in cell wall components, diminishing the remaining elongation capacity. From the analysis of the differentially expressed genes, it becomes clear that many genes identified in this response, are also involved in several other kind of stress responses. This suggests that many responses originate from individual elicitors, but that somewhere in the downstream

  9. EFFECT OF SEED XYLOGLUCANS AND DERIVATES ON THE GROWTH OF Arabidopsis thaliana

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    Adriana Tourinho Salamoni

    2009-10-01

    Full Text Available Studies on xyloglucan (XG extracted from Hymenaea courbaril L. (jatoba seeds showed that this biopolymer has biological activity that enhanced wheat coleoptiles growth. In apple tree micropropagation, the culture medium containing XG combined with agar induced a higher multiplication rate, rooting rate and root length than medium solidified with agar only. The purpose of this study was to determine the effect of XG from jatobá seeds extracted from jatoba seeds collected in Sinope/MT (XGS and Cuiabá/MT (XGC, and from XGC hydrolysed with a cellulase (XGCH, as well from Tamarindus indica seeds (XGT collected in Bahia/BA, on the growth of in vitro cultured Arabidopsis thaliana plantlets. In the first experiment, XGCH (0.25, 25 and 250 nM or XGC (0.5, 50 and 500 nM were added to a liquid half-strength MS medium. In the second experiment, XGs from several origins were compared: XGC (500 nM, XGS (1200 nM and XGT (800 nM, using culture medium solidified with 6 g.L-1agar. Arabidopsis thaliana L. seeds germinated in Petri plates for 4 to 5 days were transferred to culture media containing the different concentrations of XGs and cultured in a growing room. When the plantlets were cultured in a liquid medium, their growth was very slow in the presence of XGC and XGCH at the highest concentration tested, and it was faster at the lowest concentration. In the semi-solid culture medium, XGs also reduced growth. It was concluded that XGs can play a biological role in Arabidopsis thaliana (L. Heynh. plantlets, stimulating or inhibiting the root system growth and the lateral root formation. These opposite effects varied according to the plant specie that furnished the seeds containing XG, as well as the place where the seeds were collected, to the XG form used (hydrolyzed or not and to its concentration in the culture media. 

  10. Heterologous expression of two GPATs from Jatropha curcas alters seed oil levels in transgenic Arabidopsis thaliana.

    Science.gov (United States)

    Misra, Aparna; Khan, Kasim; Niranjan, Abhishek; Kumar, Vinod; Sane, Vidhu A

    2017-10-01

    Oils and fats are stored in endosperm during seed development in the form of triacylglycerols. Three acyltransferases: glycerol-3-phosphate acyltransferase (GPAT), lysophosphatidyl acyltransferase (LPAT) and diacylglycerol acyltransferase (DGAT) are involved in the storage lipid biosynthesis and catalyze the stepwise acylation of glycerol backbone. In this study two members of GPAT gene family (JcGPAT1 and JcGPAT2) from Jatropha seeds were identified and characterized. Sequence analysis suggested that JcGPAT1 and JcGPAT2 are homologous to Arabidopsis acyltransferase-1 (ATS1) and AtGPAT9 respectively. The sub-cellular localization studies of these two GPATs showed that JcGPAT1 localizes into plastid whereas JcGPAT2 localizes in to endoplasmic reticulum. JcGPAT1 and JcGPAT2 expressed throughout the seed development with higher expression in fully matured seed compared to immature seed. The transcript levels of JcGPAT2 were higher in comparison to JcGPAT1 in different developmental stages of seed. Over-expression of JcGPAT1 and JcGPAT2 under constitutive and seed specific promoters in Arabidopsis thaliana increased total oil content. Transgenic seeds of JcGPAT2-OE lines accumulated 43-60% more oil than control seeds whereas seeds of Arabidopsis lines over-expressing plastidial GPAT lead to only 13-20% increase in oil content. Functional characterization of GPAT homologues of Jatropha in Arabidopsis suggested that these are involved in oil biosynthesis but might have specific roles in Jatropha. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Origin of the thiazole ring of camalexin, a phytoalexin from Arabidopsis thaliana.

    Science.gov (United States)

    Zook, M; Hammerschmidt, R

    1997-02-01

    The principal phytoalexin that accumulates in Arabidopsis thaliana after infection by fungi or bacteria is 3-thiazol-2'-yl-indole (camalexin). Detached noninoculated leaves of Arabidopsis and leaves inoculated with the fungus Cochliobolus carbonum were fed [35S]cysteine (Cys) and [35S]methionine. Inoculated leaves incorporated more than a 200-fold greater amount of radioactivity from [35S]Cys into camalexin, as compared with noninoculated leaves. The amount of radioactivity from [35S]Cys that was incorporated into camalexin from inoculated Arabidopsis leaves was 10-fold greater than the amount of radioactivity that was incorporated into camalexin from [35S]methionine. Additional labeling experiments were performed to determine whether other atoms of Cys are incorporated into camalexin. [14C]Cys and [35S]Cys were incorporated into camalexin with approximately the same efficiency. Cys labeled either with deuterium (D3-Cys[2,3,3]) or 13C and 15N ([U-13C,15N]Cys) was also fed to inoculated leaves of Arabidopsis; camalexin was analyzed by mass spectroscopic analysis. The average ratio of molecular ion intensities of 203/200 for [U-13C,15N]Cys-labeled camalexin was 4.22, as compared with 0.607 for the average 203/200 ratio for unlabeled camalexin. The mass fragment-ion intensity ratios of 60/58 (thiazole ring ion fragment) and 143/142 were also higher for [U-13C,15N]Cys-labeled camalexin, as compared with unlabeled camalexin. The 59/58 and 201/200 ratios were higher for D3-Cys-labeled camalexin as compared with unlabeled camalexin. These data are consistent with the predicted formation of the thiazole ring of camalexin from Cys.

  12. CuO Nanoparticle Interaction with Arabidopsis thaliana: Toxicity, Parent-Progeny Transfer, and Gene Expression.

    Science.gov (United States)

    Wang, Zhenyu; Xu, Lina; Zhao, Jian; Wang, Xiangke; White, Jason C; Xing, Baoshan

    2016-06-07

    CuO nanoparticles (NPs) (20, 50 mg L(-1)) inhibited seedling growth of different Arabidopsis thaliana ecotypes (Col-0, Bay-0, and Ws-2), as well as the germination of their pollens and harvested seeds. For most of growth parameters (e.g., biomass, relative growth rate, root morphology change), Col-0 was the more sensitive ecotype to CuO NPs compared to Bay-0 and Ws-2. Equivalent Cu(2+) ions and CuO bulk particles had no effect on Arabidopsis growth. After CuO NPs (50 mg L(-1)) exposure, Cu was detected in the roots, leaves, flowers and harvested seeds of Arabidopsis, and its contents were significantly higher than that in CuO bulk particles (50 mg L(-1)) and Cu(2+) ions (0.15 mg L(-1)) treatments. Based on X-ray absorption near-edge spectroscopy analysis (XANES), Cu in the harvested seeds was confirmed as being mainly in the form of CuO (88.8%), which is the first observation on the presence of CuO NPs in the plant progeny. Moreover, after CuO NPs exposure, two differentially expressed genes (C-1 and C-3) that regulated root growth and reactive oxygen species generation were identified, which correlated well with the physiological root inhibition and oxidative stress data. This current study provides direct evidence for the negative effects of CuO NPs on Arabidopsis, including accumulation and parent-progeny transfer of the particles, which may have significant implications with regard to the risk of NPs to food safety and security.

  13. SnRK1 activates autophagy via the TOR signaling pathway in Arabidopsis thaliana.

    Science.gov (United States)

    Soto-Burgos, Junmarie; Bassham, Diane C

    2017-01-01

    Autophagy is a degradation process in which cells break down and recycle their cytoplasmic contents when subjected to environmental stress or during cellular remodeling. The Arabidopsis thaliana SnRK1 complex is a protein kinase that senses changes in energy levels and triggers downstream responses to enable survival. Its mammalian ortholog, AMPK, and yeast ortholog, Snf-1, activate autophagy in response to low energy conditions. We therefore hypothesized that SnRK1 may play a role in the regulation of autophagy in response to nutrient or energy deficiency in Arabidopsis. To test this hypothesis, we determined the effect of overexpression or knockout of the SnRK1 catalytic subunit KIN10 on autophagy activation by abiotic stresses, including nutrient deficiency, salt, osmotic, oxidative, and ER stress. While wild-type plants had low basal autophagy activity in control conditions, KIN10 overexpression lines had increased autophagy under these conditions, indicating activation of autophagy by SnRK1. A kin10 mutant had a basal level of autophagy under control conditions similar to wild-type plants, but activation of autophagy by most abiotic stresses was blocked, indicating that SnRK1 is required for autophagy induction by a wide variety of stress conditions. In mammals, TOR is a negative regulator of autophagy, and AMPK acts to activate autophagy both upstream of TOR, by inhibiting its activity, and in a parallel pathway. Inhibition of Arabidopsis TOR leads to activation of autophagy; inhibition of SnRK1 did not block this activation. Furthermore, an increase in SnRK1 activity was unable to induce autophagy when TOR was also activated. These results demonstrate that SnRK1 acts upstream of TOR in the activation of autophagy in Arabidopsis.

  14. The β-cyanoalanine pathway is involved in the response to water deficit in Arabidopsis thaliana.

    Science.gov (United States)

    Machingura, Marylou; Sidibe, Aissatou; Wood, Andrew J; Ebbs, Stephen D

    2013-02-01

    The β-cyanoalanine pathway is primarily responsible for detoxification of excess cyanide produced by plants. Recent evidence suggests that cyanide detoxification via this pathway may be involved in the response and tolerance to water deficit in plants. The aim of this study was to explore this role in Arabidopsis thaliana in greater detail. The first objective was to establish responsiveness of the pathway to the magnitude and duration of water deficit. The second objective was to examine how interruption of single genes (AtCysA1, AtCysC1 and AtNIT4) encoding enzymes of the pathway influenced the ability to metabolize cyanide and withstand water deficit. Arabidopsis plants were exposed to conditions which emulated acute and chronic water deficit, followed by measurement of tissue cyanide concentration, activity of enzymes, and physiological parameters. The results for wild-type Arabidopsis demonstrated a transient increase in cyanide concentration and β-cyanoalanine synthase activity, followed by a decrease in both. The increase in enzyme activity was localized to the tissue in direct proximity to the stress. The knockdown AtCysA1 mutant did not differ from wild-type while AtCysC1 mutants were slightly more sensitive to water deficit. The AtNIT4 mutant was the most sensitive showing decreased growth along with altered chlorophyll content under water deficit as compared to wild-type. Collectively, the results indicated that the pathway is responsive to water deficit although the severity of stress did not alter the nature of the response, implying that the capacity to remove cyanide generated during water deficit may contribute to tolerance to this stress in Arabidopsis. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

  15. Phytoremediation of the organic Xenobiotic simazine by p450-1a2 transgenic Arabidopsis thaliana plants.

    Science.gov (United States)

    Azab, Ehab; Hegazy, Ahmad K; El-Sharnouby, Mohamed E; Abd Elsalam, Hassan E

    2016-01-01

    The potential use of human P450-transgenic plants for phytoremediation of pesticide contaminated soils was tested in laboratory and greenhouse experiments. The transgenic P450 CYP1A2 gene Arabidopsis thaliana plants metabolize number of herbicides, insecticides and industrial chemicals. The P450 isozymes CYP1A2 expressed in A. thaliana were examined regarding the herbicide simazine (SIM). Transgenic A. thaliana plants expressing CYP1A2 gene showed significant resistance to SIM supplemented either in plant growth medium or sprayed on foliar parts. The results showed that SIM produces harmful effect on both rosette diameter and primary root length of the wild type (WT) plants. In transgenic A. thaliana lines, the rosette diameter and primary root length were not affected by SIM concentrations used in this experiment. The results indicate that CYP1A2 can be used as a selectable marker for plant transformation, allowing efficient selection of transgenic lines in growth medium and/or in soil-grown plants. The transgenic A. thaliana plants exhibited a healthy growth using doses of up to 250 μmol SIM treatments, while the non-transgenic A. thaliana plants were severely damaged with doses above 50 μmol SIM treatments. The transgenic A. thaliana plants can be used as phytoremediator of environmental SIM contaminants.

  16. [Ultrastructure of statocytes and cells of distal elongation zone of Arabidopsis thaliana under clinorotation].

    Science.gov (United States)

    Romanchuk, S M

    2010-01-01

    Results of the electron-microscopic investigation of root apices of Arabidopsis thaliana 3-, 5- and 7-days-old seedlings grown in the stationary conditions and under clinorotation are presented. It was shown the similarity in the root apex cell ultrastructure in control and under clinorotation. At the same time there were some differences in the ultrastructure of statocytes and the distal elongation zone under clinorotation. For the first time the sensitivity of ER-bodies, which are derivatives of GER and contain beta-glucosidase, to the influence of simulated microgravity was demonstrated by increased quantity and area of ER-bodies at the cell section as well as by higher variability of their form under clinorotation. A degree of these changes correlated with the duration of clinorotation. On the basis of experimental data a protective role of ER-bodies in adaptation of plants to microgravity is supposed.

  17. The correlation between the chromosome variation in callus and genotype of explants of Arabidopsis thaliana.

    Science.gov (United States)

    Fras, Alicja; Maluszynska, Jolanta

    2004-06-01

    Twelve callus lines of Arabidopsis thaliana were derived from four types of explants excised from diploid plants of two ecotypes (Columbia and Wilna) and autotetraploid plants of the Wilna ecotype. Cytogenetic analysis of the chromosome variation in particular callus lines was carried out for primary culture and callus during 5 months of culture. Ploidy levels of interphase nuclei were estimated by counting the number and size of chromocentres and nuclei of interphase cells. The first polyploid cells in all callus lines were observed during callogenesis. In primary culture the ploidy level ranged between 2 and 15x (10-75 chromosomes). The frequency of polyploid cells was higher in the 5-month old callus culture, but the ploidy level was the same. In the callus lines derived from autotetraploid plants, cells with reduced chromosome number appeared quite frequently along with diploid and polyploid cells.

  18. Recombinant ACHT1 from Arabidopsis thaliana: crystallization and X-ray crystallographic analysis.

    Science.gov (United States)

    Pan, Weimin; Wang, Junchao; Yang, Ye; Liu, Lin; Zhang, Min

    2017-07-01

    Thioredoxins (Trxs) play important roles in chloroplasts by linking photosynthetic light reactions to a series of plastid functions. They execute their function by regulating the oxidation and reduction of disulfide bonds. ACHT1 (atypical cysteine/histidine-rich Trx1) is a thylakoid-associated thioredoxin-type protein found in the Arabidopsis thaliana chloroplast. Recombinant ACHT1 protein was overexpressed in Escherichia coli, purified and crystallized by the vapour-diffusion method. The crystal diffracted to 1.7 Å resolution and a complete X-ray data set was collected. Preliminary crystallographic analysis suggested that the crystals belonged to space group C222 1 , with unit-cell parameters a = 102.7, b = 100.6, c = 92.8 Å.

  19. Gene introduction into the mitochondria of Arabidopsis thaliana via peptide-based carriers

    Science.gov (United States)

    Chuah, Jo-Ann; Yoshizumi, Takeshi; Kodama, Yutaka; Numata, Keiji

    2015-01-01

    Available methods in plant genetic transformation are nuclear and plastid transformations because similar procedures have not yet been established for the mitochondria. The double membrane and small size of the organelle, in addition to its large population in cells, are major obstacles in mitochondrial transfection. Here we report the intracellular delivery of exogenous DNA localized to the mitochondria of Arabidopsis thaliana using a combination of mitochondria-targeting peptide and cell-penetrating peptide. Low concentrations of peptides were sufficient to deliver DNA into the mitochondria and expression of imported DNA reached detectable levels within a short incubation period (12 h). We found that electrostatic interaction with the cell membrane is not a critical factor for complex internalization, instead, improved intracellular penetration of mitochondria-targeted complexes significantly enhanced gene transfer efficiency. Our results delineate a simple and effective peptide-based method, as a starting point for the development of more sophisticated plant mitochondrial transfection strategies.

  20. Modified cellulose synthase gene from Arabidopsis thaliana confers herbicide resistance to plants

    Science.gov (United States)

    Somerville, Chris R [Portola Valley, CA; Scheible, Wolf [Golm, DE

    2007-07-10

    Cellulose synthase ("CS"), a key enzyme in the biosynthesis of cellulose in plants is inhibited by herbicides comprising thiazolidinones such as 5-tert-butyl-carbamoyloxy-3-(3-trifluromethyl)phenyl-4-thiazolidinone (TZ), isoxaben and 2,6-dichlorobenzonitrile (DCB). Two mutant genes encoding isoxaben and TZ-resistant cellulose synthase have been isolated from isoxaben and TZ-resistant Arabidopsis thaliana mutants. When compared with the gene coding for isoxaben or TZ-sensitive cellulose synthase, one of the resistant CS genes contains a point mutation, wherein glycine residue 998 is replaced by an aspartic acid. The other resistant mutation is due to a threonine to isoleucine change at amino acid residue 942. The mutant CS gene can be used to impart herbicide resistance to a plant; thereby permitting the utilization of the herbicide as a single application at a concentration which ensures the complete or substantially complete killing of weeds, while leaving the transgenic crop plant essentially undamaged.

  1. ATAF1 transcription factor directly regulates abscisic acid biosynthetic gene NCED3 in Arabidopsis thaliana

    DEFF Research Database (Denmark)

    Jensen, Michael Krogh; Lindemose, Søren; De Masi, Federico

    2013-01-01

    ATAF1, an Arabidopsis thaliana NAC transcription factor, plays important roles in plant adaptation to environmental stress and development. To search for ATAF1 target genes, we used protein binding microarrays and chromatin-immunoprecipitation (ChIP). This identified T[A,C,G]CGT[A,G] and TT......[A,C,G]CGT as ATAF1 consensus binding sequences. Co-expression analysis across publicly available microarray experiments identified 25 genes co-expressed with ATAF1. The promoter regions of ATAF1 co-expressors were significantly enriched for ATAF1 binding sites, and TTGCGTA was identified in the promoter of the key...... abscisic acid (ABA) phytohormone biosynthetic gene NCED3. ChIP-qPCR and expression analysis showed that ATAF1 binding to the NCED3 promoter correlated with increased NCED3 expression and ABA hormone levels. These results indicate that ATAF1 regulates ABA biosynthesis....

  2. ups1, an Arabidopsis thaliana camalexin accumulation mutant defective in multiple defence signalling pathways.

    Science.gov (United States)

    Denby, Katherine J; Jason, Laure J M; Murray, Shane L; Last, Robert L

    2005-03-01

    We report the characterization of an Arabidopsis thaliana mutant, ups1, isolated on the basis of reduced expression of phosphoribosylanthranilate transferase, a tryptophan biosynthetic enzyme. ups1 also exhibits defects in a wide range of defence responses. After infection with Pseudomonas syringae or Botrytis cinerea, the expression of genes regulated by both the salicylic acid and jasmonic acid/ethylene pathways is reduced in ups1 compared with wild type. Camalexin accumulation in ups1 is greatly reduced after infection with these two pathogens, as well as after amino acid starvation or oxidative stress. Reactive oxygen species (ROS)-mediated gene expression is also compromised in ups1 indicating that this mutant is defective in signalling pathways activated in response to both biotic and abiotic stress. The fact that all three major defence signalling pathways are disrupted in ups1, together with the oxidative stress phenotype, leads us to suggest that UPS1 is involved in ROS signal transduction.

  3. Discovery of functional genes for systemic acquired resistance in Arabidopsis thaliana through integrated data mining.

    Science.gov (United States)

    Pan, Youlian; Pylatuik, Jeffrey D; Ouyang, Junjun; Famili, A Fazel; Fobert, Pierre R

    2004-12-01

    Various data mining techniques combined with sequence motif information in the promoter region of genes were applied to discover functional genes that are involved in the defense mechanism of systemic acquired resistance (SAR) in Arabidopsis thaliana. A series of K-Means clustering with difference-in-shape as distance measure was initially applied. A stability measure was used to validate this clustering process. A decision tree algorithm with the discover-and-mask technique was used to identify a group of most informative genes. Appearance and abundance of various transcription factor binding sites in the promoter region of the genes were studied. Through the combination of these techniques, we were able to identify 24 candidate genes involved in the SAR defense mechanism. The candidate genes fell into 2 highly resolved categories, each category showing significantly unique profiles of regulatory elements in their promoter regions. This study demonstrates the strength of such integration methods and suggests a broader application of this approach.

  4. Isolation of mutations affecting the development of freezing tolerance in Arabidopsis thaliana (L.) Heynh.

    Science.gov (United States)

    Warren, G; McKown, R; Marin, A L; Teutonico, R

    1996-08-01

    We screened for mutations deleterious to the freezing tolerance of Arabidopsis thaliana (L.) Heynh. ecotype Columbia. Tolerance was assayed by the vigor and regrowth of intact plants after cold acclimation and freezing. From a chemically mutagenized population, we obtained 13 lines of mutants with highly penetrant phenotypes. In 5 of these, freezing sensitivity was attributable to chilling injury sustained during cold acclimation, but in the remaining 8 lines, the absence of injury prior to freezing suggested that they were affected specifically in the development of freezing tolerance. In backcrosses, freezing sensitivity from each line segregated as a single nuclear mutation. Complementation tests indicated that the 8 lines contained mutations in 7 different genes. The mutants' freezing sensitivity was also detectable in the leakage of electrolytes from frozen leaves. However, 1 mutant line that displayed a strong phenotype at the whole-plant level showed a relatively weak phenotype by the electrolyte leakage assay.

  5. Transmembrane topology of FRO2, a ferric chelate reductase from Arabidopsis thaliana.

    Science.gov (United States)

    Schagerlöf, Ulrika; Wilson, Greer; Hebert, Hans; Al-Karadaghi, Salam; Hägerhäll, Cecilia

    2006-09-01

    Iron uptake in Arabidopsis thaliana is mediated by ferric chelate reductase FRO2, a transmembrane protein belonging to the flavocytochrome b family. There is no high resolution structural information available for any member of this family. We have determined the transmembrane topology of FRO2 experimentally using the alkaline phosphatase fusion method. The resulting topology is different from that obtained by theoretical predictions and contains 8 transmembrane helices, 4 of which build up the highly conserved core of the protein. This core is present in the entire flavocytochrome b family. The large water soluble domain of FRO2, which contains NADPH, FAD and oxidoreductase sequence motifs, was located on the inside of the membrane.

  6. Sugar regulation of SUGAR TRANSPORTER PROTEIN 1 (STP1) expression in Arabidopsis thaliana

    Science.gov (United States)

    Cordoba, Elizabeth; Aceves-Zamudio, Denise Lizeth; Hernández-Bernal, Alma Fabiola; Ramos-Vega, Maricela; León, Patricia

    2015-01-01

    Sugars regulate the expression of many genes at the transcriptional level. In Arabidopsis thaliana, sugars induce or repress the expression of >1800 genes, including the STP1 (SUGAR TRANSPORTER PROTEIN 1) gene, which encodes an H+/monosaccharide cotransporter. STP1 transcript levels decrease more rapidly after the addition of low concentrations of sugars than the levels of other repressed genes, such as DIN6 (DARK-INDUCED 6). We found that this regulation is exerted at the transcriptional level and is initiated by phosphorylatable sugars. Interestingly, the sugar signal that modulates STP1 expression is transmitted through a HEXOKINASE 1-independent signalling pathway. Finally, analysis of the STP1 5′ regulatory region allowed us to delimit a region of 309bp that contains the cis elements implicated in the glucose regulation of STP1 expression. Putative cis-acting elements involved in this response were identified. PMID:25281700

  7. The Structure of Sucrose Synthase-1 from Arabidopsis thaliana and Its Functional Implications

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, Yi; Anderson, Spencer; Zhang, Yanfeng; Garavito, R. Michael (MSU); (NWU)

    2014-10-02

    Sucrose transport is the central system for the allocation of carbon resources in vascular plants. During growth and development, plants control carbon distribution by coordinating sites of sucrose synthesis and cleavage in different plant organs and different cellular locations. Sucrose synthase, which reversibly catalyzes sucrose synthesis and cleavage, provides a direct and reversible means to regulate sucrose flux. Depending on the metabolic environment, sucrose synthase alters its cellular location to participate in cellulose, callose, and starch biosynthesis through its interactions with membranes, organelles, and cytoskeletal actin. The x-ray crystal structure of sucrose synthase isoform 1 from Arabidopsis thaliana (AtSus1) has been determined as a complex with UDP-glucose and as a complex with UDP and fructose, at 2.8- and 2.85-{angstrom} resolutions, respectively. The AtSus1 structure provides insights into sucrose catalysis and cleavage, as well as the regulation of sucrose synthase and its interactions with cellular targets.

  8. Spatiotemporal expression control correlates with intragenic scaffold matrix attachment regions (S/MARs in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Igor V Tetko

    2006-03-01

    Full Text Available Scaffold/matrix attachment regions (S/MARs are essential for structural organization of the chromatin within the nucleus and serve as anchors of chromatin loop domains. A significant fraction of genes in Arabidopsis thaliana contains intragenic S/MAR elements and a significant correlation of S/MAR presence and overall expression strength has been demonstrated. In this study, we undertook a genome scale analysis of expression level and spatiotemporal expression differences in correlation with the presence or absence of genic S/MAR elements. We demonstrate that genes containing intragenic S/MARs are prone to pronounced spatiotemporal expression regulation. This characteristic is found to be even more pronounced for transcription factor genes. Our observations illustrate the importance of S/MARs in transcriptional regulation and the role of chromatin structural characteristics for gene regulation. Our findings open new perspectives for the understanding of tissue- and organ-specific regulation of gene expression.

  9. Effect of salt stress on genes encoding translation-associated proteins in Arabidopsis thaliana.

    Science.gov (United States)

    Omidbakhshfard, Mohammad Amin; Omranian, Nooshin; Ahmadi, Farajollah Shahriari; Nikoloski, Zoran; Mueller-Roeber, Bernd

    2012-09-01

    Salinity negatively affects plant growth and disturbs chloroplast integrity. Here, we aimed at identifying salt-responsive translation-related genes in Arabidopsis thaliana with an emphasis on those encoding plastid-located proteins. We used quantitative real-time PCR to test the expression of 170 genes after short-term salt stress (up to 24 h) and identified several genes affected by the stress including: PRPL11, encoding plastid ribosomal protein L11, ATAB2, encoding a chloroplast-located RNA-binding protein presumably functioning as an activator of translation, and PDF1B, encoding a peptide deformylase involved in N-formyl group removal from nascent proteins synthesized in chloroplasts. These genes were previously shown to have important functions in chloroplast biology and may therefore represent new targets for biotechnological optimization of salinity tolerance.

  10. Towards annotating the plant epigenome: the Arabidopsis thaliana small RNA locus map.

    Science.gov (United States)

    Hardcastle, Thomas J; Müller, Sebastian Y; Baulcombe, David C

    2018-04-20

    Based on 98 public and internal small RNA high throughput sequencing libraries, we mapped small RNAs to the genome of the model organism Arabidopsis thaliana and defined loci based on their expression using an empirical Bayesian approach. The resulting loci were subsequently classified based on their genetic and epigenetic context as well as their expression properties. We present the results of this classification, which broadly conforms to previously reported divisions between transcriptional and post-transcriptional gene silencing small RNAs, and to PolIV and PolV dependencies. However, we are able to demonstrate the existence of further subdivisions in the small RNA population of functional significance. Moreover, we present a framework for similar analyses of small RNA populations in all species.

  11. Seed coat mucilage cells of Arabidopsis thaliana as a model for plant cell wall research.

    Science.gov (United States)

    Arsovski, Andrej A; Haughn, George W; Western, Tamara L

    2010-07-01

    Plant cells are encased within a complex polysaccharide wall that strengthens the cell and has key roles in all aspects of plant cell growth, differentiation, and interaction with the environment. This dynamic structure is under continual modification during plant development, and its synthesis and modification require the activity of a myriad of enzymes. The mucilage secretory cells (MSCs) of the Arabidopsis thaliana seed coat provide a model for the discovery of novel genes involved in the synthesis, secretion and modification of cell wall components, particularly pectin. These cells synthesize copious amounts of pectinaceous mucilage during development and, upon hydration of the desiccated seed, the mucilage rapidly swells, bursts from the MSCs and surrounds the seed in a gelatinous capsule. Several genes affecting MSC differentiation, pectin synthesis, and mucilage release have been identified and additional genes involved in these and related processes including pectin secretion and the mechanical alteration of cell walls await to be discovered.

  12. ERECTA controls low light intensity-inducd differential petiole growth independent of phytochrome B and chryptochrome 2 action in Arabidopsis thaliana

    NARCIS (Netherlands)

    Zanten, van M.; Snoek, L.B.; Eck-Stouten, van E.; Proveniers, M.C.G.; Torii, K.U.; Voesenek, L.A.C.J.; Millenaar, F.F.; Peeters, A.J.M.

    2010-01-01

    Plants can respond quickly and profoundly to changes in their environment. Several species, including Arabidopsis thaliana, are capable of differential petiole growth driven upward leaf movement (hyponastic growth) to escape from detrimental environmental conditions. Recently, we demonstrated that

  13. X-ray and fast neutron-induced mutations in Arabidopsis thaliana, and the effect of dithiothreitol upon the mutant spectrum

    International Nuclear Information System (INIS)

    Dellaert, L.M.W.

    1980-01-01

    The author discusses the genetic effects of X-ray and fast neutron seed-irradiation of Arabidopsis thaliana (L.) Heynh., and the influence of a pre-irradiation treatment with the radio-protector dithiothreitol (DTT). (Auth.)

  14. DOG1 expression is predicted by the seed-maturation envornment and contributes to geographical variation in germination in Arabidopsis thaliana

    NARCIS (Netherlands)

    Chiang, G.C.K.; Bartsch, M.; Barua, D.; Nakabayashi, K.; Debieu, M.; Kronholm, I.; Koornneef, M.; Soppe, W.J.J.; Donohue, K.; Meaux, De J.

    2011-01-01

    Seasonal germination timing of Arabidopsis thaliana strongly influences overall life history expression and is the target of intense natural selection. This seasonal germination timing depends strongly on the interaction between genetics and seasonal environments both before and after seed

  15. Metabolic labeling and membrane fractionation for comparative proteomic analysis of Arabidopsis thaliana suspension cell cultures.

    Science.gov (United States)

    Szymanski, Witold G; Kierszniowska, Sylwia; Schulze, Waltraud X

    2013-09-28

    Plasma membrane microdomains are features based on the physical properties of the lipid and sterol environment and have particular roles in signaling processes. Extracting sterol-enriched membrane microdomains from plant cells for proteomic analysis is a difficult task mainly due to multiple preparation steps and sources for contaminations from other cellular compartments. The plasma membrane constitutes only about 5-20% of all the membranes in a plant cell, and therefore isolation of highly purified plasma membrane fraction is challenging. A frequently used method involves aqueous two-phase partitioning in polyethylene glycol and dextran, which yields plasma membrane vesicles with a purity of 95% (1). Sterol-rich membrane microdomains within the plasma membrane are insoluble upon treatment with cold nonionic detergents at alkaline pH. This detergent-resistant membrane fraction can be separated from the bulk plasma membrane by ultracentrifugation in a sucrose gradient (2). Subsequently, proteins can be extracted from the low density band of the sucrose gradient by methanol/chloroform precipitation. Extracted protein will then be trypsin digested, desalted and finally analyzed by LC-MS/MS. Our extraction protocol for sterol-rich microdomains is optimized for the preparation of clean detergent-resistant membrane fractions from Arabidopsis thaliana cell cultures. We use full metabolic labeling of Arabidopsis thaliana suspension cell cultures with K(15)NO3 as the only nitrogen source for quantitative comparative proteomic studies following biological treatment of interest (3). By mixing equal ratios of labeled and unlabeled cell cultures for joint protein extraction the influence of preparation steps on final quantitative result is kept at a minimum. Also loss of material during extraction will affect both control and treatment samples in the same way, and therefore the ratio of light and heave peptide will remain constant. In the proposed method either labeled or

  16. Photoprotective mechanism of the non-target organism Arabidopsis thaliana to paraquat exposure.

    Science.gov (United States)

    Moustaka, Julietta; Moustakas, Michael

    2014-05-01

    The response of photosystem II (PSII), of the non-target organism Arabidopsis thaliana, to paraquat (Pq) exposure was studied by chlorophyll fluorescence imaging. Effects of 1mM Pq application by spray on A. thaliana leaves were monitored as soon as 20min after application at the deposit areas of the droplets. A decline in the effective quantum yield of photochemical energy conversion in PSII (ΦPSII) was accompanied by an increase in the quantum yield for dissipation by down regulation in PSII (ΦNPQ). The concomitant decrease in the quantum yield of non-regulated energy loss in PSII (ΦNO) pointed out a quick effective photoprotection mechanism to Pq exposure. Even 1h after Pq spray, when the maximum Pq effect was observed, the decrease of electron transport rate (ETR) and the increase in non-photochemical quenching (NPQ) resulted to maintain almost the same redox state of quinone A (QA) as control plants. Thus, maximal photoprotection was achieved since NPQ was regulated in such a way that PSII reaction centers remained open. Arabidopsis plants were protected from Pq exposure, by increasing NPQ that dissipates light energy and decreases the efficiency of photochemical reactions of photosynthesis (down regulation of PSII) via the "water-water cycle". PSII photochemistry began to recover 4h after Pq exposure, and this was evident from the increase of ΦPSII, the simultaneous decrease of ΦNPQ, and the concomitant decrease of ΦNO. Yet, ETR began to increase, as well as the fraction of open PSII reaction centers. Copyright © 2014 Elsevier Inc. All rights reserved.

  17. Tailoring high-density oligonucleotide arrays for transcript profiling of different Arabidopsis thaliana accessions using a sequence-based approach.

    Science.gov (United States)

    Boudichevskaia, Anastassia; Cao, Hieu Xuan; Schmidt, Renate

    2017-08-01

    Excluding polymorphic probes from GeneChip ® transcript profiling experiments via a sequence-based approach results in improved detection of differentially expressed genes in developing seeds of Arabidopsis thaliana accessions Col-0 and C24. GeneChip ® arrays represent a powerful tool for transcript profiling experiments. The ATH1 GeneChip ® has been designed based on the sequence of the Arabidopsis thaliana reference genome Col-0, hence the features on the array exactly match the sequences of Col-0 transcripts. In contrast, transcripts of other A. thaliana accessions or related species may show nucleotide differences and/or insertions/deletions when compared to the corresponding Col-0 transcripts, therefore, comparisons of transcript abundance involving different A. thaliana accessions or related species may be compromised for a certain number of transcripts. To tackle this limitation, a sequence-based strategy was developed. Only features on the array that were identical in sequence for the specimen to be compared were considered for transcript profiling. The impact of the proposed strategy was evaluated for transcript profiles that were established for developing seeds of A. thaliana accessions Col-0 and C24.

  18. Beneficial Bacteria Isolated from Grapevine Inner Tissues Shape Arabidopsis thaliana Roots

    Science.gov (United States)

    Baldan, Enrico; Nigris, Sebastiano; Romualdi, Chiara; D’Alessandro, Stefano; Clocchiatti, Anna; Zottini, Michela; Stevanato, Piergiorgio; Squartini, Andrea; Baldan, Barbara

    2015-01-01

    We investigated the potential plant growth-promoting traits of 377 culturable endophytic bacteria, isolated from Vitis vinifera cv. Glera, as good biofertilizer candidates in vineyard management. Endophyte ability in promoting plant growth was assessed in vitro by testing ammonia production, phosphate solubilization, indole-3-acetic acid (IAA) and IAA-like molecule biosynthesis, siderophore and lytic enzyme secretion. Many of the isolates were able to mobilize phosphate (33%), release ammonium (39%), secrete siderophores (38%) and a limited part of them synthetized IAA and IAA-like molecules (5%). Effects of each of the 377 grapevine beneficial bacteria on Arabidopsis thaliana root development were also analyzed to discern plant growth-promoting abilities (PGP) of the different strains, that often exhibit more than one PGP trait. A supervised model-based clustering analysis highlighted six different classes of PGP effects on root architecture. A. thaliana DR5::GUS plantlets, inoculated with IAA-producing endophytes, resulted in altered root growth and enhanced auxin response. Overall, the results indicate that the Glera PGP endospheric culturable microbiome could contribute, by structural root changes, to obtain water and nutrients increasing plant adaptation and survival. From the complete cultivable collection, twelve promising endophytes mainly belonging to the Bacillus but also to Micrococcus and Pantoea genera, were selected for further investigations in the grapevine host plants towards future application in sustainable management of vineyards. PMID:26473358

  19. Discordant longitudinal clines in flowering time and phytochrome C in Arabidopsis thaliana.

    Science.gov (United States)

    Samis, Karen E; Heath, Katy D; Stinchcombe, John R

    2008-12-01

    Using seasonal cues to time reproduction appropriately is crucial for many organisms. Plants in particular often use photoperiod to signal the time to transition to flowering. Because seasonality varies latitudinally, adaptation to local climate is expected to result in corresponding clines in photoperiod-related traits. By experimentally manipulating photoperiod cues and measuring the flowering responses and photoperiod plasticity of 138 Eurasian accessions of Arabidopsis thaliana, we detected strong longitudinal but not latitudinal clines in flowering responses. The presence of longitudinal clines suggests that critical photoperiod cues vary among populations occurring at similar latitudes. Haplotypes at PHYC, a locus hypothesized to play a role in adaptation to light cues, were also longitudinally differentiated. Controlling for neutral population structure revealed that PHYC haplotype influenced flowering time; however, the distribution of PHYC haplotypes occurred in the opposite direction to the phenotypic cline, suggesting that loci other than PHYC are responsible for the longitudinal pattern in photoperiod response. Our results provide previously missing empirical support for the importance of PHYC in mediating photoperiod sensitivity in natural populations of A. thaliana. However, they also suggest that other loci and epistatic interactions likely play a role in the determination of flowering time and that the environmental factors influencing photoperiod in plants vary longitudinally as well as latitudinally.

  20. Genome wide transcriptional profiling of acclimation to photoperiod in high-latitude accessions of Arabidopsis thaliana.

    Science.gov (United States)

    Lewandowska-Sabat, Anna Monika; Winge, Per; Fjellheim, Siri; Dørum, Guro; Bones, Atle Magnar; Rognli, Odd Arne

    2012-04-01

    Three Arabidopsis thaliana accessions originating from the northernmost boundary of the species distribution in Norway (59-68°N) were used to study global wide transcriptional responses to 16 and 24 h photoperiods during flower initiation. Significant analysis of microarrays (SAM), analyses of statistically overrepresented gene ontologies (GOstat) and gene set enrichment analyses (GSEA) were used to identify candidate genes and genetic pathways underlying phenotypic adaptations of accessions to different photoperiods. Statistical analyses identified 732 and 258 differentially expressed genes between accessions in 16 and 24 h photoperiod, respectively. Among significantly expressed genes, ethylene mediated signaling pathway was significantly overrepresented in 16 h photoperiod, while genes involved in response to auxin stimulus were found to be significantly overrepresented in 24 h photoperiod. Several gene sets were found to be differentially expressed among accessions, e.g. cold acclimation, dehydration response, phytochrome signaling, vernalization response and circadian clock regulated flowering time genes. These results revealed several candidate genes and pathways likely involved in transcriptional control of photoperiodic response. In particular, ethylene and auxin signaling pathway may represent candidate genes contributing to local adaptation of high-latitude accessions of A. thaliana. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  1. Ultraviolet-B- and ozone-induced biochemical changes in antioxidant enzymes of Arabidopsis thaliana

    International Nuclear Information System (INIS)

    Rao, M.V.; Paliyath, G.; Ormrod, D.P.

    1996-01-01

    Earlier studies with Arabidopsis thaliana exposed to ultraviolet B (UV-B) and ozone (O 3 ) have indicated the differential responses of superoxide dismutase and glutathione reductase. In this study, we have investigated whether A. thaliana genotype Landsberg erecta and its flavonoid-deficient mutant transparent testa (tt5) is capable of metabolizing UV-B- and O 3 -induced activated oxygen species by invoking similar antioxidant enzymes. UV-B exposure preferentially enhanced guaiacol-peroxidases, ascorbate peroxidase, and peroxidases specific to coniferyl alcohol and modified the substrate affinity of ascorbate peroxidase. O 3 exposure enhanced superoxide dismutase, peroxidases, glutathione reductase, and ascorbate peroxidase to a similar degree and modified the substrate affinity of both glutathione reductase and ascorbate peroxidase. Both UV-B and O 3 exposure enhanced similar Cu,Zn-superoxide dismutase isoforms. New isoforms of peroxidases and ascorbate peroxidase were synthesized in tt5 plants irradiated with UV-B. UV-B radiation, in contrast to O 3 , enhanced the activation oxygen species by increasing membrane-localized NADPH-oxidase activity and decreasing catalase activities. These results collectively suggest that (a) UV-B exposure preferentially induces peroxidase-related enzymes, whereas O 3 exposure invokes the enzymes of superoxide dismutase/ascorbate-glutathione cycle, and (b) in contrast to O 3 , UV-B exposure generated activated oxygen species by increasing NADPH-oxidase activity. 10 figs., 4 tabs

  2. Crystal structure of glutamate-1-semialdehyde-2,1-aminomutase from Arabidopsis thaliana

    Energy Technology Data Exchange (ETDEWEB)

    Song, Yingxian; Pu, Hua; Jiang, Tian; Zhang, Lixin; Ouyang, Min, E-mail: ouyangmin@ibcas.ac.cn [Chinese Academy of Sciences, Beijing 100093, People’s Republic of (China)

    2016-05-23

    A structural study of A. thaliana glutamate-1-semialdehyde-2,1-aminomutase (GSAM) has revealed asymmetry in cofactor binding as well as in the gating-loop orientation, which supports the previously proposed negative cooperativity between monomers of GSAM. Glutamate-1-semialdehyde-2,1-aminomutase (GSAM) catalyzes the isomerization of glutamate-1-semialdehyde (GSA) to 5-aminolevulinate (ALA) and is distributed in archaea, most bacteria and plants. Although structures of GSAM from archaea and bacteria have been resolved, a GSAM structure from a higher plant is not available, preventing further structure–function analysis. Here, the structure of GSAM from Arabidopsis thaliana (AtGSA1) obtained by X-ray crystallography is reported at 1.25 Å resolution. AtGSA1 forms an asymmetric dimer and displays asymmetry in cofactor binding as well as in the gating-loop orientation, which is consistent with previously reported Synechococcus GSAM structures. While one monomer binds PMP with the gating loop fixed in the open state, the other monomer binds either PMP or PLP and the gating loop is ready to close. The data also reveal the mobility of residues Gly163, Ser164 and Gly165, which are important for reorientation of the gating loop. Furthermore, the asymmetry of the AtGSA1 structure supports the previously proposed negative cooperativity between monomers of GSAM.

  3. Root-knot nematodes induce pattern-triggered immunity in Arabidopsis thaliana roots.

    Science.gov (United States)

    Teixeira, Marcella A; Wei, Lihui; Kaloshian, Isgouhi

    2016-07-01

    Root-knot nematodes (RKNs; Meloidogyne spp.) are plant parasites with a broad host range causing great losses worldwide. To parasitize their hosts, RKNs establish feeding sites in roots known as giant cells. The majority of work studying plant-RKN interactions in susceptible hosts addresses establishment of the giant cells and there is limited information on the early defense responses. Here we characterized early defense or pattern-triggered immunity (PTI) against RKNs in Arabidopsis thaliana. To address PTI, we evaluated known canonical PTI signaling mutants with RKNs and investigated the expression of PTI marker genes after RKN infection using both quantitative PCR and β-glucuronidase reporter transgenic lines. We showed that PTI-compromised plants have enhanced susceptibility to RKNs, including the bak1-5 mutant. BAK1 is a common partner of distinct receptors of microbe- and damage-associated molecular patterns. Furthermore, our data indicated that nematode recognition leading to PTI responses involves camalexin and glucosinolate biosynthesis. While the RKN-induced glucosinolate biosynthetic pathway was BAK1-dependent, the camalexin biosynthetic pathway was only partially dependent on BAK1. Combined, our results indicate the presence of BAK1-dependent and -independent PTI against RKNs in A. thaliana, suggesting the existence of diverse nematode recognition mechanisms. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

  4. Expression of pH-sensitive green fluorescent protein in Arabidopsis thaliana

    Science.gov (United States)

    Moseyko, N.; Feldman, L. J.

    2001-01-01

    This is the first report on using green fluorescent protein (GFP) as a pH reporter in plants. Proton fluxes and pH regulation play important roles in plant cellular activity and therefore, it would be extremely helpful to have a plant gene reporter system for rapid, non-invasive visualization of intracellular pH changes. In order to develop such a system, we constructed three vectors for transient and stable transformation of plant cells with a pH-sensitive derivative of green fluorescent protein. Using these vectors, transgenic Arabidopsis thaliana and tobacco plants were produced. Here the application of pH-sensitive GFP technology in plants is described and, for the first time, the visualization of pH gradients between different developmental compartments in intact whole-root tissues of A. thaliana is reported. The utility of pH-sensitive GFP in revealing rapid, environmentally induced changes in cytoplasmic pH in roots is also demonstrated.

  5. The novel elicitor AsES triggers a defense response against Botrytis cinerea in Arabidopsis thaliana.

    Science.gov (United States)

    Hael-Conrad, V; Abou-Mansour, E; Díaz-Ricci, J-C; Métraux, J-P; Serrano, M

    2015-12-01

    AsES (Acremonium strictum Elicitor and Subtilisin) is a novel extracellular elicitor protein produced by the avirulent isolate SS71 of the opportunist strawberry fungal pathogen A. strictum. Here we describe the activity of AsES in the plant-pathogen system Arabidopsis thaliana-Botrytis cinerea. We show that AsES renders A. thaliana plants resistant to the necrotrophic pathogen B. cinerea, both locally and systemically and the defense response observed is dose-dependent. Systemic, but not local resistance is dependent on the length of exposure to AsES. The germination of the spores in vitro was not inhibited by AsES, implying that protection to B. cinerea is due to the induction of the plant defenses. These results were further supported by the findings that AsES differentially affects mutants impaired in the response to salicylic acid, jasmonic acid and ethylene, suggesting that AsES triggers the defense response through these three signaling pathways. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  6. Putrescine accumulation in Arabidopsis thaliana transgenic lines enhances tolerance to dehydration and freezing stress

    Science.gov (United States)

    Alet, Analía I; Sanchez, Diego H; Cuevas, Juan C; del Valle, Secundino; Altabella, Teresa; Tiburcio, Antonio F; Marco, Francisco; Ferrando, Alejandro; Espasandín, Fabiana D; González, María E; Carrasco, Pedro

    2011-01-01

    Polyamines have been globally associated to plant responses to abiotic stress. Particularly, putrescine has been related to a better response to cold and dehydration stresses. It is known that this polyamine is involved in cold tolerance, since Arabidopsis thaliana plants mutated in the key enzyme responsible for putrescine synthesis (arginine decarboxilase, ADC; EC 4.1.1.19) are more sensitive than the wild type to this stress. Although it is speculated that the overexpression of ADC genes may confer tolerance, this is hampered by pleiotropic effects arising from the constitutive expression of enzymes from the polyamine metabolism. Here, we present our work using A. thaliana transgenic plants harboring the ADC gene from oat under the control of a stress-inducible promoter (pRD29A) instead of a constitutive promoter. The transgenic lines presented in this work were more resistant to both cold and dehydration stresses, associated with a concomitant increment in endogenous putrescine levels under stress. Furthermore, the increment in putrescine upon cold treatment correlates with the induction of known stress-responsive genes, and suggests that putrescine may be directly or indirectly involved in ABA metabolism and gene expression. PMID:21330789

  7. ARA-PEPs: a repository of putative sORF-encoded peptides in Arabidopsis thaliana.

    Science.gov (United States)

    Hazarika, Rashmi R; De Coninck, Barbara; Yamamoto, Lidia R; Martin, Laura R; Cammue, Bruno P A; van Noort, Vera

    2017-01-17

    Many eukaryotic RNAs have been considered non-coding as they only contain short open reading frames (sORFs). However, there is increasing evidence for the translation of these sORFs into bioactive peptides with potent signaling, antimicrobial, developmental, antioxidant roles etc. Yet only a few peptides encoded by sORFs are annotated in the model organism Arabidopsis thaliana. To aid the functional annotation of these peptides, we have developed ARA-PEPs (available at http://www.biw.kuleuven.be/CSB/ARA-PEPs ), a repository of putative peptides encoded by sORFs in the A. thaliana genome starting from in-house Tiling arrays, RNA-seq data and other publicly available datasets. ARA-PEPs currently lists 13,748 sORF-encoded peptides with transcriptional evidence. In addition to existing data, we have identified 100 novel transcriptionally active regions (TARs) that might encode 341 novel stress-induced peptides (SIPs). To aid in identification of bioactivity, we add functional annotation and sequence conservation to predicted peptides. To our knowledge, this is the largest repository of plant peptides encoded by sORFs with transcript evidence, publicly available and this resource will help scientists to effortlessly navigate the list of experimentally studied peptides, the experimental and computational evidence supporting the activity of these peptides and gain new perspectives for peptide discovery.

  8. Characterizing genomic variation of Arabidopsis thaliana: the roles of geography and climate.

    Science.gov (United States)

    Lasky, Jesse R; Des Marais, David L; McKay, John K; Richards, James H; Juenger, Thomas E; Keitt, Timothy H

    2012-11-01

    Arabidopsis thaliana inhabits diverse climates and exhibits varied phenology across its range. Although A. thaliana is an extremely well-studied model species, the relationship between geography, growing season climate and its genetic variation is poorly characterized. We used redundancy analysis (RDA) to quantify the association of genomic variation [214 051 single nucleotide polymorphisms (SNPs)] with geography and climate among 1003 accessions collected from 447 locations in Eurasia. We identified climate variables most correlated with genomic variation, which may be important selective gradients related to local adaptation across the species range. Climate variation among sites of origin explained slightly more genomic variation than geographical distance. Large-scale spatial gradients and early spring temperatures explained the most genomic variation, while growing season and summer conditions explained the most after controlling for spatial structure. SNP variation in Scandinavia showed the greatest climate structure among regions, possibly because of relatively consistent phenology and life history of populations in this region. Climate variation explained more variation among nonsynonymous SNPs than expected by chance, suggesting that much of the climatic structure of SNP correlations is due to changes in coding sequence that may underlie local adaptation. © 2012 Blackwell Publishing Ltd.

  9. Effects of elevated carbon dioxide and sucrose concentrations on Arabidopsis thaliana root architecture and anatomy

    International Nuclear Information System (INIS)

    Lee-Ho, E.; Walton, L.J.; Reid, D.M.; Yeung, E.C.; Kurepin, L.V.

    2007-01-01

    Plant root growth is known to be influenced by higher levels of atmospheric carbon dioxide (CO 2 ). Roots of some species grown in hydroponics under elevated CO 2 concentrations may be more competitive sinks for photosynthetic assimilates than roots grown under lower CO 2 conditions. Root branching patterns may also be influenced by elevated CO 2 concentrations. Studies have also shown that factors such as soil compaction, salinity and the availability of nitrate, phosphorous, oxygen and water also influence root growth, and the effects of higher CO 2 on roots can be confounded by such environmental factors. This study evaluated the effects of elevated carbon dioxide and sucrose concentrations on Arabidopsis thaliana root growth, morphology, and architecture. Both ambient and elevated CO 2 levels were used along with various sucrose concentrations. The study revealed that A. thaliana plants grown on a phytagar medium in small chambers with elevated CO 2 had longer roots, more lateral root growth than plants grown in ambient CO 2 . Roots in elevated CO 2 were found to have wider root diameters, and more secondary growth. The addition of sucrose to the media closely resembled the effects of elevated CO 2 . In addition, the increase in sucrose concentration had a bigger effect on root morphology under ambient, than elevated CO 2 . Therefore, both elevated CO 2 and increased sucrose concentrations promote root growth by increasing their number, length, and diameter. The dichotomy branching index (DBI) also dropped resulting in a more dichotomous branching pattern. 34 refs., 5 figs

  10. Evaluation of glyphosate resistance in Arabidopsis thaliana expressing an altered target site EPSPS.

    Science.gov (United States)

    Sammons, R Douglas; You, Jinsong; Qi, Youlin; Flasinski, Stanislaw; Kavanaugh, Christina; Washam, Jeannie; Ostrander, Elizabeth; Wang, Dafu; Heck, Greg

    2018-05-01

    Glyphosate-resistant goosegrass has recently evolved and is homozygous for the double mutant of EPSPS (T 102 I, P 106 S or TIPS). These same mutations combined with EPSPS overexpression, have been used to create transgenic glyphosate-resistant crops. Arabidopsis thaliana (Wt EPSPS K i ∼ 0.5 μM) was engineered to express a variant AtEPSPS-T 102 I, P 106 A (TIPA K i = 150 μM) to determine the resistance magnitude for a more potent variant EPSPS that might evolve in weeds. Transgenic A. thaliana plants, homozygous for one, two or four copies of AtEPSPS-TIPA, had resistance (IC 50 values, R/S) as measured by seed production ranging from 4.3- to 16-fold. Plants treated in reproductive stage were male sterile with a range of R/S from 10.1- to 40.6-fold. A significant hormesis (∼ 63% gain in fresh weight) was observed for all genotypes when treated at the initiation of reproductive stage with 0.013 kg ha -1 . AtEPSPS-TIPA enzyme activity was proportional to copy number and correlated with resistance magnitude. A. thaliana, as a model weed expressing one copy of AtEPSPS-TIPA (300-fold more resistant), had only 4.3-fold resistance to glyphosate for seed production. Resistance behaved as a single dominant allele. Vegetative tissue resistance was 4.7-fold greater than reproductive tissue resistance and was linear with gene copy number. © 2017 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. © 2017 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

  11. Chromosome-level assembly of Arabidopsis thaliana Ler reveals the extent of translocation and inversion polymorphisms

    Science.gov (United States)

    Zapata, Luis; Ding, Jia; Willing, Eva-Maria; Hartwig, Benjamin; Bezdan, Daniela; Jiao, Wen-Biao; Patel, Vipul; Velikkakam James, Geo; Koornneef, Maarten; Ossowski, Stephan; Schneeberger, Korbinian

    2016-01-01

    Resequencing or reference-based assemblies reveal large parts of the small-scale sequence variation. However, they typically fail to separate such local variation into colinear and rearranged variation, because they usually do not recover the complement of large-scale rearrangements, including transpositions and inversions. Besides the availability of hundreds of genomes of diverse Arabidopsis thaliana accessions, there is so far only one full-length assembled genome: the reference sequence. We have assembled 117 Mb of the A. thaliana Landsberg erecta (Ler) genome into five chromosome-equivalent sequences using a combination of short Illumina reads, long PacBio reads, and linkage information. Whole-genome comparison against the reference sequence revealed 564 transpositions and 47 inversions comprising ∼3.6 Mb, in addition to 4.1 Mb of nonreference sequence, mostly originating from duplications. Although rearranged regions are not different in local divergence from colinear regions, they are drastically depleted for meiotic recombination in heterozygotes. Using a 1.2-Mb inversion as an example, we show that such rearrangement-mediated reduction of meiotic recombination can lead to genetically isolated haplotypes in the worldwide population of A. thaliana. Moreover, we found 105 single-copy genes, which were only present in the reference sequence or the Ler assembly, and 334 single-copy orthologs, which showed an additional copy in only one of the genomes. To our knowledge, this work gives first insights into the degree and type of variation, which will be revealed once complete assemblies will replace resequencing or other reference-dependent methods. PMID:27354520

  12. Exogenous auxin-induced NO synthesis is nitrate reductase-associated in Arabidopsis thaliana root primordia.

    Science.gov (United States)

    Kolbert, Zsuzsanna; Bartha, Bernadett; Erdei, László

    2008-06-16

    Nitric oxide (NO) functions in various physiological and developmental processes in plants. However, the source of this signaling molecule in the diversity of plant responses is not well understood. It is known that NO mediates auxin-induced adventitious and lateral root (LR) formation. In this paper, we provide genetic and pharmacological evidence that the production of NO is associated with the nitrate reductase (NR) enzyme during indole-3-butyric acid (IBA)-induced lateral root development in Arabidopsis thaliana L. NO production was detected using 4,5-diaminofluorescein diacetate (DAF-2DA) in the NR-deficient nia1, nia2 and Atnoa1 (former Atnos1) mutants of A. thaliana. An inhibitor for nitric oxide synthase (NOS) N(G)-monomethyl-l-arginine (l-NMMA) was applied. Our data clearly show that IBA increased LR frequency in the wild-type plant and the LR initials emitted intensive NO-dependent fluorescence of the triazol product of NO and DAF-2DA. Increased levels of NO were restricted only to the LR initials in contrast to primary root (PR) sections, where NO remained at the control level. The mutants had different NO levels in their control state (i.e. without IBA treatment): nia1, nia2 showed lower NO fluorescence than Atnoa1 or the wild-type plant. The role of NR in IBA-induced NO formation in the wild type was shown by the zero effects of the NOS inhibitors l-NMMA. Finally, it was clearly demonstrated that IBA was able to induce NO generation in both the wild-type and Atnoa1 plants, but failed to induce NO in the NR-deficient mutant. It is concluded that the IBA-induced NO production is nitrate reductase-associated during lateral root development in A. thaliana.

  13. Introduction of tri-antennary N-glycans in Arabidopsis thaliana plants.

    Science.gov (United States)

    Nagels, Bieke; Van Damme, Els J M; Callewaert, Nico; Weterings, Koen

    2012-04-01

    Because the pathway for protein synthesis is largely conserved between plants and animals, plants provide an attractive platform for the cost effective and flexible production of biopharmaceuticals. However, there are some differences in glycosylation between plants and humans that need to be considered before plants can be used as an efficient expression platform. In the presented research the human genes encoding α1,3-mannosyl-β1,4-N-acetylglucosaminyltransferase (GnT-IV) and α1,6-mannosyl-β1,6-N-acetylglucosaminyltransferase (GnT-V) were introduced in the fast cycling model plant Arabidopsis thaliana to synthesize tri-antennary N-glycans. The GnT-IV and -V enzymes were targeted to the Golgi apparatus with plant-specific localization signals. The experiments were performed both in a wild type background, as well as in plants lacking β1,2-xylosyltransferase (XylT) and α1,3-fucosyltransferase (FucT) activity. Glycan analysis of endogenous proteins in the transgenic lines using CE-LIF showed that tri-antennary N-glycans could be produced in the XylT/FucT deficient line, while these structures were not found in the wild type background. Since β-N-acetylhexosaminidases, that remove terminal GlcNAcs, are active in A. thaliana plants, the specificity of these enzymes for different GlcNAc linkages was tested. The results showed that there is no pronounced preference of the A. thaliana hexosaminidases for human-type GlcNAc-linkages. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  14. Characterisation of the first enzymes committed to lysine biosynthesis in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Michael D W Griffin

    Full Text Available In plants, the lysine biosynthetic pathway is an attractive target for both the development of herbicides and increasing the nutritional value of crops given that lysine is a limiting amino acid in cereals. Dihydrodipicolinate synthase (DHDPS and dihydrodipicolinate reductase (DHDPR catalyse the first two committed steps of lysine biosynthesis. Here, we carry out for the first time a comprehensive characterisation of the structure and activity of both DHDPS and DHDPR from Arabidopsis thaliana. The A. thaliana DHDPS enzyme (At-DHDPS2 has similar activity to the bacterial form of the enzyme, but is more strongly allosterically inhibited by (S-lysine. Structural studies of At-DHDPS2 show (S-lysine bound at a cleft between two monomers, highlighting the allosteric site; however, unlike previous studies, binding is not accompanied by conformational changes, suggesting that binding may cause changes in protein dynamics rather than large conformation changes. DHDPR from A. thaliana (At-DHDPR2 has similar specificity for both NADH and NADPH during catalysis, and has tighter binding of substrate than has previously been reported. While all known bacterial DHDPR enzymes have a tetrameric structure, analytical ultracentrifugation, and scattering data unequivocally show that At-DHDPR2 exists as a dimer in solution. The exact arrangement of the dimeric protein is as yet unknown, but ab initio modelling of x-ray scattering data is consistent with an elongated structure in solution, which does not correspond to any of the possible dimeric pairings observed in the X-ray crystal structure of DHDPR from other organisms. This increased knowledge of the structure and function of plant lysine biosynthetic enzymes will aid future work aimed at improving primary production.

  15. Caracterización de las respuestas de defensa inducidas por hongos del género Trichoderma en Arabidopsis thaliana

    OpenAIRE

    Contreras Cornejo, Hexon Angel

    2012-01-01

    Los hongos filamentosos del género Trichoderma han sido reconocidos como agentes para el biocontrol de enfermedades vegetales. En este trabajo, investigamos los mecanismos implicados en las respuestas de defensa en Arabidopsis thaliana inoculadas con Trichoderma virens y Trichoderma atroviride. La interacción de Arabidopsis thaliana con Trichoderma indujo el crecimiento vegetal y activó respuestas de defensa. Estos resultados indican que ambos procesos no son inherentemente ...

  16. Phytoalexins and phytoanticipins from the wild crucifers Thellungiella halophila and Arabidopsis thaliana: rapalexin A, wasalexins and camalexin.

    Science.gov (United States)

    Pedras, M Soledade C; Adio, Adewale M

    2008-02-01

    Investigation of phytoalexin production using abiotic elicitation showed that the phytoalexin rapalexin A was produced by both Thellungiella halophila and Arabidopsis thaliana, but while A. thaliana produced camalexin, T. halophila produced wasalexins A and B and methoxybrassenin B. Considering that the genome of T. halophila is being sequenced currently and that the wasalexin pathway present in T. halophila is expected to involve a number of genes also present in Brassica species, our discovery should facilitate the isolation of genes involved in biosynthetic pathways of phytoalexins of the most economically important crucifer species.

  17. Genetic and Phenotypic Analysis of Lateral Root Development in Arabidopsis thaliana.

    Science.gov (United States)

    Napsucialy-Mendivil, Selene; Dubrovsky, Joseph G

    2018-01-01

    Root system formation to a great extent depends on lateral root (LR) formation. In Arabidopsis thaliana, LRs are initiated within a parent root in pericycle that is an external tissue of the stele. LR initiation takes place in a strictly acropetal pattern, whereas posterior lateral root primordium (LRP) formation is asynchronous. In this chapter, we focus on methods of genetic and phenotypic analysis of LR initiation, LRP morphogenesis, and LR emergence in Arabidopsis. We provide details on how to make cleared root preparations and how to identify the LRP stages. We also pay attention to the categorization of the LRP developmental stages and their variations and to the normalization of the number of LRs and LRPs formed, per length of the primary root, and per number of cells produced within a root. Hormonal misbalances and mutations affect LRP morphogenesis significantly, and the evaluation of LRP abnormalities is addressed as well. Finally, we deal with various molecular markers that can be used for genetic and phenotypic analyses of LR development.

  18. Arabidopsis thaliana WAPL is essential for the prophase removal of cohesin during meiosis.

    Directory of Open Access Journals (Sweden)

    Kuntal De

    2014-07-01

    Full Text Available Sister chromatid cohesion, which is mediated by the cohesin complex, is essential for the proper segregation of chromosomes in mitosis and meiosis. The establishment of stable sister chromatid cohesion occurs during DNA replication and involves acetylation of the complex by the acetyltransferase CTF7. In higher eukaryotes, the majority of cohesin complexes are removed from chromosomes during prophase. Studies in fly and human have shown that this process involves the WAPL mediated opening of the cohesin ring at the junction between the SMC3 ATPase domain and the N-terminal domain of cohesin's α-kleisin subunit. We report here the isolation and detailed characterization of WAPL in Arabidopsis thaliana. We show that Arabidopsis contains two WAPL genes, which share overlapping functions. Plants in which both WAPL genes contain T-DNA insertions show relatively normal growth and development but exhibit a significant reduction in male and female fertility. The removal of cohesin from chromosomes during meiotic prophase is blocked in Atwapl mutants resulting in chromosome bridges, broken chromosomes and uneven chromosome segregation. In contrast, while subtle mitotic alterations are observed in some somatic cells, cohesin complexes appear to be removed normally. Finally, we show that mutations in AtWAPL suppress the lethality associated with inactivation of AtCTF7. Taken together our results demonstrate that WAPL plays a critical role in meiosis and raises the possibility that mechanisms involved in the prophase removal of cohesin may vary between mitosis and meiosis in plants.

  19. Life cycle of Arabidopsis thaliana under microgravity condition in the International Space Station Kibo module

    Science.gov (United States)

    Karahara, Ichirou; Soga, Kouichi; Hoson, Takayuki; Kamisaka, Seiichiro; Yano, Sachiko; Shimazu, Toru; Tamaoki, Daisuke; Tanigaki, Fumiaki; Kasahara, Haruo; Yashiro, Umi; Suto, Takamichi; Yamaguchi, Takashi; Kasahara, Hirokazu

    2012-07-01

    Gravity is an important environmental factors for growth and development of plants throughout their life cycle. We have designed an experiment, which is called Space Seed, to examine the effects of microgravity on the seed to seed life cycle of plants. We have carried out this experiment using a newly developed apparatus, which is called the Plant Experiment Unit (PEU) and installed in the Cell Biology Experiment Facility (CBEF) onboard International Space Station (ISS). The CBEF is equipped with a turntable generating artificial gravity to perform 1-G control experiment as well as micro-G experiment on board. Arabidopsis thaliana seeds sown on dry rockwool in PEUs were transported from Kennedy Space Center to the ISS Kibo module by Space Shuttle Discovery in STS-128 mission. This experiment was started on Sep. 10, 2009 and terminated on Nov. 11, 2009. Arabidopsis seeds successfully germinated, and the plants passed through both vegetative and reproductive processes, such as formation of rosette leaves, bolting of inflorescence stems, flowering, formation of siliques and seeds. Vegetative and reproductive growth were compared among micro-G plants, 1-G control, and the ground control.

  20. Characterization of a mitochondrially targeted single-stranded DNA-binding protein in Arabidopsis thaliana.

    Science.gov (United States)

    Edmondson, Andrew C; Song, Daqing; Alvarez, Luis A; Wall, Melisa K; Almond, David; McClellan, David A; Maxwell, Anthony; Nielsen, Brent L

    2005-04-01

    A gene encoding a predicted mitochondrially targeted single-stranded DNA binding protein (mtSSB) was identified in the Arabidopsis thaliana genome sequence. This gene (At4g11060) codes for a protein of 201 amino acids, including a 28-residue putative mitochondrial targeting transit peptide. Protein sequence alignment shows high similarity between the mtSSB protein and single-stranded DNA binding proteins (SSB) from bacteria, including residues conserved for SSB function. Phylogenetic analysis indicates a close relationship between this protein and other mitochondrially targeted SSB proteins. The predicted targeting sequence was fused with the GFP coding region, and the organellar localization of the expressed fusion protein was determined. Specific targeting to mitochondria was observed in in-vitro import experiments and by transient expression of a GFP fusion construct in Arabidopsis leaves after microprojectile bombardment. The mature mtSSB coding region was overexpressed in Escherichia coli and the protein was purified for biochemical characterization. The purified protein binds single-stranded, but not double-stranded, DNA. MtSSB stimulates the homologous strand-exchange activity of E. coli RecA. These results indicate that mtSSB is a functional homologue of the E. coli SSB, and that it may play a role in mitochondrial DNA recombination.

  1. Selenite-induced nitro-oxidative stress processes in Arabidopsis thaliana and Brassica juncea.

    Science.gov (United States)

    Molnár, Árpád; Kolbert, Zsuzsanna; Kéri, Krisztina; Feigl, Gábor; Ördög, Attila; Szőllősi, Réka; Erdei, László

    2018-02-01

    Extremes of selenium (Se) exert toxic effects on plants' physiological processes; although plant species tolerate Se differently. This study focuses on the effect of Se (0, 20, 50 or 100μM sodium selenite) on secondary nitro-oxidative stress processes mainly using in situ microscopic methods in non-accumulator Arabidopsis thaliana and secondary Se accumulator Brassica juncea. Relative Se tolerance or sensitivity of the species was evaluated based on growth parameters (fresh and dry weight, root growth) and cell viability. Besides, selenite-triggered cell wall modifications (pectin, callose) and stomatal regulations were determined for the first time. In case of Arabidopsis, relative selenite sensitivity was accompanied by decreased stomatal density and induced stomatal opening, callose accumulation, pronounced oxidative stress and moderate nitrosative modifications. In contrast, the selenite-treated, relatively tolerant Brassica juncea showed larger number of more opened stomata, pectin accumulation, moderate oxidative and intense nitrosative stress. These suggest that selenite tolerance or sensitivity is rather associated with oxidative processes than secondary nitrosative modifications in higher plants. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Dynamic Acclimation to High Light in Arabidopsis thaliana Involves Widespread Reengineering of the Leaf Proteome

    Directory of Open Access Journals (Sweden)

    Matthew A. E. Miller

    2017-07-01

    Full Text Available Leaves of Arabidopsis thaliana transferred from low to high light increase their capacity for photosynthesis, a process of dynamic acclimation. A mutant, gpt2, lacking a chloroplast glucose-6-phosphate/phosphate translocator, is deficient in its ability to acclimate to increased light. Here, we have used a label-free proteomics approach, to perform relative quantitation of 1993 proteins from Arabidopsis wild type and gpt2 leaves exposed to increased light. Data are available via ProteomeXchange with identifier PXD006598. Acclimation to light is shown to involve increases in electron transport and carbon metabolism but no change in the abundance of photosynthetic reaction centers. The gpt2 mutant shows a similar increase in total protein content to wild type but differences in the extent of change of certain proteins, including in the relative abundance of the cytochrome b6f complex and plastocyanin, the thylakoid ATPase and selected Benson-Calvin cycle enzymes. Changes in leaf metabolite content as plants acclimate can be explained by changes in the abundance of enzymes involved in metabolism, which were reduced in gpt2 in some cases. Plants of gpt2 invest more in stress-related proteins, suggesting that their reduced ability to acclimate photosynthetic capacity results in increased stress.

  3. PARVUS affects aluminium sensitivity by modulating the structure of glucuronoxylan in Arabidopsis thaliana.

    Science.gov (United States)

    Zhu, Xiao Fang; Wan, Jiang Xue; Wu, Qi; Zhao, Xu Sheng; Zheng, Shao Jian; Shen, Ren Fang

    2017-09-01

    Glucuronoxylan (GX), an important component of hemicellulose in the cell wall, appears to affect aluminium (Al) sensitivity in plants. To investigate the role of GX in cell-wall-localized xylan, we examined the Arabidopsis thaliana parvus mutant in detail. This mutant lacks α-D-glucuronic acid (GlcA) side chains in GX and has greater resistance to Al stress than wild-type (WT) plants. The parvus mutant accumulated lower levels of Al in its roots and cell walls than WT despite having cell wall pectin content and pectin methylesterase (PME) activity similar to those of WT. Our results suggest that the altered properties of hemicellulose in the mutant contribute to its decreased Al accumulation. Although we observed almost no differences in hemicellulose content between parvus and WT under control conditions, less Al was retained in parvus hemicellulose than in WT. This observation is consistent with the finding that GlcA substitutions in WT GX, but not mutant GX, were increased under Al stress. Taken together, these results suggest that the modulation of GlcA levels in GX affects Al resistance by influencing the Al binding capacity of the root cell wall in Arabidopsis. © 2017 John Wiley & Sons Ltd.

  4. UV-B-inducible and temperature-sensitive photoreactivation of cyclobutane pyrimidine dimers in Arabidopsis thaliana

    International Nuclear Information System (INIS)

    Pang, Qishen; Hays, J.B.

    1991-01-01

    Removal of cyclobutane pyrimidine dimers (CBPDs) in vivo from the DNA of UV-irradiated eight-leaf seedlings of Arabidopsis thaliana was rapid in the presence of visible light (half-life about 1 hour); removal of CBPDs in the dark, presumably via excision repair, was an order of magnitude slower. Extracts of plants contained significant photolyase in vitro, as assayed by restoration of transforming activity to UV-irradiated Escherichia coli plasmids; activity was maximal from four-leaf to 12-leaf stages. UV-B treatment of seedlings for 6 hours increased photolyase specific activity in extracts twofold. Arabidopsis photolyase was markedly temperature-sensitive, both in vitro (half-life at 30C about 12 minutes) and in vivo (half-life at 30C, 30 to 45 minutes). The wavelength dependency of the photoreactivation cross-section showed a broad peak at 375 to 400 nm, and is thus similar to that for maize pollen; it overlaps bacterial and yeast photolyase action spectra

  5. Gene expression and hormone autonomy in radiation-induced tumors of Arabidopsis thaliana

    International Nuclear Information System (INIS)

    Persinger, S.M.; Town, C.D.

    1989-01-01

    In order to study the molecular genetics of factor controlling plant cell growth, we have isolated a group of radiation-induced tumors from Arabidopsis thaliana. Tumors appeared on plants derived from 60 Co gamma-irradiated seed or seedlings, and are capable of hormone-autonomous growth in culture. We have used vertebrate oncogene probes to explore the hypothesis that the tumors arose by the radiation-induced activation of growth-regulating plant oncogenes. One probe, int-2, was used to isolate cDNA clones representing an mRNA differentially expressed between tumors and hormone-dependent callus tissue. The genomic organization and function of this and other differentially expressed Arabidopsis sequences are being further characterized. A second area of study concerns the hormonal status of individual tumors. Tumor tissue varies in color, texture, and degree of differentiation: while some tumors appear undifferentiated, one consistently produces roots, and others occasionally develop shoots or leaflets. The tumors have characteristic growth rates on hormone-free medium, and growth in response to exogenous hormones differs among the tumors themselves and from wild-type. Characterization of the relationships between hormonal status, morphogenesis, and gene expression should yield valuable insights into the mechanisms regulating plant growth and development

  6. Transcriptomic variation among six Arabidopsis thaliana accessions identified several novel genes controlling aluminium tolerance.

    Science.gov (United States)

    Kusunoki, Kazutaka; Nakano, Yuki; Tanaka, Keisuke; Sakata, Yoichi; Koyama, Hiroyuki; Kobayashi, Yuriko

    2017-02-01

    Differences in the expression levels of aluminium (Al) tolerance genes are a known determinant of Al tolerance among plant varieties. We combined transcriptomic analysis of six Arabidopsis thaliana accessions with contrasting Al tolerance and a reverse genetic approach to identify Al-tolerance genes responsible for differences in Al tolerance between accession groups. Gene expression variation increased in the signal transduction process under Al stress and in growth-related processes in the absence of stress. Co-expression analysis and promoter single nucleotide polymorphism searching suggested that both trans-acting polymorphisms of Al signal transduction pathway and cis-acting polymorphisms in the promoter sequences caused the variations in gene expression associated with Al tolerance. Compared with the wild type, Al sensitivity increased in T-DNA knockout (KO) lines for five genes, including TARGET OF AVRB OPERATION1 (TAO1) and an unannotated gene (At5g22530). These were identified from 53 Al-inducible genes showing significantly higher expression in tolerant accessions than in sensitive accessions. These results indicate that the difference in transcriptional signalling is partly associated with the natural variation in Al tolerance in Arabidopsis. Our study also demonstrates the feasibility of comparative transcriptome analysis by using natural genetic variation for the identification of genes responsible for Al stress tolerance. © 2016 John Wiley & Sons Ltd.

  7. Purifying selection acts on coding and non-coding sequences of paralogous genes in Arabidopsis thaliana.

    Science.gov (United States)

    Hoffmann, Robert D; Palmgren, Michael

    2016-06-13

    Whole-genome duplications in the ancestors of many diverse species provided the genetic material for evolutionary novelty. Several models explain the retention of paralogous genes. However, how these models are reflected in the evolution of coding and non-coding sequences of paralogous genes is unknown. Here, we analyzed the coding and non-coding sequences of paralogous genes in Arabidopsis thaliana and compared these sequences with those of orthologous genes in Arabidopsis lyrata. Paralogs with lower expression than their duplicate had more nonsynonymous substitutions, were more likely to fractionate, and exhibited less similar expression patterns with their orthologs in the other species. Also, lower-expressed genes had greater tissue specificity. Orthologous conserved non-coding sequences in the promoters, introns, and 3' untranslated regions were less abundant at lower-expressed genes compared to their higher-expressed paralogs. A gene ontology (GO) term enrichment analysis showed that paralogs with similar expression levels were enriched in GO terms related to ribosomes, whereas paralogs with different expression levels were enriched in terms associated with stress responses. Loss of conserved non-coding sequences in one gene of a paralogous gene pair correlates with reduced expression levels that are more tissue specific. Together with increased mutation rates in the coding sequences, this suggests that similar forces of purifying selection act on coding and non-coding sequences. We propose that coding and non-coding sequences evolve concurrently following gene duplication.

  8. Identification and Partial Characterization of an L-Tyrosine Aminotransferase (TAT from Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Pranav R. Prabhu

    2010-01-01

    Full Text Available The aminotransferase gene family in the model plant Arabidopsis thaliana consists of 44 genes. Twenty six of these enzymes are classified as characterized meaning that the reaction(s that the enzyme catalyzes are documented using experimental means. The remaining 18 enzymes are uncharacterized and are therefore deemed putative. Our laboratory is interested in elucidating the function(s of the remaining putative aminotransferase enzymes. To this end, we have identified and partially characterized an aminotransferase (TAT enzyme from Arabidopsis annotated by the locus tag At5g36160. The full-length cDNA was cloned and the purified recombinant enzyme was characterized using in vitro and in vivo experiments. In vitro analysis showed that the enzyme is capable of interconverting L-Tyrosine and 4-hydroxyphenylpyruvate, and L-Phenylalanine and phenylpyruvate. In vivo analysis by functional complementation showed that the gene was able to complement an E. coli with a background of aminotransferase mutations that confers auxotrophy for L-Tyrosine and L-Phenylalanine.

  9. The aba mutant of Arabidopsis thaliana is impaired in epoxy-carotenoid biosynthesis

    Energy Technology Data Exchange (ETDEWEB)

    Rock, C.D.; Zeevaart, J.A.D. (Michigan State Univ., East Lansing (United States))

    1991-09-01

    The three mutant alleles of the ABA locus of Arabidopsis thaliana result in plants that are deficient in the plant growth regulator abscisic acid (ABA). The authors have used {sup 18}O{sub 2} to label ABA in water-stressed leaves of mutant and wild-type Arabidopsis. Analysis by selected ion monitoring and tandem mass spectrometry of ({sup 18}O)ABA and its catabolites, phaseic acid and ABA-glucose ester ({beta}-D-glucopyranosyl abscisate), indicates that the aba genotypes are impaired in ABA biosynthesis and have a small ABA precursor pool of compounds that contain oxygens on the rings, presumably oxygenated carotenoids (xanthophylls). Quantitation of the carotenoids form mutant and wild-type leaves establishes that the aba alleles cause a deficiency of the epoxy-carotenoids violaxanthin and neoxanthin and an accumulation of their biosynthetic precursor, zeaxanthin. These results provide evidence that ABA is synthesized by oxidative cleavage of epoxy-carotenoids (the indirect pathway). Furthermore the carotenoid mutant they describe undergoes normal greening. Thus the aba alleles provide an opportunity to study the physiological roles of epoxy-carotenoids in photosynthesis in a higher plants.

  10. Camalexin Quantification inArabidopsis thalianaLeaves Infected withBotrytis cinerea.

    Science.gov (United States)

    Savatin, Daniel V; Bisceglia, Nora Gigli; Gravino, Matteo; Fabbri, Claudia; Pontiggia, Daniela; Mattei, Benedetta

    2015-01-20

    Phytoalexins are heterogeneous low molecular mass secondary metabolites with antimicrobial activity produced at the infection site in response to pathogen invasion and represent an important part of the plant defense repertoire. Camalexin (3-Thiazol-2'-yl-indole) is a known phytoalexin first detected and isolated in Camelina sativa , from which it takes its name, infected with Alternaria brassicae (Browne et al. , 1991). Production of camalexin is also induced in Arabidopsis thaliana leaves by a range of biotrophic and necrotrophic plant pathogens (bacteria, oomycetes, fungi and viruses) (Ahuja et al. , 2012) as well as by abiotic stresses, such as UV and chemicals ( e.g. acifluorfen, paraquat, chlorsulfuron and α-amino butyric acid) (Zhao et al. , 1998; Tierens et al. , 2002). Camalexin originates from tryptophan and CYP79B2 and CYP71B15 (PAD3) are P450 enzymes that catalyze important steps in its biosynthetic pathway (Glawischnig, 2007). The detection and quantification of camalexin content is required to understand how it is produced upon various stress conditions. Here we describe an easy method for camalexin extraction from Arabidopsis leaves infected with the necrotrophic fungus Botrytis cinerea , and further determination of camalexin levels by liquid chromatography-mass spectrometry (LC-MS). The method is sensitive enough to trace amount of camalexin down to the low pico-gram (10 pg/mg FW) range.

  11. Glutathione-Indole-3-Acetonitrile Is Required for Camalexin Biosynthesis in Arabidopsis thaliana[W][OA

    Science.gov (United States)

    Su, Tongbing; Xu, Juan; Li, Yuan; Lei, Lei; Zhao, Luo; Yang, Hailian; Feng, Jidong; Liu, Guoqin; Ren, Dongtao

    2011-01-01

    Camalexin, a major phytoalexin in Arabidopsis thaliana, consists of an indole ring and a thiazole ring. The indole ring is produced from Trp, which is converted to indole-3-acetonitrile (IAN) by CYP79B2/CYP79B3 and CYP71A13. Conversion of Cys(IAN) to dihydrocamalexic acid and subsequently to camalexin is catalyzed by CYP71B15. Recent studies proposed that Cys derivative, not Cys itself, is the precursor of the thiazole ring that conjugates with IAN. The nature of the Cys derivative and how it conjugates to IAN and subsequently forms Cys(IAN) remain obscure. We found that protein accumulation of multiple glutathione S-transferases (GSTs), elevation of GST activity, and consumption of glutathione (GSH) coincided with camalexin production. GSTF6 overexpression increased and GSTF6-knockout reduced camalexin production. Arabidopsis GSTF6 expressed in yeast cells catalyzed GSH(IAN) formation. GSH(IAN), (IAN)CysGly, and γGluCys(IAN) were determined to be intermediates within the camalexin biosynthetic pathway. Inhibitor treatments and mutant analyses revealed the involvement of γ-glutamyl transpeptidases (GGTs) and phytochelatin synthase (PCS) in the catabolism of GSH(IAN). The expression of GSTF6, GGT1, GGT2, and PCS1 was coordinately upregulated during camalexin biosynthesis. These results suggest that GSH is the Cys derivative used during camalexin biosynthesis, that the conjugation of GSH with IAN is catalyzed by GSTF6, and that GGTs and PCS are involved in camalexin biosynthesis. PMID:21239642

  12. Glutathione-indole-3-acetonitrile is required for camalexin biosynthesis in Arabidopsis thaliana.

    Science.gov (United States)

    Su, Tongbing; Xu, Juan; Li, Yuan; Lei, Lei; Zhao, Luo; Yang, Hailian; Feng, Jidong; Liu, Guoqin; Ren, Dongtao

    2011-01-01

    Camalexin, a major phytoalexin in Arabidopsis thaliana, consists of an indole ring and a thiazole ring. The indole ring is produced from Trp, which is converted to indole-3-acetonitrile (IAN) by CYP79B2/CYP79B3 and CYP71A13. Conversion of Cys(IAN) to dihydrocamalexic acid and subsequently to camalexin is catalyzed by CYP71B15. Recent studies proposed that Cys derivative, not Cys itself, is the precursor of the thiazole ring that conjugates with IAN. The nature of the Cys derivative and how it conjugates to IAN and subsequently forms Cys(IAN) remain obscure. We found that protein accumulation of multiple glutathione S-transferases (GSTs), elevation of GST activity, and consumption of glutathione (GSH) coincided with camalexin production. GSTF6 overexpression increased and GSTF6-knockout reduced camalexin production. Arabidopsis GSTF6 expressed in yeast cells catalyzed GSH(IAN) formation. GSH(IAN), (IAN)CysGly, and γGluCys(IAN) were determined to be intermediates within the camalexin biosynthetic pathway. Inhibitor treatments and mutant analyses revealed the involvement of γ-glutamyl transpeptidases (GGTs) and phytochelatin synthase (PCS) in the catabolism of GSH(IAN). The expression of GSTF6, GGT1, GGT2, and PCS1 was coordinately upregulated during camalexin biosynthesis. These results suggest that GSH is the Cys derivative used during camalexin biosynthesis, that the conjugation of GSH with IAN is catalyzed by GSTF6, and that GGTs and PCS are involved in camalexin biosynthesis.

  13. Genome-Wide Analysis of the Distinct Types of Chromatin Interactions in Arabidopsis thaliana.

    Science.gov (United States)

    Wang, Jingjing; Zhou, Yincong; Li, Xue; Meng, Xianwen; Fan, Miao; Chen, Hongjun; Xue, Jitong; Chen, Ming

    2017-01-01

    The three-dimensional shapes of chromosomes regulate gene expression and genome function. Our knowledge of the role of chromatin interaction is evolving rapidly. Here, we present a study of global chromatin interaction patterns in Arabidopsis thaliana. High-throughput experimental techniques have been developed to map long-range interactions within chromatin. We have integrated data from multiple experimental sources including Hi-C, BS-seq, ChIP-chip and ChIP-seq data for 17 epigenetic marks and 35 transcription factors. We identified seven groups of interacting loci, which can be distinguished by their epigenetic profiles. Furthermore, the seven groups of interacting loci can be divided into three types of chromatin linkages based on expression status. We observed that two interacting loci sometimes share common epigenetic and transcription factor-binding profiles. Different groups of loci display very different relationships between epigenetic marks and the binding of transcription factors. Distinctive types of chromatin linkages exhibit different gene expression profiles. Our study unveils an entirely unexplored regulatory interaction, linking epigenetic profiles, transcription factor binding and the three-dimensional spatial organization of the Arabidopsis nuclear genome. © The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  14. Susceptibility of intact germinating Arabidopsis thaliana to human fungal pathogens Cryptococcus neoformans and C. gattii.

    Science.gov (United States)

    Warpeha, Katherine M; Park, Yoon-Dong; Williamson, Peter R

    2013-05-01

    The fungus Cryptococcus contributes a large global burden of infectious death in both HIV-infected and healthy individuals. As Cryptococcus is an opportunistic pathogen, much of the evolutionary pressure shaping virulence occurs in environments in contact with plants and soil. The present studies investigated inoculation of intact seeds of the common weed Arabidopsis thaliana with fungal cells over a 21-day period. C. gattii was the more virulent plant pathogen, resulting in disrupted germination as well as increased stem lodging, fungal burden, and plant tissue colocalization. C. neoformans was a less virulent plant pathogen but exhibited prolonged tissue residence within the cuticle and vascular spaces. Arabidopsis mutants of the PRN1 gene, which is involved in abiotic and biotic signaling affecting phenylalanine-derived flavonoids, showed altered susceptibility to cryptoccocal infections, suggesting roles for this pathway in cryptococcal defense. The fungal virulence factor laccase was also implicated in plant pathogenesis, as a cryptococcal lac1Δ strain was less virulent than wild-type fungi and was unable to colonize seedlings. In conclusion, these studies expand knowledge concerning the ecological niche of Cryptococcus by demonstrating the pathogenic capacity of the anamorphic form of cryptococcal cells against healthy seedlings under physiologically relevant conditions. In addition, an important role of laccase in plant as well as human virulence may suggest mechanisms for laccase retention and optimization during evolution of this fungal pathogen.

  15. Mapping quantitative trait loci affecting Arabidopsis thaliana seed morphology features extracted computationally from images.

    Science.gov (United States)

    Moore, Candace R; Gronwall, David S; Miller, Nathan D; Spalding, Edgar P

    2013-01-01

    Seeds are studied to understand dispersal and establishment of the next generation, as units of agricultural yield, and for other important reasons. Thus, elucidating the genetic architecture of seed size and shape traits will benefit basic and applied plant biology research. This study sought quantitative trait loci (QTL) controlling the size and shape of Arabidopsis thaliana seeds by computational analysis of seed phenotypes in recombinant inbred lines derived from the small-seeded Landsberg erecta × large-seeded Cape Verde Islands accessions. On the order of 10(3) seeds from each recombinant inbred line were automatically measured with flatbed photo scanners and custom image analysis software. The eight significant QTL affecting seed area explained 63% of the variation, and overlapped with five of the six major-axis (length) QTL and three of the five minor-axis (width) QTL, which accounted for 57% and 38% of the variation in those traits, respectively. Because the Arabidopsis seed is exalbuminous, lacking an endosperm at maturity, the results are relatable to embryo length and width. The Cvi allele generally had a positive effect of 2.6-4.0%. Analysis of variance showed heritability of the three traits ranged between 60% and 73%. Repeating the experiment with 2.2 million seeds from a separate harvest of the RIL population and approximately 0.5 million seeds from 92 near-isogenic lines confirmed the aforementioned results. Structured for download are files containing phenotype measurements, all sets of seed images, and the seed trait measuring tool.

  16. A Comparison of Global Gene Expression Measurement Technologies in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Blake Meyers

    2006-03-01

    Full Text Available Microarrays and tag-based transcriptional profiling technologies represent diverse but complementary data types. We are currently conducting a comparison of high-density in situ synthesized microarrays and massively-parallel signature sequencing (MPSS data in the model plant, Arabidopsis thaliana. The MPSS data (available at http://mpss.udel.edu/at and the microarray data have been compiled using the same RNA source material. In this review, we outline the experimental strategy that we are using, and present preliminary data and interpretations from the transcriptional profiles of Arabidopsis leaves and roots. The preliminary data indicate that the log ratio differences of transcripts between leaves and roots measured by microarray data are in better agreement with the MPSS data than the absolute intensities measured for individual microarrays hybridized to only one of the cRNA populations. The correlation was substantially improved by focusing on a subset of genes excluding those with very low expression levels; this selection may have removed noisy data. Future reports will incorporate more than 10 tissues that have been sampled by MPSS.

  17. Proteomic and phosphoproteomic analyses of chromatin-associated proteins from Arabidopsis thaliana

    KAUST Repository

    Bigeard, Jean

    2014-07-10

    The nucleus is the organelle where basically all DNA-related processes take place in eukaryotes, such as replication, transcription, and splicing as well as epigenetic regulation. The identification and description of the nuclear proteins is one of the requisites toward a comprehensive understanding of the biological functions accomplished in the nucleus. Many of the regulatory mechanisms of protein functions rely on their PTMs among which phosphorylation is probably one of the most important properties affecting enzymatic activity, interaction with other molecules, localization, or stability. So far, the nuclear and subnuclear proteome and phosphoproteome of the model plant Arabidopsis thaliana have been the subject of very few studies. In this work, we developed a purification protocol of Arabidopsis chromatin-associated proteins and performed proteomic and phosphoproteomic analyses identifying a total of 879 proteins of which 198 were phosphoproteins that were mainly involved in chromatin remodeling, transcriptional regulation, and RNA processing. From 230 precisely localized phosphorylation sites (phosphosites), 52 correspond to hitherto unidentified sites. This protocol and data thereby obtained should be a valuable resource for many domains of plant research.

  18. Chronical influence of radiation and lead on mutation rates in plants of Arabidopsis Thaliana (L.) Heynh

    International Nuclear Information System (INIS)

    Kryukov, V.I.; Shishkin, V.A.; Sokolenko, S.F.

    1996-01-01

    Plants of Arabidopsis thaliana were grown in a laboratory conditions on the soil (black earth, chernozem) which was polluted with a radioactive isotopes of cesium, 134+137 Cs. Increase in specific activity of samples from 217 to 1025 and 2529 Bq/kg resulted in increase of embryonic mutation rate in Arabidopsis from 8.2 to 20.2 and 51.6 % respectively. Bringing Pb 2+ in a dose of 16 mg into the soil resulted in statistically significant decrease in mutation rate. Further increase of lead concentration in radioactive soils to 32, 64, 96, 160 and 320 mg/kg resulted in growth of the mutation rates in the plants which were grown on the soil with low and middle specific activity of cesium, and in decrease of the mutation rates in the plants which were grown on the soil with high specific radioactivity. The last process apparently was connected with the intensive growth in the number of sterile seeds in the pods. 19 refs.; 2 figs.; 4 tabs

  19. Genome-wide analysis of protein disorder in Arabidopsis thaliana: implications for plant environmental adaptation.

    Science.gov (United States)

    Pietrosemoli, Natalia; García-Martín, Juan A; Solano, Roberto; Pazos, Florencio

    2013-01-01

    Intrinsically disordered proteins/regions (IDPs/IDRs) are currently recognized as a widespread phenomenon having key cellular functions. Still, many aspects of the function of these proteins need to be unveiled. IDPs conformational flexibility allows them to recognize and interact with multiple partners, and confers them larger interaction surfaces that may increase interaction speed. For this reason, molecular interactions mediated by IDPs/IDRs are particularly abundant in certain types of protein interactions, such as those of signaling and cell cycle control. We present the first large-scale study of IDPs in Arabidopsis thaliana, the most widely used model organism in plant biology, in order to get insight into the biological roles of these proteins in plants. The work includes a comparative analysis with the human proteome to highlight the differential use of disorder in both species. Results show that while human proteins are in general more disordered, certain functional classes, mainly related to environmental response, are significantly more enriched in disorder in Arabidopsis. We propose that because plants cannot escape from environmental conditions as animals do, they use disorder as a simple and fast mechanism, independent of transcriptional control, for introducing versatility in the interaction networks underlying these biological processes so that they can quickly adapt and respond to challenging environmental conditions.

  20. Co-ordinate regulation of genes involved in storage lipid mobilization in Arabidopsis thaliana.

    Science.gov (United States)

    Rylott, E L; Hooks, M A; Graham, I A

    2001-05-01

    Molecular genetic approaches in the model plant Arabidopsis thaliana (Col0) are shedding new light on the role and control of the pathways associated with the mobilization of lipid reserves during oilseed germination and post-germinative growth. Numerous independent studies have reported on the expression of individual genes encoding enzymes from the three major pathways: beta-oxidation, the glyoxylate cycle and gluconeogenesis. However, a single comprehensive study of representative genes and enzymes from the different pathways in a single plant species has not been done. Here we present results from Arabidopsis that demonstrate the co-ordinate regulation of gene expression and enzyme activities for the acyl-CoA oxidase- and 3-ketoacyl-CoA thiolase-mediated steps of beta-oxidation, the isocitrate lyase and malate synthase steps of the glyoxylate cycle and the phosphoenolpyruvate carboxykinase step of gluconeogenesis. The mRNA abundance and enzyme activities increase to a peak at stage 2, 48 h after the onset of seed germination, and decline thereafter either to undetectable levels (for malate synthase and isocitrate lyase) or low basal levels (for the genes of beta-oxidation and gluconeogenesis). The co-ordinate induction of all these genes at the onset of germination raises the possibility that a global regulatory mechanism operates to induce the expression of genes associated with the mobilization of storage reserves during the heterotrophic growth period.

  1. Arabidopsis thaliana ICE2 gene: phylogeny, structural evolution and functional diversification from ICE1.

    Science.gov (United States)

    Kurbidaeva, Amina; Ezhova, Tatiana; Novokreshchenova, Maria

    2014-12-01

    The ability to tolerate environmental stresses is crucial for all living organisms, and gene duplication is one of the sources for evolutionary novelties. Arabidopsis thaliana INDUCER OF CBF EXPRESSION1 and 2 (ICE1 and ICE2) encode MYC-type bHLH (basic helix-loop-helix) transcription factors. They confer cold stress tolerance by induction of the CBF/DREB1 regulon and regulate stomata formation. Although ICE2 is closely related to ICE1, its origin and role in cold response remains uncertain. Here, we used a bioinformatics/phylogenetic approach to uncover the ICE2 evolutionary history, structural evolution and functional divergence from the putative ancestral gene. Sequence diversification from ICE1 included the gain of cis-acting elements in ICE2 promoter sequence that may provide meristem-specific and defense-related gene expression. By analyzing transgenic Arabidopsis lines with ICE2 over-expression we showed that it contributes to stomata formation, flowering time regulation and cold response. Constitutive ICE2 expression led to induced meristem freezing tolerance, resulting from activation of CBF1 and CBF3 genes and ABA biosynthesis by NCED3 induction. We presume that ICE2 gene has originated from a duplication event about 17.9MYA followed by sub- and neofunctionalization of the ancestral ICE1 gene. Moreover, we predict its role in pathogen resistance and flowering time regulation. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  2. Inference of the Genetic Network Regulating Lateral Root Initiation in Arabidopsis thaliana

    KAUST Repository

    Muraro, D.

    2013-01-01

    Regulation of gene expression is crucial for organism growth, and it is one of the challenges in systems biology to reconstruct the underlying regulatory biological networks from transcriptomic data. The formation of lateral roots in Arabidopsis thaliana is stimulated by a cascade of regulators of which only the interactions of its initial elements have been identified. Using simulated gene expression data with known network topology, we compare the performance of inference algorithms, based on different approaches, for which ready-to-use software is available. We show that their performance improves with the network size and the inclusion of mutants. We then analyze two sets of genes, whose activity is likely to be relevant to lateral root initiation in Arabidopsis, and assess causality of their regulatory interactions by integrating sequence analysis with the intersection of the results of the best performing methods on time series and mutants. The methods applied capture known interactions between genes that are candidate regulators at early stages of development. The network inferred from genes significantly expressed during lateral root formation exhibits distinct scale free, small world and hierarchical properties and the nodes with a high out-degree may warrant further investigation. © 2004-2012 IEEE.

  3. Agrobacterium tumefaciens promotes tumor induction by modulating pathogen defense in Arabidopsis thaliana.

    Science.gov (United States)

    Lee, Chil-Woo; Efetova, Marina; Engelmann, Julia C; Kramell, Robert; Wasternack, Claus; Ludwig-Müller, Jutta; Hedrich, Rainer; Deeken, Rosalia

    2009-09-01

    Agrobacterium tumefaciens causes crown gall disease by transferring and integrating bacterial DNA (T-DNA) into the plant genome. To examine the physiological changes and adaptations during Agrobacterium-induced tumor development, we compared the profiles of salicylic acid (SA), ethylene (ET), jasmonic acid (JA), and auxin (indole-3-acetic acid [IAA]) with changes in the Arabidopsis thaliana transcriptome. Our data indicate that host responses were much stronger toward the oncogenic strain C58 than to the disarmed strain GV3101 and that auxin acts as a key modulator of the Arabidopsis-Agrobacterium interaction. At initiation of infection, elevated levels of IAA and ET were associated with the induction of host genes involved in IAA, but not ET signaling. After T-DNA integration, SA as well as IAA and ET accumulated, but JA did not. This did not correlate with SA-controlled pathogenesis-related gene expression in the host, although high SA levels in mutant plants prevented tumor development, while low levels promoted it. Our data are consistent with a scenario in which ET and later on SA control virulence of agrobacteria, whereas ET and auxin stimulate neovascularization during tumor formation. We suggest that crosstalk among IAA, ET, and SA balances pathogen defense launched by the host and tumor growth initiated by agrobacteria.

  4. Evaluation of Arabidopsis thaliana as a model host for Xylella fastidiosa.

    Science.gov (United States)

    Rogers, Elizabeth E

    2012-06-01

    The bacterium Xylella fastidiosa causes a number of plant diseases of significant economic impact. To date, progress determining mechanisms of host-plant susceptibility, tolerance, or resistance has been slow, due in large part to the long generation time and limited available genetic resources for grape, almond, and other known hosts of X. fastidiosa. To overcome many of these limitations, Arabidopsis thaliana has been evaluated as a host for X. fastidiosa. A pin-prick inoculation method has been developed to infect Arabidopsis with X. fastidiosa. Following infection, X. fastidiosa multiplies and can be detected by microscopy, polymerase chain reaction, and isolation. The ecotypes Van-0, LL-0, and Tsu-1 all allow more growth of strain X. fastidiosa Temecula than the reference ecotype Col-0. Affymetrix ATH1 microarray analysis of inoculated vs. noninoculated Tsu-1 reveals gene expression changes that differ greatly from changes seen after infection with apoplast-colonizing bacteria such as Psuedomonas syringae pvs. tomato or syringae. Many genes responsive to oxidative stress are differentially regulated, while classic pathogenesis-related genes are not induced by X. fastidiosa infection.

  5. Cloning and sequencing of cDNAs specifying a novel class of phosphoribosyl diphosphate synthase in Arabidopsis thaliana

    DEFF Research Database (Denmark)

    Krath, Britta N.; Eriksen, Tina A.; Poulsen, Tim S.

    1999-01-01

    cDNAs specifying four active phosphoribosyl diphosphate synthase isozymes were isolated from an Arabidopsis thaliana cDNA library. In contrast to other phosphoribosyl diphosphate synthases the activity of two of the A. thaliana isozymes are independent of Pi. Amino acid sequence comparison...

  6. Identifying the transition to the maturation zone in three ecotypes of Arabidopsis thaliana roots.

    Science.gov (United States)

    Cajero Sánchez, Wendy; García-Ponce, Berenice; Sánchez, María de la Paz; Álvarez-Buylla, Elena R; Garay-Arroyo, Adriana

    2018-01-01

    The Arabidopsis thaliana (hereafter Arabidopsis) root has become a useful model for studying how organ morphogenesis emerge from the coordination and balance of cell proliferation and differentiation, as both processes may be observed and quantified in the root at different stages of development. Hence, being able to objectively identify and delimit the different stages of root development has been very important. Up to now, three different zones along the longitudinal axis of the primary root of Arabidopsis, have been identified: the root apical meristematic zone (RAM) with two domains [the proliferative (PD) and the transition domain (TD)], the elongation zone (EZ) and the maturation zone (MZ). We previously reported a method to quantify the length of the cells of the meristematic and the elongation zone, as well as the boundaries or transitions between the root domains along the growing part of the Arabidopsis root. In this study, we provide a more accurate criterion to identify the MZ. Traditionally, the transition between the EZ to the MZ has been established by the emergence of the first root-hair bulge in the epidermis, because this emergence coincides with cell maturation in this cell type. But we have found here that after the emergence of the first root-hair bulge some cells continue to elongate and we have confirmed this in three different Arabidopsis ecotypes. We established the limit between the EZ and the MZ by looking for the closest cortical cell with a longer length than the average cell length of 10 cells after the cortical cell closest to the epidermal cell with the first root-hair bulge in these three ecotypes. In Col-0 and Ws this cell is four cells above the one with the root hair bulge and, in the Ler ecotype, this cell is five cells above. To unambiguously identifying the site at which cells stop elongating and attain their final length and fate at the MZ, we propose to calculate the length of completely elongated cortical cells counting 10

  7. Impacts of high ATP supply from chloroplasts and mitochondria on the leaf metabolism of Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Chao eLiang

    2015-10-01

    Full Text Available Chloroplasts and mitochondria are the major ATP producing organelles in plant leaves. Arabidopsis thaliana purple acid phosphatase 2 (AtPAP2 is a phosphatase dually targeted to the outer membranes of both organelles and it plays a role in the import of selected nuclear-encoded proteins into these two organelles. Overexpression (OE of AtPAP2 in Arabidopsis thaliana accelerates plant growth and promotes flowering, seed yield and biomass at maturity. Measurement of ADP/ATP/NADP+/NADPH contents in the leaves of 20-day-old OE and wild-type lines at the end of night and at 1 and 8 h following illumination in a 16/8 h photoperiod revealed that the ATP levels and ATP/NADPH ratios were significantly increased in the OE line at all three time points. The AtPAP2 OE line is therefore a good model to investigate the impact of high energy on the global molecular status of Arabidopsis. In this study, transcriptome, proteome and metabolome profiles of the high ATP transgenic line were examined and compared with those of wild-type plants. A comparison of OE and WT at the end of the night provide valuable information on the impact of higher ATP output from mitochondria on plant physiology, as mitochondrial respiration is the major source of ATP in the dark in leaves. Similarly, comparison of OE and WT following illumination will provide information on the impact of higher energy output from chloroplasts on plant physiology. Overexpression of AtPAP2 was found to significantly affect the transcript and protein abundances of genes encoded by the two organellar genomes. For example, the protein abundances of many ribosomal proteins encoded by the chloroplast genome were higher in the AtPAP2 OE line under both light and dark conditions, while the protein abundances of multiple components of the photosynthetic complexes were lower. RNA-seq data also showed that the transcription of the mitochondrial genome is greatly affected by the availability of energy. These data

  8. Distinct physiological and molecular responses in Arabidopsis thaliana exposed to aluminum oxide nanoparticles and ionic aluminum.

    Science.gov (United States)

    Jin, Yujian; Fan, Xiaoji; Li, Xingxing; Zhang, Zhenyan; Sun, Liwei; Fu, Zhengwei; Lavoie, Michel; Pan, Xiangliang; Qian, Haifeng

    2017-09-01

    Nano-aluminium oxide (nAl 2 O 3 ) is one of the most widely used nanomaterials. However, nAl 2 O 3 toxicity mechanisms and potential beneficial effects on terrestrial plant physiology remain poorly understood. Such knowledge is essential for the development of robust nAl 2 O 3 risk assessment. In this study, we studied the influence of a 10-d exposure to a total selected concentration of 98 μM nAl 2 O 3 or to the equivalent molar concentration of ionic Al (AlCl 3 ) (196 μM) on the model plant Arabidopsis thaliana on the physiology (e.g., growth and photosynthesis, membrane damage) and the transcriptome using a high throughput state-of-the-art technology, RNA-seq. We found no evidence of nAl 2 O 3 toxicity on photosynthesis, growth and lipid peroxidation. Rather the nAl 2 O 3 treatment stimulated root weight and length by 48% and 39%, respectively as well as photosynthesis opening up the door to the use of nAl 2 O 3 in biotechnology and nano agriculture. Transcriptomic analyses indicate that the beneficial effect of nAl 2 O 3 was related to an increase in the transcription of several genes involved in root growth as well as in root nutrient uptake (e.g., up-regulation of the root hair-specific gene family and root development genes, POLARIS protein). By contrast, the ionic Al treatment decreased shoot and root weight of Arabidopsis thaliana by 57.01% and 45.15%, respectively. This toxic effect was coupled to a range of response at the gene transcription level including increase transcription of antioxidant-related genes and transcription of genes involved in plant defense response to pathogens. This work provides an integrated understanding at the molecular and physiological level of the effects of nAl 2 O 3 and ionic Al in Arabidopsis. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Identification and Expression Profiling of Radiation-sensitive Genes Using Plant Model System, Arabidopsis thaliana

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Dong-Sub; Kang, Si-Yong; Lee, Geung-Joo; Kim, Jin-Baek

    2008-06-15

    The purpose of this study is to characterize genes specifically expressed in response to ionizing energy (gamma-rays) of acute irradiation and elucidate signalling mechanisms via functional analysis of isolated genes in Arabidopsis thaliana. Recent improvements in DNA microarray technologies and bioinformatics have made it possible to look for common features of ionizing radiation-responsive genes and their regulatory regions. It has produced massive quantities of gene expression and other functional genomics data, and its application will increase in plant genomics. In this study, we used oligonucleotide microarrays to detect the Arabidopsis genes expressed differentially by a gamma-irradiation during the vegetative (VT, 21 DAG) and reproductive (RT, 28 DAG) stages. Wild-type (Ler) Arabidopsis was irradiated with gamma-rays with 100 and 800 Gy doses. Among the 21,500 genes represented in the Agilent chip, approximately 13,500 ({sup {approx}}61.4 %) responsive genes to {nu} -irradiation were expressed with signal intensity greater than 192 when compared to the combined control (non-irradiated vegetative and reproductive pool). Expression patterns of several radiation inducible genes were confirmed by RT-PCR and Northern blotting. Our microarray results may contribute to an overall understanding of the type and quantities of genes that are expressed by an acute gamma-irradiation. In addition, to investigate the oxidative damage caused by irradiation, RT-PCR analysis for the expression of antioxidant isoenzyme genes, and a Transmission Electron Microscope (TEM) observation for visualizing the H{sub 2}O{sub 2} scavenging activity in leaves were applied.

  10. Synthesis of oleyl oleate wax esters in Arabidopsis thaliana and Camelina sativa seed oil.

    Science.gov (United States)

    Iven, Tim; Hornung, Ellen; Heilmann, Mareike; Feussner, Ivo

    2016-01-01

    Seed oil composed of wax esters with long-chain monoenoic acyl moieties represents a high-value commodity for industry. Such plant-derived sperm oil-like liquid wax esters are biodegradable and can have excellent properties for lubrication. In addition, wax ester oil may represent a superior substrate for biodiesel production. In this study, we demonstrate that the low-input oil seed crop Camelina sativa can serve as a biotechnological platform for environmentally benign wax ester production. Two biosynthetic steps catalysed by a fatty alcohol-forming acyl-CoA reductase (FAR) and a wax ester synthase (WS) are sufficient to achieve wax ester accumulation from acyl-CoA substrates. To produce plant-derived sperm oil-like liquid wax esters, the WS from Mus musculus (MmWS) or Simmondsia chinensis (ScWS) were expressed in combination with the FAR from Mus musculus (MmFAR1) or Marinobacter aquaeolei (MaFAR) in seeds of Arabidopsis thaliana and Camelina sativa. The three analysed enzyme combinations Oleo3:mCherry:MmFAR1∆c/Oleo3:EYFP:MmWS, Oleo3:mCherry:MmFAR1∆c/ScWS and MaFAR/ScWS showed differences in the wax ester molecular species profiles and overall biosynthetic performance. By expressing MaFAR/ScWS in Arabidopsis or Camelina up to 59% or 21% of the seed oil TAGs were replaced by wax esters, respectively. This combination also yielded wax ester molecular species with highest content of monounsaturated acyl moieties. Expression of the enzyme combinations in the Arabidopsis fae1 fad2 mutant background high in oleic acid resulted in wax ester accumulation enriched in oleyl oleate (18:1/18:1 > 60%), suggesting that similar values may be obtained with a Camelina high oleic acid line. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

  11. A circadian oscillator in the fungus Botrytis cinerea regulates virulence when infecting Arabidopsis thaliana.

    Science.gov (United States)

    Hevia, Montserrat A; Canessa, Paulo; Müller-Esparza, Hanna; Larrondo, Luis F

    2015-07-14

    The circadian clock of the plant model Arabidopsis thaliana modulates defense mechanisms impacting plant-pathogen interactions. Nevertheless, the effect of clock regulation on pathogenic traits has not been explored in detail. Moreover, molecular description of clocks in pathogenic fungi--or fungi in general other than the model ascomycete Neurospora crassa--has been neglected, leaving this type of question largely unaddressed. We sought to characterize, therefore, the circadian system of the plant pathogen Botrytis cinerea to assess if such oscillatory machinery can modulate its virulence potential. Herein, we show the existence of a functional clock in B. cinerea, which shares similar components and circuitry with the Neurospora circadian system, although we found that its core negative clock element FREQUENCY (BcFRQ1) serves additional roles, suggesting extracircadian functions for this protein. We observe that the lesions produced by this necrotrophic fungus on Arabidopsis leaves are smaller when the interaction between these two organisms occurs at dawn. Remarkably, this effect does not depend solely on the plant clock, but instead largely relies on the pathogen circadian system. Genetic disruption of the B. cinerea oscillator by mutation, overexpression of BcFRQ1, or by suppression of its rhythmicity by constant light, abrogates circadian regulation of fungal virulence. By conducting experiments with out-of-phase light:dark cycles, we confirm that indeed, it is the fungal clock that plays the main role in defining the outcome of the Arabidopsis-Botrytis interaction, providing to our knowledge the first evidence of a microbial clock modulating pathogenic traits at specific times of the day.

  12. Identification and Expression Profiling of Radiation-sensitive Genes Using Plant Model System, Arabidopsis thaliana

    International Nuclear Information System (INIS)

    Kim, Dong-Sub; Kang, Si-Yong; Lee, Geung-Joo; Kim, Jin-Baek

    2008-06-01

    The purpose of this study is to characterize genes specifically expressed in response to ionizing energy (gamma-rays) of acute irradiation and elucidate signalling mechanisms via functional analysis of isolated genes in Arabidopsis thaliana. Recent improvements in DNA microarray technologies and bioinformatics have made it possible to look for common features of ionizing radiation-responsive genes and their regulatory regions. It has produced massive quantities of gene expression and other functional genomics data, and its application will increase in plant genomics. In this study, we used oligonucleotide microarrays to detect the Arabidopsis genes expressed differentially by a gamma-irradiation during the vegetative (VT, 21 DAG) and reproductive (RT, 28 DAG) stages. Wild-type (Ler) Arabidopsis was irradiated with gamma-rays with 100 and 800 Gy doses. Among the 21,500 genes represented in the Agilent chip, approximately 13,500 ( ∼ 61.4 %) responsive genes to ν -irradiation were expressed with signal intensity greater than 192 when compared to the combined control (non-irradiated vegetative and reproductive pool). Expression patterns of several radiation inducible genes were confirmed by RT-PCR and Northern blotting. Our microarray results may contribute to an overall understanding of the type and quantities of genes that are expressed by an acute gamma-irradiation. In addition, to investigate the oxidative damage caused by irradiation, RT-PCR analysis for the expression of antioxidant isoenzyme genes, and a Transmission Electron Microscope (TEM) observation for visualizing the H 2 O 2 scavenging activity in leaves were applied

  13. LEA (Late Embryogenesis Abundant proteins and their encoding genes in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Hincha Dirk K

    2008-03-01

    Full Text Available Abstract Background LEA (late embryogenesis abundant proteins have first been described about 25 years ago as accumulating late in plant seed development. They were later found in vegetative plant tissues following environmental stress and also in desiccation tolerant bacteria and invertebrates. Although they are widely assumed to play crucial roles in cellular dehydration tolerance, their physiological and biochemical functions are largely unknown. Results We present a genome-wide analysis of LEA proteins and their encoding genes in Arabidopsis thaliana. We identified 51 LEA protein encoding genes in the Arabidopsis genome that could be classified into nine distinct groups. Expression studies were performed on all genes at different developmental stages, in different plant organs and under different stress and hormone treatments using quantitative RT-PCR. We found evidence of expression for all 51 genes. There was only little overlap between genes expressed in vegetative tissues and in seeds and expression levels were generally higher in seeds. Most genes encoding LEA proteins had abscisic acid response (ABRE and/or low temperature response (LTRE elements in their promoters and many genes containing the respective promoter elements were induced by abscisic acid, cold or drought. We also found that 33% of all Arabidopsis LEA protein encoding genes are arranged in tandem repeats and that 43% are part of homeologous pairs. The majority of LEA proteins were predicted to be highly hydrophilic and natively unstructured, but some were predicted to be folded. Conclusion The analyses indicate a wide range of sequence diversity, intracellular localizations, and expression patterns. The high fraction of retained duplicate genes and the inferred functional diversification indicate that they confer an evolutionary advantage for an organism under varying stressful environmental conditions. This comprehensive analysis will be an important starting point for

  14. Arabidopsis thaliana: A model host plant to study plant-pathogen interaction using Chilean field isolates of Botrytis cinerea

    Directory of Open Access Journals (Sweden)

    JUAN GONZÁLEZ

    2006-01-01

    Full Text Available One of the fungal pathogens that causes more agriculture damage is Botrytis cinerea. Botrytis is a constant threat to crops because the fungus infects a wide range of host species, both native and cultivated. Furthermore, Botrytis persists on plant debris in and on the soil. Some of the most serious diseases caused by Botrytis include gray mold on vegetables and fruits, such as grapes and strawberries. Botrytis also causes secondary soft rot of fruits and vegetables during storage, transit and at the market. In many plant-pathogen interactions, resistance often is associated with the deposition of callose, accumulation of autofluorescent compounds, the synthesis and accumulation of salicylic acid as well as pathogenesis-related proteins. Arabidopsis thaliana has been used as a plant model to study plant-pathogen interaction. The genome of Arabidopsis has been completely sequenced and this plant serves as a good genetic and molecular model. In this study, we demonstrate that Chilean field isolates infect Arabidopsis thaliana and that Arabidopsis subsequently activates several defense response mechanisms associated with a hypersensitive response. Furthermore, we propose that Arabidopsis may be used as a model host species to analyze the diversity associated with infectivity among populations of Botrytis cinerea field isolates

  15. Arabidopsis thaliana: a model host plant to study plant-pathogen interaction using Chilean field isolates of Botrytis cinerea.

    Science.gov (United States)

    González, Juan; Reyes, Francisca; Salas, Carlos; Santiag, Margarita; Codriansky, Yael; Coliheuque, Nelson; Silva, Herman

    2006-01-01

    One of the fungal pathogens that causes more agriculture damage is Botrytis cinerea. Botrytis is a constant threat to crops because the fungus infects a wide range of host species, both native and cultivated. Furthermore, Botrytis persists on plant debris in and on the soil. Some of the most serious diseases caused by Botrytis include gray mold on vegetables and fruits, such as grapes and strawberries. Botrytis also causes secondary soft rot of fruits and vegetables during storage, transit and at the market. In many plant-pathogen interactions, resistance often is associated with the deposition of callose, accumulation of autofluorescent compounds, the synthesis and accumulation of salicylic acid as well as pathogenesis-related proteins. Arabidopsis thaliana has been used as a plant model to study plant-pathogen interaction. The genome of Arabidopsis has been completely sequenced and this plant serves as a good genetic and molecular model. In this study, we demonstrate that Chilean field isolates infect Arabidopsis thaliana and that Arabidopsis subsequently activates several defense response mechanisms associated with a hypersensitive response. Furthermore, we propose that Arabidopsis may be used as a model host species to analyze the diversity associated with infectivity among populations of Botrytis cinerea field isolates.

  16. Intraspecific plant-soil feedback and intraspecific overyielding in Arabidopsis thaliana.

    Science.gov (United States)

    Bukowski, Alexandra R; Petermann, Jana S

    2014-06-01

    Understanding the mechanisms of community coexistence and ecosystem functioning may help to counteract the current biodiversity loss and its potentially harmful consequences. In recent years, plant-soil feedback that can, for example, be caused by below-ground microorganisms has been suggested to play a role in maintaining plant coexistence and to be a potential driver of the positive relationship between plant diversity and ecosystem functioning. Most of the studies addressing these topics have focused on the species level. However, in addition to interspecific interactions, intraspecific interactions might be important for the structure of natural communities. Here, we examine intraspecific coexistence and intraspecific diversity effects using 10 natural accessions of the model species Arabidopsis thaliana (L.) Heynh. We assessed morphological intraspecific diversity by measuring several above- and below-ground traits. We performed a plant-soil feedback experiment that was based on these trait differences between the accessions in order to determine whether A. thaliana experiences feedback at intraspecific level as a result of trait differences. We also experimentally tested the diversity-productivity relationship at intraspecific level. We found strong differences in above- and below-ground traits between the A. thaliana accessions. Overall, plant-soil feedback occurred at intraspecific level. However, accessions differed in the direction and strength of this feedback: Some accessions grew better on their own soils, some on soils from other accessions. Furthermore, we found positive diversity effects within A. thaliana: Accession mixtures produced a higher total above-ground biomass than accession monocultures. Differences between accessions in their feedback response could not be explained by morphological traits. Therefore, we suggest that they might have been caused by accession-specific accumulated soil communities, by root exudates, or by accession

  17. Temperature fine-tunes Mediterranean Arabidopsis thaliana life-cycle phenology geographically.

    Science.gov (United States)

    Marcer, A; Vidigal, D S; James, P M A; Fortin, M-J; Méndez-Vigo, B; Hilhorst, H W M; Bentsink, L; Alonso-Blanco, C; Picó, F X

    2018-01-01

    To understand how adaptive evolution in life-cycle phenology operates in plants, we need to unravel the effects of geographic variation in putative agents of natural selection on life-cycle phenology by considering all key developmental transitions and their co-variation patterns. We address this goal by quantifying the temperature-driven and geographically varying relationship between seed dormancy and flowering time in the annual Arabidopsis thaliana across the Iberian Peninsula. We used data on genetic variation in two major life-cycle traits, seed dormancy (DSDS50) and flowering time (FT), in a collection of 300 A. thaliana accessions from the Iberian Peninsula. The geographically varying relationship between life-cycle traits and minimum temperature, a major driver of variation in DSDS50 and FT, was explored with geographically weighted regressions (GWR). The environmentally varying correlation between DSDS50 and FT was analysed by means of sliding window analysis across a minimum temperature gradient. Maximum local adjustments between minimum temperature and life-cycle traits were obtained in the southwest Iberian Peninsula, an area with the highest minimum temperatures. In contrast, in off-southwest locations, the effects of minimum temperature on DSDS50 were rather constant across the region, whereas those of minimum temperature on FT were more variable, with peaks of strong local adjustments of GWR models in central and northwest Spain. Sliding window analysis identified a minimum temperature turning point in the relationship between DSDS50 and FT around a minimum temperature of 7.2 °C. Above this minimum temperature turning point, the variation in the FT/DSDS50 ratio became rapidly constrained and the negative correlation between FT and DSDS50 did not increase any further with increasing minimum temperatures. The southwest Iberian Peninsula emerges as an area where variation in life-cycle phenology appears to be restricted by the duration and severity

  18. Expression differences for genes involved in lignin, glutathione and sulphate metabolism in response to cadmium in Arabidopsis thaliana and the related Zn/Cd-hyperaccumulator Thlaspi caerulescens

    NARCIS (Netherlands)

    van de Mortel, Judith E.; Schat, Henk; Moerland, Perry D.; Ver Loren van Themaat, Emiel; van der Ent, Sjoerd; Blankestijn, Hetty; Ghandilyan, Artak; Tsiatsiani, Styliani; Aarts, Mark G. M.

    2008-01-01

    Cadmium (Cd) is a widespread, naturally occurring element present in soil, rock, water, plants and animals. Cd is a non-essential element for plants and is toxic at higher concentrations. Transcript profiles of roots of Arabidopsis thaliana (Arabidopsis) and Thlaspi caerulescens plants exposed to Cd

  19. Root hydrotropism and thigmotropism in Arabidopsis thaliana are differentially controlled by redox status

    OpenAIRE

    Ponce, Georgina; Corkidi, Gabriel; Eapen, Delfeena; Lledías, Fernando; Cárdenas, Luis; Cassab, Gladys

    2017-01-01

    Factors that affect the direction of root growth in response to environmental signals influence crop productivity. We analyzed the root tropic responses of thioredoxin (trxs), thigmotropic (wav2-1), and hydrotropic (ahr1 and nhr1) Arabidopsis thaliana mutants treated with low concentrations of paraquat (PQ), which induces mild oxidative stress, and established a new method for evaluating root waviness (root bending effort, RBE). This method estimates root bending by measuring and summing loca...

  20. Loss of membrane fluidity and endocytosis inhibition are involved in rapid aluminum-induced root growth cessation in Arabidopsis thaliana

    Czech Academy of Sciences Publication Activity Database

    Krtková, J.; Havelková, L.; Křepelová, A.; Fišer, R.; Vosolsobě, S.; Novotná, Z.; Martinec, Jan; Schwarzerová, K.

    2012-01-01

    Roč. 60, Nov 2012 (2012), s. 88-97 ISSN 0981-9428 R&D Projects: GA ČR GA522/05/0340 Grant - others:GA ČR(CZ) GPP207/12/P890 Program:GP Institutional research plan: CEZ:AV0Z50380511 Keywords : Aluminum toxicity * Arabidopsis thaliana * Cortical microtubules Subject RIV: ED - Physiology Impact factor: 2.775, year: 2012

  1. The Arabidopsis thaliana non-specific phospholipase C2 is involved in the response to Pseudomonas syringae attack

    Czech Academy of Sciences Publication Activity Database

    Krčková, Zuzana; Kocourková, Daniela; Daněk, Michal; Brouzdová, Jitka; Pejchar, Přemysl; Janda, Martin; Pokotylo, I.; Ott, P.G.; Valentová, O.; Martinec, Jan

    2018-01-01

    Roč. 121, č. 2 (2018), s. 297-310 ISSN 0305-7364 R&D Projects: GA ČR(CZ) GAP501/12/1942 Institutional support: RVO:61389030 Keywords : Arabidopsis thaliana * effector-triggered immunity * flagellin * MAMP-triggered immunity * non-specific phospholipase C * phosphatidylcholine-specific phospholipase C * Pseudomonas syringae * reactive oxygen species Subject RIV: ED - Physiology OBOR OECD: Plant sciences, botany Impact factor: 4.041, year: 2016

  2. Expression of Cucumber mosaic virus suppressor 2b alters FWA methylation and its siRNA accumulation in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Sadia Hamera

    2016-11-01

    Full Text Available The Cucumber mosaic virus (CMV suppressor 2b co-localizes with AGO4 in cytoplasmic and nuclear fractions of Arabidopsis thaliana. Biochemical fractionation of A. thaliana cellular extracts revealed that 2b and AGO4 coexist in multiple size exclusions. 2b transgenic A. thaliana exhibited an enhanced accumulation of 24nt siRNAs from flowering wageningen (FWA and other heterochromatic loci. These plants also exhibited hypo-methylation of an endogenous- as well as transgene-FWA promoter at non-CG sites. In corroboration, both transgenic 2b and CMV infection affected the regulation of transposons which mimics the ago4 phenotype. In conclusion, 2b perturbs plant defense by interfering with AGO4-regulated transcriptional gene silencing.

  3. Early effects of salt stress on the physiological and oxidative status of Cakile maritima (halophyte) and Arabidopsis thaliana (glycophyte).

    Science.gov (United States)

    Ellouzi, Hasna; Hamed, Karim Ben; Cela, Jana; Munné-Bosch, Sergi; Abdelly, Chedly

    2011-06-01

    Early changes in physiological and oxidative status induced by salt stress were monitored in two Brassicaceae plants differing in their tolerance to salinity, Cakile maritima (halophyte) and Arabidopsis thaliana (glycophyte). Growth response and antioxidant defense of C. maritima under 400 mM NaCl were compared with those of A. thaliana exposed to 100 mM NaCl. Salinity induced early growth reduction that is less pronounced in C. maritima than in A. thaliana. Maximum hydrogen peroxide (H₂O₂) level occurred in the leaves of both species 4 h after the onset of salt treatment. A rapid decline in H₂O₂ concentration was observed thereafter in C. maritima, whereas it remained high in A. thaliana. Correlatively, superoxide dismutase, catalase and peroxidase activities increased at 4 h of treatment in C. maritima and decreased thereafter. However, the activity of these enzymes remained higher in treated plants than that in controls, regardless of the duration of treatment, in A. thaliana. The concentrations of malondialdehyde (MDA) reached maximum values at 24 h of salt stress in both species. Again, MDA levels decreased later in C. maritima, but remained high in A. thaliana. The contents of α-tocopherol remained constant during salt stress in C. maritima and decreased during the first 24 h of salt stress and then remained low in A. thaliana. The results clearly showed that C. maritima, in contrast to A. thaliana, can rapidly evolve physiological and antioxidant mechanisms to adapt to salt and manage the oxidative stress. This may explain, at least partially, the difference in salt tolerance between halophytes and glycophytes. Copyright © Physiologia Plantarum 2011.

  4. A trio of viral proteins tunes aphid-plant interactions in Arabidopsis thaliana.

    Science.gov (United States)

    Westwood, Jack H; Groen, Simon C; Du, Zhiyou; Murphy, Alex M; Anggoro, Damar Tri; Tungadi, Trisna; Luang-In, Vijitra; Lewsey, Mathew G; Rossiter, John T; Powell, Glen; Smith, Alison G; Carr, John P

    2013-01-01

    Virus-induced deterrence to aphid feeding is believed to promote plant virus transmission by encouraging migration of virus-bearing insects away from infected plants. We investigated the effects of infection by an aphid-transmitted virus, cucumber mosaic virus (CMV), on the interaction of Arabidopsis thaliana, one of the natural hosts for CMV, with Myzus persicae (common names: 'peach-potato aphid', 'green peach aphid'). Infection of Arabidopsis (ecotype Col-0) with CMV strain Fny (Fny-CMV) induced biosynthesis of the aphid feeding-deterrent 4-methoxy-indol-3-yl-methylglucosinolate (4MI3M). 4MI3M inhibited phloem ingestion by aphids and consequently discouraged aphid settling. The CMV 2b protein is a suppressor of antiviral RNA silencing, which has previously been implicated in altering plant-aphid interactions. Its presence in infected hosts enhances the accumulation of CMV and the other four viral proteins. Another viral gene product, the 2a protein (an RNA-dependent RNA polymerase), triggers defensive signaling, leading to increased 4MI3M accumulation. The 2b protein can inhibit ARGONAUTE1 (AGO1), a host factor that both positively-regulates 4MI3M biosynthesis and negatively-regulates accumulation of substance(s) toxic to aphids. However, the 1a replicase protein moderated 2b-mediated inhibition of AGO1, ensuring that aphids were deterred from feeding but not poisoned. The LS strain of CMV did not induce feeding deterrence in Arabidopsis ecotype Col-0. Inhibition of AGO1 by the 2b protein could act as a booby trap since this will trigger antibiosis against aphids. However, for Fny-CMV the interplay of three viral proteins (1a, 2a and 2b) appears to balance the need of the virus to inhibit antiviral silencing, while inducing a mild resistance (antixenosis) that is thought to promote transmission. The strain-specific effects of CMV on Arabidopsis-aphid interactions, and differences between the effects of Fny-CMV on this plant and those seen previously in tobacco

  5. A Trio of Viral Proteins Tunes Aphid-Plant Interactions in Arabidopsis thaliana

    Science.gov (United States)

    Du, Zhiyou; Murphy, Alex M.; Anggoro, Damar Tri; Tungadi, Trisna; Luang-In, Vijitra; Lewsey, Mathew G.; Rossiter, John T.; Powell, Glen; Smith, Alison G.; Carr, John P.

    2013-01-01

    Background Virus-induced deterrence to aphid feeding is believed to promote plant virus transmission by encouraging migration of virus-bearing insects away from infected plants. We investigated the effects of infection by an aphid-transmitted virus, cucumber mosaic virus (CMV), on the interaction of Arabidopsis thaliana, one of the natural hosts for CMV, with Myzus persicae (common names: ‘peach-potato aphid’, ‘green peach aphid’). Methodology/Principal Findings Infection of Arabidopsis (ecotype Col-0) with CMV strain Fny (Fny-CMV) induced biosynthesis of the aphid feeding-deterrent 4-methoxy-indol-3-yl-methylglucosinolate (4MI3M). 4MI3M inhibited phloem ingestion by aphids and consequently discouraged aphid settling. The CMV 2b protein is a suppressor of antiviral RNA silencing, which has previously been implicated in altering plant-aphid interactions. Its presence in infected hosts enhances the accumulation of CMV and the other four viral proteins. Another viral gene product, the 2a protein (an RNA-dependent RNA polymerase), triggers defensive signaling, leading to increased 4MI3M accumulation. The 2b protein can inhibit ARGONAUTE1 (AGO1), a host factor that both positively-regulates 4MI3M biosynthesis and negatively-regulates accumulation of substance(s) toxic to aphids. However, the 1a replicase protein moderated 2b-mediated inhibition of AGO1, ensuring that aphids were deterred from feeding but not poisoned. The LS strain of CMV did not induce feeding deterrence in Arabidopsis ecotype Col-0. Conclusions/Significance Inhibition of AGO1 by the 2b protein could act as a booby trap since this will trigger antibiosis against aphids. However, for Fny-CMV the interplay of three viral proteins (1a, 2a and 2b) appears to balance the need of the virus to inhibit antiviral silencing, while inducing a mild resistance (antixenosis) that is thought to promote transmission. The strain-specific effects of CMV on Arabidopsis-aphid interactions, and differences between

  6. Structural and Functional Characterization of the Protein Kinase Mps1 in Arabidopsis thaliana

    Science.gov (United States)

    de Oliveira, Eduardo Alves Gamosa; Romeiro, Nelilma Correia; Ribeiro, Elane da Silva; Santa-Catarina, Claudete; Oliveira, Antônia Elenir Amâncio; Silveira, Vanildo; de Souza Filho, Gonçalo Apolinário; Venancio, Thiago Motta; Cruz, Marco Antônio Lopes

    2012-01-01

    In eukaryotes, protein kinases catalyze the transfer of a gamma-phosphate from ATP (or GTP) to specific amino acids in protein targets. In plants, protein kinases have been shown to participate in signaling cascades driving responses to environmental stimuli and developmental processes. Plant meristems are undifferentiated tissues that provide the major source of cells that will form organs throughout development. However, non-dividing specialized cells can also dedifferentiate and re-initiate cell division if exposed to appropriate conditions. Mps1 (Monopolar spindle) is a dual-specificity protein kinase that plays a critical role in monitoring the accuracy of chromosome segregation in the mitotic checkpoint mechanism. Although Mps1 functions have been clearly demonstrated in animals and fungi, its role in plants is so far unclear. Here, using structural and biochemical analyses here we show that Mps1 has highly similar homologs in many plant genomes across distinct lineages (e.g. AtMps1 in Arabidopsis thaliana). Several structural features (i.e. catalytic site, DFG motif and threonine triad) are clearly conserved in plant Mps1 kinases. Structural and sequence analysis also suggest that AtMps1 interact with other cell cycle proteins, such as Mad2 and MAPK1. By using a very specific Mps1 inhibitor (SP600125) we show that compromised AtMps1 activity hampers the development of A. thaliana seedlings in a dose-dependent manner, especially in secondary roots. Moreover, concomitant administration of the auxin IAA neutralizes the AtMps1 inhibition phenotype, allowing secondary root development. These observations let us to hypothesize that AtMps1 might be a downstream regulator of IAA signaling in the formation of secondary roots. Our results indicate that Mps1 might be a universal component of the Spindle Assembly Checkpoint machinery across very distant lineages of eukaryotes. PMID:23049844

  7. Arabidopsis thaliana GYRB3 does not encode a DNA gyrase subunit.

    Directory of Open Access Journals (Sweden)

    Katherine M Evans-Roberts

    2010-03-01

    Full Text Available DNA topoisomerases are enzymes that control the topology of DNA in all cells. DNA gyrase is unique among the topoisomerases in that it is the only enzyme that can actively supercoil DNA using the free energy of ATP hydrolysis. Until recently gyrase was thought to be unique to bacteria, but has now been discovered in plants. The genome of the model plant, Arabidopsis thaliana, is predicted to encode four gyrase subunits: AtGyrA, AtGyrB1, AtGyrB2 and AtGyrB3.We found, contrary to previous data, that AtGyrB3 is not essential to the survival of A. thaliana. Bioinformatic analysis suggests AtGyrB3 is considerably shorter than other gyrase B subunits, lacking part of the ATPase domain and other key motifs found in all type II topoisomerases; but it does contain a putative DNA-binding domain. Partially purified AtGyrB3 cannot bind E. coli GyrA or support supercoiling. AtGyrB3 cannot complement an E. coli gyrB temperature-sensitive strain, whereas AtGyrB2 can. Yeast two-hybrid analysis suggests that AtGyrB3 cannot bind to AtGyrA or form a dimer.These data strongly suggest that AtGyrB3 is not a gyrase subunit but has another unknown function. One possibility is that it is a nuclear protein with a role in meiosis in pollen.

  8. Seed dormancy cycling and mortality differ between two locally adapted populations of Arabidopsis thaliana.

    Science.gov (United States)

    Postma, Froukje M; Lundemo, Sverre; Ågren, Jon

    2016-02-01

    Intraspecific variation in seed bank dynamics should contribute to local adaptation, but is not well studied. The extent to which genetic and environmental factors affect dormancy cycling and seed mortality was investigated in the annual herb Arabidopsis thaliana by conducting a reciprocal seed burial experiment. Seeds from two locally adapted populations (from Italy and Sweden) were buried at both of the sites of origin, and seed mortality and germinability were determined during the following 2 years for initially non-dormant glasshouse-matured seeds and dormant field-matured seeds. Mean soil temperature was higher at the Italian site compared with the Swedish site throughout the year, and the germination proportions were in general higher for seeds buried in Italy than in Sweden. The rate of secondary dormancy induction of the Italian genotype was faster than that of the Swedish genotype at both sites, while the opposite was true for the rate of dormancy release, at least at the Swedish site. The comparison of non-dormant glasshouse seeds with dormant field seeds demonstrated that A. thaliana seeds can adjust their dormancy levels to current environmental conditions, and suggests that maternal environmental conditions have only minor effects on dormancy cycles. At both sites, locally produced seeds had low germinability in the first year compared with the second year, suggesting that a considerable fraction of the seeds would enter the seed bank. In Italy, but not in Sweden, seed mortality increased rapidly during the second year of burial. This is the first demonstration of intraspecific genetic differentiation in the annual seed dormancy cycle of any species, and the documented difference is likely to contribute to local adaptation. The results suggest that the contribution of a seed bank to seedling recruitment should vary among environments due to differences in the rate of seed mortality. © The Author 2015. Published by Oxford University Press on behalf of

  9. Modulation of modeled microgravity on radiation-induced bystander effects in Arabidopsis thaliana

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Ting [Key Laboratory of Ion Beam Bio-engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences and Anhui Province, Hefei, Anhui 230031 (China); Sun, Qiao [Space Molecular Biological Lab, China Academy of Space Technology, Beijing 100086 (China); Xu, Wei; Li, Fanghua [Key Laboratory of Ion Beam Bio-engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences and Anhui Province, Hefei, Anhui 230031 (China); Li, Huasheng; Lu, Jinying [Space Molecular Biological Lab, China Academy of Space Technology, Beijing 100086 (China); Wu, Lijun; Wu, Yuejin [Key Laboratory of Ion Beam Bio-engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences and Anhui Province, Hefei, Anhui 230031 (China); Liu, Min [Space Molecular Biological Lab, China Academy of Space Technology, Beijing 100086 (China); Bian, Po [Key Laboratory of Ion Beam Bio-engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences and Anhui Province, Hefei, Anhui 230031 (China)

    2015-03-15

    Highlights: • The effects of microgravity on the radiation-induced bystander effects (RIBE) were definitely demonstrated. • The effects of microgravity on RIBE might be divergent for different biological events. • The microgravity mainly modified the generation or transport of bystander signals at early stage. - Abstract: Both space radiation and microgravity have been demonstrated to have inevitable impact on living organisms during space flights and should be considered as important factors for estimating the potential health risk for astronauts. Therefore, the question whether radiation effects could be modulated by microgravity is an important aspect in such risk evaluation. Space particles at low dose and fluence rate, directly affect only a fraction of cells in the whole organism, which implement radiation-induced bystander effects (RIBE) in cellular response to space radiation exposure. The fact that all of the RIBE experiments are carried out in a normal gravity condition bring forward the need for evidence regarding the effect of microgravity on RIBE. In the present study, a two-dimensional rotation clinostat was adopted to demonstrate RIBE in microgravity conditions, in which the RIBE was assayed using an experimental system of root-localized irradiation of Arabidopsis thaliana (A. thaliana) plants. The results showed that the modeled microgravity inhibited significantly the RIBE-mediated up-regulation of expression of the AtRAD54 and AtRAD51 genes, generation of reactive oxygen species (ROS) and transcriptional activation of multicopy P35S:GUS, but made no difference to the induction of homologous recombination by RIBE, showing divergent responses of RIBE to the microgravity conditions. The time course of interaction between the modeled microgravity and RIBE was further investigated, and the results showed that the microgravity mainly modulated the processes of the generation or translocation of the bystander signal(s) in roots.

  10. Effects of elevated carbon dioxide and sucrose concentrations on Arabidopsis thaliana root architecture and anatomy

    Energy Technology Data Exchange (ETDEWEB)

    Lee-Ho, E.; Walton, L.J.; Reid, D.M.; Yeung, E.C.; Kurepin, L.V. [Calgary Univ., AB (Canada). Dept. of Biology

    2007-03-15

    Plant root growth is known to be influenced by higher levels of atmospheric carbon dioxide (CO{sub 2}). Roots of some species grown in hydroponics under elevated CO{sub 2} concentrations may be more competitive sinks for photosynthetic assimilates than roots grown under lower CO{sub 2} conditions. Root branching patterns may also be influenced by elevated CO{sub 2} concentrations. Studies have also shown that factors such as soil compaction, salinity and the availability of nitrate, phosphorous, oxygen and water also influence root growth, and the effects of higher CO{sub 2} on roots can be confounded by such environmental factors. This study evaluated the effects of elevated carbon dioxide and sucrose concentrations on Arabidopsis thaliana root growth, morphology, and architecture. Both ambient and elevated CO{sub 2} levels were used along with various sucrose concentrations. The study revealed that A. thaliana plants grown on a phytagar medium in small chambers with elevated CO{sub 2} had longer roots, more lateral root growth than plants grown in ambient CO{sub 2}. Roots in elevated CO{sub 2} were found to have wider root diameters, and more secondary growth. The addition of sucrose to the media closely resembled the effects of elevated CO{sub 2}. In addition, the increase in sucrose concentration had a bigger effect on root morphology under ambient, than elevated CO{sub 2}. Therefore, both elevated CO{sub 2} and increased sucrose concentrations promote root growth by increasing their number, length, and diameter. The dichotomy branching index (DBI) also dropped resulting in a more dichotomous branching pattern. 34 refs., 5 figs.

  11. Environmental regulation of leaf colour in red 35S:PAP1 Arabidopsis thaliana.

    Science.gov (United States)

    Rowan, Daryl D; Cao, Mingshu; Lin-Wang, Kui; Cooney, Janine M; Jensen, Dwayne J; Austin, Paul T; Hunt, Martin B; Norling, Cara; Hellens, Roger P; Schaffer, Robert J; Allan, Andrew C

    2009-01-01

    * High-temperature, low-light (HTLL) treatment of 35S:PAP1 Arabidopsis thaliana over-expressing the PAP1 (Production of Anthocyanin Pigment 1) gene results in reversible reduction of red colouration, suggesting the action of additional anthocyanin regulators. High-performance liquid chromatography (HPLC), liquid chromatography mass spectrometry (LCMS) and Affimetrix-based microarrays were used to measure changes in anthocyanin, flavonoids, and gene expression in response to HTLL. * HTLL treatment of control and 35S:PAP1 A. thaliana resulted in a reversible reduction in the concentrations of major anthocyanins despite ongoing over-expression of the PAP1 MYB transcription factor. Twenty-one anthocyanins including eight cis-coumaryl esters were identified by LCMS. The concentrations of nine anthocyanins were reduced and those of three were increased, consistent with a sequential process of anthocyanin degradation. Analysis of gene expression showed down-regulation of flavonol and anthocyanin biosynthesis and of transport-related genes within 24 h of HTLL treatment. No catabolic genes up-regulated by HTLL were found. * Reductions in the concentrations of anthocyanins and down-regulation of the genes of anthocyanin biosynthesis were achieved by environmental manipulation, despite ongoing over-expression of PAP1. Quantitative PCR showed reduced expression of three genes (TT8, TTG1 and EGL3) of the PAP1 transcriptional complex, and increased expression of the potential transcriptional repressors AtMYB3, AtMYB6 and AtMYBL2 coincided with HTLL-induced down-regulation of anthocyanin biosynthesis. * HTLL treatment offers a model system with which to explore anthocyanin catabolism and to discover novel genes involved in the environmental control of anthocyanins.

  12. Overexpression of IRM1 enhances resistance to aphids in Arabidopsis thaliana.

    Science.gov (United States)

    Chen, Xi; Zhang, Zhao; Visser, Richard G F; Broekgaarden, Colette; Vosman, Ben

    2013-01-01

    Aphids are insects that cause direct damage to crops by the removal of phloem sap, but more importantly they spread devastating viruses. Aphids use their sophisticated mouthpart (i.e. stylet) to feed from the phloem sieve elements of the host plant. To identify genes that affect host plant resistance to aphids, we previously screened an Arabidopsis thaliana activation tag mutant collection. In such mutants, tagged genes are overexpressed by a strong 35S enhancer adjacent to the natural promoter, resulting in a dominant gain-of-function phenotype. We previously identified several of these mutants on which the aphid Myzus persicae showed a reduced population development compared with wild type. In the present study we show that the gene responsible for the phenotype of one of the mutants is At5g65040 and named this gene Increased Resistance to Myzus persicae 1 (IRM1). Overexpression of the cloned IRM1 gene conferred a phenotype identical to that of the original mutant. Conversely, an IRM1 knockout mutant promoted aphid population development compared to the wild type. We performed Electrical Penetration Graph analysis to investigate how probing and feeding behaviour of aphids was affected on plants that either overexpressed IRM1 or contained a knockout mutation in this gene. The EPG results indicated that the aphids encounter resistance factors while reaching for the phloem on the overexpressing line. This resistance mechanism also affected other aphid species and is suggested to be of mechanical nature. Interestingly, genetic variation for IRM1 expression in response to aphid attack was observed. Upon aphid attack the expression of IRM1 was initially (after 6 hours) induced in ecotype Wassilewskija followed by suppression. In Columbia-0, IRM1 expression was already suppressed six hours after the start of the infestation. The resistance conferred by the overexpression of IRM1 in A. thaliana trades off with plant growth.

  13. Overexpression of IRM1 enhances resistance to aphids in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Xi Chen

    Full Text Available Aphids are insects that cause direct damage to crops by the removal of phloem sap, but more importantly they spread devastating viruses. Aphids use their sophisticated mouthpart (i.e. stylet to feed from the phloem sieve elements of the host plant. To identify genes that affect host plant resistance to aphids, we previously screened an Arabidopsis thaliana activation tag mutant collection. In such mutants, tagged genes are overexpressed by a strong 35S enhancer adjacent to the natural promoter, resulting in a dominant gain-of-function phenotype. We previously identified several of these mutants on which the aphid Myzus persicae showed a reduced population development compared with wild type. In the present study we show that the gene responsible for the phenotype of one of the mutants is At5g65040 and named this gene Increased Resistance to Myzus persicae 1 (IRM1. Overexpression of the cloned IRM1 gene conferred a phenotype identical to that of the original mutant. Conversely, an IRM1 knockout mutant promoted aphid population development compared to the wild type. We performed Electrical Penetration Graph analysis to investigate how probing and feeding behaviour of aphids was affected on plants that either overexpressed IRM1 or contained a knockout mutation in this gene. The EPG results indicated that the aphids encounter resistance factors while reaching for the phloem on the overexpressing line. This resistance mechanism also affected other aphid species and is suggested to be of mechanical nature. Interestingly, genetic variation for IRM1 expression in response to aphid attack was observed. Upon aphid attack the expression of IRM1 was initially (after 6 hours induced in ecotype Wassilewskija followed by suppression. In Columbia-0, IRM1 expression was already suppressed six hours after the start of the infestation. The resistance conferred by the overexpression of IRM1 in A. thaliana trades off with plant growth.

  14. Effect of modeled microgravity on radiation-induced adaptive response of root growth in Arabidopsis thaliana

    International Nuclear Information System (INIS)

    Deng, Chenguang; Wang, Ting; Wu, Jingjing; Xu, Wei; Li, Huasheng; Liu, Min

    2017-01-01

    Highlights: • The radio-adaptive response (RAR) of A. thaliana root growth is modulated in microgravity. • The DNA damage repairs in RAR are regulated by microgravity. • The phytohormone auxin plays a regulatory role in the modulation of microgravity on RAR of root growth. - Abstract: Space particles have an inevitable impact on organisms during space missions; radio-adaptive response (RAR) is a critical radiation effect due to both low-dose background and sudden high-dose radiation exposure during solar storms. Although it is relevant to consider RAR within the context of microgravity, another major space environmental factor, there is no existing evidence as to its effects on RAR. In the present study, we established an experimental method for detecting the effects of gamma-irradiation on the primary root growth of Arabidopsis thaliana, in which RAR of root growth was significantly induced by several dose combinations. Microgravity was simulated using a two-dimensional rotation clinostat. It was shown that RAR of root growth was significantly inhibited under the modeled microgravity condition, and was absent in pgm-1 plants that had impaired gravity sensing in root tips. These results suggest that RAR could be modulated in microgravity. Time course analysis showed that microgravity affected either the development of radio-resistance induced by priming irradiation, or the responses of plants to challenging irradiation. After treatment with the modeled microgravity, attenuation in priming irradiation-induced expressions of DNA repair genes (AtKu70 and AtRAD54), and reduced DNA repair efficiency in response to challenging irradiation were observed. In plant roots, the polar transportation of the phytohormone auxin is regulated by gravity, and treatment with an exogenous auxin (indole-3-acetic acid) prevented the induction of RAR of root growth, suggesting that auxin might play a regulatory role in the interaction between microgravity and RAR of root growth.

  15. Expression of the dspA/E gene of Erwinia amylovora in non-host plant Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Hasan Murat Aksoy

    2017-01-01

    Full Text Available In the Erwinia amylovora genome, the hrp gene cluster containing the dspA/E/EB/F operon plays a crucial role in mediating the pathogenicity and the hypersensitive response (HR in the host plant. The role of the dspA/E gene derived from E. amylovora was investigated by monitoring the expression of the β-glucuronidase (GUS reporter system in transgenic Arabidopsis thaliana cv. Pri-Gus seedlings. A mutant ΔdspA/E strain of E. amylovora was generated to contain a deletion of the dspA/E gene for the purpose of this study. Two-week-old seedlings of GUS transgenic Arabidopsis were vacuum-infiltrated with the wild-type and the mutant (ΔdspA/E E. amylovora strains. The Arabidopsis seedlings were fixed and stained for GUS activity after 3–5 days following infiltration. The appearance of dense spots with blue staining on the Arabidopsis leaves indicated the typical characteristic of GUS activity. This observation indicated that the wild-type E. amylovora strain had induced a successful and efficient infection on the A. thaliana Pri-Gus leaves. In contrast, there was no visible GUS expression on leaf tissues which were inoculated with the ΔdspA/E mutant E. amylovora strain. These results indicate that the dspA/E gene is required by the bacterial cells to induce HR in non-host plants.

  16. YUCCA6 over-expression demonstrates auxin function in delaying leaf senescence in Arabidopsis thaliana

    Science.gov (United States)

    Kim, Jeong Im; Murphy, Angus S.; Baek, Dongwon; Lee, Shin-Woo; Yun, Dae-Jin; Bressan, Ray A.; Narasimhan, Meena L.

    2011-01-01

    The Arabidopsis thaliana YUCCA family of flavin monooxygenase proteins catalyses a rate-limiting step in de novo auxin biosynthesis. A YUCCA6 activation mutant, yuc6-1D, has been shown to contain an elevated free IAA level and to display typical high-auxin phenotypes. It is reported here that Arabidopsis plants over-expressing YUCCA6, such as the yuc6-1D activation mutant and 35S:YUC6 transgenic plants, displayed dramatic longevity. In addition, plants over-expressing YUCCA6 exhibited classical, delayed dark-induced and hormone-induced senescence in assays using detached rosette leaves. However, plants over-expressing an allele of YUCCA6, that carries mutations in the NADPH cofactor binding site, exhibited neither delayed leaf senescence phenotypes nor phenotypes typical of auxin overproduction. When the level of free IAA was reduced in yuc6-1D by conjugation to lysine, yuc6-1D leaves senesced at a rate similar to the wild-type leaves. Dark-induced senescence in detached leaves was accompanied by a decrease in their free IAA content, by the reduced expression of auxin biosynthesis enzymes such as YUCCA1 and YUCCA6 that increase cellular free IAA levels, and by the increased expression of auxin-conjugating enzymes encoded by the GH3 genes that reduce the cellular free auxin levels. Reduced transcript abundances of SAG12, NAC1, and NAC6 during senescence in yuc6-1D compared with the wild type suggested that auxin delays senescence by directly or indirectly regulating the expression of senescence-associated genes. PMID:21511905

  17. N-terminal Proteomics Assisted Profiling of the Unexplored Translation Initiation Landscape in Arabidopsis thaliana.

    Science.gov (United States)

    Willems, Patrick; Ndah, Elvis; Jonckheere, Veronique; Stael, Simon; Sticker, Adriaan; Martens, Lennart; Van Breusegem, Frank; Gevaert, Kris; Van Damme, Petra

    2017-06-01

    Proteogenomics is an emerging research field yet lacking a uniform method of analysis. Proteogenomic studies in which N-terminal proteomics and ribosome profiling are combined, suggest that a high number of protein start sites are currently missing in genome annotations. We constructed a proteogenomic pipeline specific for the analysis of N-terminal proteomics data, with the aim of discovering novel translational start sites outside annotated protein coding regions. In summary, unidentified MS/MS spectra were matched to a specific N-terminal peptide library encompassing protein N termini encoded in the Arabidopsis thaliana genome. After a stringent false discovery rate filtering, 117 protein N termini compliant with N-terminal methionine excision specificity and indicative of translation initiation were found. These include N-terminal protein extensions and translation from transposable elements and pseudogenes. Gene prediction provided supporting protein-coding models for approximately half of the protein N termini. Besides the prediction of functional domains (partially) contained within the newly predicted ORFs, further supporting evidence of translation was found in the recently released Araport11 genome re-annotation of Arabidopsis and computational translations of sequences stored in public repositories. Most interestingly, complementary evidence by ribosome profiling was found for 23 protein N termini. Finally, by analyzing protein N-terminal peptides, an in silico analysis demonstrates the applicability of our N-terminal proteogenomics strategy in revealing protein-coding potential in species with well- and poorly-annotated genomes. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  18. UGT74D1 is a novel auxin glycosyltransferase from Arabidopsis thaliana.

    Science.gov (United States)

    Jin, Shang-Hui; Ma, Xin-Mei; Han, Ping; Wang, Bo; Sun, Yan-Guo; Zhang, Gui-Zhi; Li, Yan-Jie; Hou, Bing-Kai

    2013-01-01

    Auxin is one type of phytohormones that plays important roles in nearly all aspects of plant growth and developmental processes. The glycosylation of auxins is considered to be an essential mechanism to control the level of active auxins. Thus, the identification of auxin glycosyltransferases is of great significance for further understanding the auxin regulation. In this study, we biochemically screened the group L of Arabidopsis thaliana glycosyltransferase superfamily for enzymatic activity toward auxins. UGT74D1 was identified to be a novel auxin glycosyltransferase. Through HPLC and LC-MS analysis of reaction products in vitro by testing eight substrates including auxins and other compounds, we found that UGT74D1 had a strong glucosylating activity toward indole-3-butyric acid [IBA], indole-3-propionic acid [IPA], indole-3-acetic acid [IAA] and naphthaleneacetic acid [NAA], catalyzing them to form corresponding glucose esters. Biochemical characterization showed that this enzyme had a maximum activity in HEPES buffer at pH 6.0 and 37°C. In addition, the enzymatic activity analysis of crude protein and the IBA metabolite analysis from transgenic Arabidopsis plants overexpressing UGT74D1 gene were also carried out. Experimental results indicated that over-production of the UGT74D1 in plants indeed led to increased level of the glucose conjugate of IBA. Moreover, UGT74D1 overexpression lines displayed curling leaf phenotype, suggesting a physiological role of UGT74D1 in affecting the activity of auxins. Our current data provide a new target gene for further genetic studies to understand the auxin regulation by glycosylation in plants.

  19. Autophagy Deficiency Compromises Alternative Pathways of Respiration following Energy Deprivation inArabidopsis thaliana.

    Science.gov (United States)

    Barros, Jessica A S; Cavalcanti, João Henrique F; Medeiros, David B; Nunes-Nesi, Adriano; Avin-Wittenberg, Tamar; Fernie, Alisdair R; Araújo, Wagner L

    2017-09-01

    Under heterotrophic conditions, carbohydrate oxidation inside the mitochondrion is the primary energy source for cellular metabolism. However, during energy-limited conditions, alternative substrates are required to support respiration. Amino acid oxidation in plant cells plays a key role in this by generating electrons that can be transferred to the mitochondrial electron transport chain via the electron transfer flavoprotein/ubiquinone oxidoreductase system. Autophagy, a catabolic mechanism for macromolecule and protein recycling, allows the maintenance of amino acid pools and nutrient remobilization. Although the association between autophagy and alternative respiratory substrates has been suggested, the extent to which autophagy and primary metabolism interact to support plant respiration remains unclear. To investigate the metabolic importance of autophagy during development and under extended darkness, Arabidopsis ( Arabidopsis thaliana ) mutants with disruption of autophagy ( atg mutants) were used. Under normal growth conditions, atg mutants showed lower growth and seed production with no impact on photosynthesis. Following extended darkness, atg mutants were characterized by signatures of early senescence, including decreased chlorophyll content and maximum photochemical efficiency of photosystem II coupled with increases in dark respiration. Transcript levels of genes involved in alternative pathways of respiration and amino acid catabolism were up-regulated in atg mutants. The metabolite profiles of dark-treated leaves revealed an extensive metabolic reprogramming in which increases in amino acid levels were partially compromised in atg mutants. Although an enhanced respiration in atg mutants was observed during extended darkness, autophagy deficiency compromises protein degradation and the generation of amino acids used as alternative substrates to the respiration. © 2017 American Society of Plant Biologists. All Rights Reserved.

  20. A novel blue-light phototropic response is revealed in roots of Arabidopsis thaliana in microgravity.

    Science.gov (United States)

    Vandenbrink, Joshua P; Herranz, Raul; Medina, F Javier; Edelmann, Richard E; Kiss, John Z

    2016-12-01

    Blue-light positive phototropism in roots is masked by gravity and revealed in conditions of microgravity. In addition, the magnitude of red-light positive phototropic curvature is correlated to the magnitude of gravity. Due to their sessile nature, plants utilize environmental cues to grow and respond to their surroundings. Two of these cues, light and gravity, play a substantial role in plant orientation and directed growth movements (tropisms). However, very little is currently known about the interaction between light- (phototropic) and gravity (gravitropic)-mediated growth responses. Utilizing the European Modular Cultivation System on board the International Space Station, we investigated the interaction between phototropic and gravitropic responses in three Arabidopsis thaliana genotypes, Landsberg wild type, as well as mutants of phytochrome A and phytochrome B. Onboard centrifuges were used to create a fractional gravity gradient ranging from reduced gravity up to 1g. A novel positive blue-light phototropic response of roots was observed during conditions of microgravity, and this response was attenuated at 0.1g. In addition, a red-light pretreatment of plants enhanced the magnitude of positive phototropic curvature of roots in response to blue illumination. In addition, a positive phototropic response of roots was observed when exposed to red light, and a decrease in response was gradual and correlated with the increase in gravity. The positive red-light phototropic curvature of hypocotyls when exposed to red light was also confirmed. Both red-light and blue-light phototropic responses were also shown to be affected by directional light intensity. To our knowledge, this is the first characterization of a positive blue-light phototropic response in Arabidopsis roots, as well as the first description of the relationship between these phototropic responses in fractional or reduced gravities.

  1. YUCCA6 over-expression demonstrates auxin function in delaying leaf senescence in Arabidopsis thaliana

    KAUST Repository

    Kim, Jeong Im

    2011-04-21

    The Arabidopsis thaliana YUCCA family of flavin monooxygenase proteins catalyses a rate-limiting step in de novo auxin biosynthesis. A YUCCA6 activation mutant, yuc6-1D, has been shown to contain an elevated free IAA level and to display typical high-auxin phenotypes. It is reported here that Arabidopsis plants over-expressing YUCCA6, such as the yuc6-1D activation mutant and 35S:YUC6 transgenic plants, displayed dramatic longevity. In addition, plants over-expressing YUCCA6 exhibited classical, delayed dark-induced and hormone-induced senescence in assays using detached rosette leaves. However, plants over-expressing an allele of YUCCA6, that carries mutations in the NADPH cofactor binding site, exhibited neither delayed leaf senescence phenotypes nor phenotypes typical of auxin overproduction. When the level of free IAA was reduced in yuc6-1D by conjugation to lysine, yuc6-1D leaves senesced at a rate similar to the wild-type leaves. Dark-induced senescence in detached leaves was accompanied by a decrease in their free IAA content, by the reduced expression of auxin biosynthesis enzymes such as YUCCA1 and YUCCA6 that increase cellular free IAA levels, and by the increased expression of auxin-conjugating enzymes encoded by the GH3 genes that reduce the cellular free auxin levels. Reduced transcript abundances of SAG12, NAC1, and NAC6 during senescence in yuc6-1D compared with the wild type suggested that auxin delays senescence by directly or indirectly regulating the expression of senescence-associated genes. 2011 The Author(s).

  2. Contribution of the GABA shunt to hypoxia-induced alanine accumulation in roots of Arabidopsis thaliana.

    Science.gov (United States)

    Miyashita, Yo; Good, Allen G

    2008-01-01

    When subjected to low oxygen stress, plants accumulate alanine and gamma-aminobutyric acid (GABA). To investigate the function of GABA metabolism under hypoxia and its contribution to alanine accumulation, we studied the genes that encode the two key enzymes of the GABA shunt, glutamate decarboxylase (GAD) and GABA transaminase (GABA-T). Among the five homologous GAD genes found in Arabidopsis thaliana, GAD1 expression was predominantly found in roots, while GAD2 expression was evident in all organs. Expression of the other three GAD genes was generally weak. In response to hypoxia, transcriptional induction was observed for GAD4 only. For GABA-T1, its expression was detected in all organs, but there was no significant transcriptional change under hypoxic conditions. Moreover, we have isolated and characterized Arabidopsis mutants defective in GAD1 and GABA-T1. In gad1 mutants, GAD activity was significantly reduced in roots but was not affected in shoots. In the gaba-t1 mutant, GABA-T activity was decreased to negligible levels in both shoots and roots. These mutants were phenotypically normal under normal growth conditions except for the reduced seed production of the pop2 mutants as described previously. However, metabolite analysis revealed significant changes in GABA content in gad1 and gaba-t1 mutants. The levels of alanine under hypoxic conditions were also affected in the roots of gad1 and gaba-t1 mutants. The partial inhibition of the hypoxia-induced alanine accumulation in roots of these mutants suggests that the GABA shunt is, in part, responsible for the alanine accumulation under hypoxia.

  3. Superoxide-responsive gene expression in Arabidopsis thaliana and Zea mays.

    Science.gov (United States)

    Xu, Junhuan; Tran, Thu; Padilla Marcia, Carmen S; Braun, David M; Goggin, Fiona L

    2017-08-01

    Superoxide (O 2 - ) and other reactive oxygen species (ROS) are generated in response to numerous biotic and abiotic stresses. Different ROS have been reported to elicit different transcriptional responses in plants, and so ROS-responsive marker genes and promoter::reporter gene fusions have been proposed as indirect means of detecting ROS and discriminating among different species. However, further information about the specificity of transcriptional responses to O 2 - is needed in order to assess potential markers for this critical stress-responsive signaling molecule. Using qRT-PCR, the expression of 12 genes previously reported to be upregulated by O 2 - was measured in Arabidopsis thaliana plants exposed to elicitors of common stress-responsive ROS: methyl viologen (an inducer of O 2 - ), rose bengal (an inducer of singlet oxygen, 1 ΔO 2 ), and exogenous hydrogen peroxide (H 2 O 2 ). Surprisingly, Zinc-Finger Protein 12 (AtZAT12), which had previously been used as a reporter for H 2 O 2 , responded more strongly to O 2 - than to H 2 O 2 ; moreover, the expression of an AtZAT12 promoter-reporter fusion (AtZAT12::Luc) was enhanced by diethyldithiocarbamate, which inhibits dismutation of O 2 - to H 2 O 2 . These results suggest that AtZAT12 is transcriptionally upregulated in response to O 2 - , and that AtZAT12::Luc may be a useful biosensor for detecting O 2 - generation in vivo. In addition, transcripts encoding uncoupling proteins (AtUCPs) showed selectivity for O 2 - in Arabidopsis, and an AtUCP homolog upregulated by methyl viologen was also identified in maize (Zea mays L.), indicating that there are O 2 - -responsive members of this family in monocots. These results expand our limited knowledge of ROS-responsive gene expression in monocots, as well as O 2 - -selective responses in dicots. Copyright © 2017 The Authors. Published by Elsevier Masson SAS.. All rights reserved.

  4. One-step analysis of seed storage data and the longevity of Arabidopsis thaliana seeds.

    Science.gov (United States)

    Hay, Fiona R; Mead, Andrew; Manger, Kirstine; Wilson, Fiona J

    2003-03-01

    Seeds of two ecotypes of Arabidopsis thaliana, NW20 and N1601, were aged over a range of saturated salt solutions at temperatures between 6 degrees C and 55 degrees C. For each ecotype, the results from 37 storage experiments were summarized using the Ellis and Roberts viability equations and a modified version of these equations which allows for a proportion of 'non-respondents'. For both models, two approaches were taken in order to model the effect of moisture content (MC) and temperature on seed longevity. The first, a two-step approach, involved fitting individual survival curves and then multiple regression analysis of the fitted parameters on moisture content and temperature. For the second approach, the full viability models were fitted in one step, including the multiple regression for the effects of MC and temperature within the generalized linear model used to describe each survival curve. This one-step approach takes into account the full variability of the data and provides the best predictions of seed longevity based on the original assumptions of the Ellis and Roberts viability equations. As a consequence of taking into account all the variation, this one-step approach is more sensitive and thus more likely to detect changes due to reducing the number of parameters in the model as being significant. Whilst both approaches indicated that seeds from the two Arabidopsis ecotypes have the same response to MC and temperature, parameter values did differ between the approaches, with the one-step approach providing the better fit. The best model for these two ecotypes, from the one-step approach, confirmed a quadratic relationship between temperature and longevity, but the magnitude of the non-linearity is not as large as indicated by the universal value for the quadratic term.

  5. UGT74D1 is a novel auxin glycosyltransferase from Arabidopsis thaliana.

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    Shang-Hui Jin

    Full Text Available Auxin is one type of phytohormones that plays important roles in nearly all aspects of plant growth and developmental processes. The glycosylation of auxins is considered to be an essential mechanism to control the level of active auxins. Thus, the identification of auxin glycosyltransferases is of great significance for further understanding the auxin regulation. In this study, we biochemically screened the group L of Arabidopsis thaliana glycosyltransferase superfamily for enzymatic activity toward auxins. UGT74D1 was identified to be a novel auxin glycosyltransferase. Through HPLC and LC-MS analysis of reaction products in vitro by testing eight substrates including auxins and other compounds, we found that UGT74D1 had a strong glucosylating activity toward indole-3-butyric acid [IBA], indole-3-propionic acid [IPA], indole-3-acetic acid [IAA] and naphthaleneacetic acid [NAA], catalyzing them to form corresponding glucose esters. Biochemical characterization showed that this enzyme had a maximum activity in HEPES buffer at pH 6.0 and 37°C. In addition, the enzymatic activity analysis of crude protein and the IBA metabolite analysis from transgenic Arabidopsis plants overexpressing UGT74D1 gene were also carried out. Experimental results indicated that over-production of the UGT74D1 in plants indeed led to increased level of the glucose conjugate of IBA. Moreover, UGT74D1 overexpression lines displayed curling leaf phenotype, suggesting a physiological role of UGT74D1 in affecting the activity of auxins. Our current data provide a new target gene for further genetic studies to understand the auxin regulation by glycosylation in plants.

  6. Effects of aneuploidy on genome structure, expression, and interphase organization in Arabidopsis thaliana.

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    Bruno Huettel

    2008-10-01

    Full Text Available Aneuploidy refers to losses and/or gains of individual chromosomes from the normal chromosome set. The resulting gene dosage imbalance has a noticeable affect on the phenotype, as illustrated by aneuploid syndromes, including Down syndrome in humans, and by human solid tumor cells, which are highly aneuploid. Although the phenotypic manifestations of aneuploidy are usually apparent, information about the underlying alterations in structure, expression, and interphase organization of unbalanced chromosome sets is still sparse. Plants generally tolerate aneuploidy better than animals, and, through colchicine treatment and breeding strategies, it is possible to obtain inbred sibling plants with different numbers of chromosomes. This possibility, combined with the genetic and genomics tools available for Arabidopsis thaliana, provides a powerful means to assess systematically the molecular and cytological consequences of aberrant numbers of specific chromosomes. Here, we report on the generation of Arabidopsis plants in which chromosome 5 is present in triplicate. We compare the global transcript profiles of normal diploids and chromosome 5 trisomics, and assess genome integrity using array comparative genome hybridization. We use live cell imaging to determine the interphase 3D arrangement of transgene-encoded fluorescent tags on chromosome 5 in trisomic and triploid plants. The results indicate that trisomy 5 disrupts gene expression throughout the genome and supports the production and/or retention of truncated copies of chromosome 5. Although trisomy 5 does not grossly distort the interphase arrangement of fluorescent-tagged sites on chromosome 5, it may somewhat enhance associations between transgene alleles. Our analysis reveals the complex genomic changes that can occur in aneuploids and underscores the importance of using multiple experimental approaches to investigate how chromosome numerical changes condition abnormal phenotypes and

  7. Complexes with mixed primary and secondary cellulose synthases are functional in Arabidopsis thaliana plants

    Energy Technology Data Exchange (ETDEWEB)

    Carroll, Andrew; Mansoori, N; Li, Shundai; Lei, Lei; Vernhettes, Samantha; Visser, Richard G. F.; Somerville, Chris R; Gu, Ying; Trindade, Luisa M.

    2012-10-01

    In higher plants, cellulose is synthesized by so-called rosette protein complexes with cellulose synthases (CESAs) as catalytic subunits of the complex. The CESAs are divided into two distinct families, three of which are thought to be specialized for the primary cell wall and three for the secondary cell wall. In this article, the potential of primary and secondary CESAs forming a functional rosette complex has been investigated. The membrane-based yeast two-hybrid and biomolecular fluorescence systems were used to assess the interactions between three primary (CESA1, CESA3, CESA6), and three secondary (CESA4, CESA7, CESA8) Arabidopsis (Arabidopsis thaliana) CESAs. The results showed that all primary CESAs can physically interact both in vitro and in planta with all secondary CESAs. Although CESAs are broadly capable of interacting in pairwise combinations, they are not all able to form functional complexes in planta. Analysis of transgenic lines showed that CESA7 can partially rescue defects in the primary cell wall biosynthesis in a weak cesa3 mutant. Green fluorescent protein-CESA protein fusions revealed that when CESA3 was replaced by CESA7 in the primary rosette, the velocity of the mixed complexes was slightly faster than the native primary complexes. CESA1 in turn can partly rescue defects in secondary cell wall biosynthesis in a cesa8ko mutant, resulting in an increase of cellulose content relative to cesa8ko. These results demonstrate that sufficient parallels exist between the primary and secondary complexes for cross-functionality and open the possibility that mixed complexes of primary and secondary CESAs may occur at particular times.

  8. Apparent homology of expressed genes from wood-forming tissues of loblolly pine (Pinus taeda L.) with Arabidopsis thaliana.

    Science.gov (United States)

    Kirst, Matias; Johnson, Arthur F; Baucom, Christie; Ulrich, Erin; Hubbard, Kristy; Staggs, Rod; Paule, Charles; Retzel, Ernest; Whetten, Ross; Sederoff, Ronald

    2003-06-10

    Pinus taeda L. (loblolly pine) and Arabidopsis thaliana differ greatly in form, ecological niche, evolutionary history, and genome size. Arabidopsis is a small, herbaceous, annual dicotyledon, whereas pines are large, long-lived, coniferous forest trees. Such diverse plants might be expected to differ in a large number of functional genes. We have obtained and analyzed 59,797 expressed sequence tags (ESTs) from wood-forming tissues of loblolly pine and compared them to the gene sequences inferred from the complete sequence of the Arabidopsis genome. Approximately 50% of pine ESTs have no apparent homologs in Arabidopsis or any other angiosperm in public databases. When evaluated by using contigs containing long, high-quality sequences, we find a higher level of apparent homology between the inferred genes of these two species. For those contigs 1,100 bp or longer, approximately 90% have an apparent Arabidopsis homolog (E value < 10-10). Pines and Arabidopsis last shared a common ancestor approximately 300 million years ago. Few genes would be expected to retain high sequence similarity for this time if they did not have essential functions. These observations suggest substantial conservation of gene sequence in seed plants.

  9. The mitochondrial phosphate transporters modulate plant responses to salt stress via affecting ATP and gibberellin metabolism in Arabidopsis thaliana.

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    Wei Zhu

    Full Text Available The mitochondrial phosphate transporter (MPT plays crucial roles in ATP production in plant cells. Three MPT genes have been identified in Arabidopsis thaliana. Here we report that the mRNA accumulations of AtMPTs were up-regulated by high salinity stress in A. thaliana seedlings. And the transgenic lines overexpressing AtMPTs displayed increased sensitivity to salt stress compared with the wild-type plants during seed germination and seedling establishment stages. ATP content and energy charge was higher in overexpressing plants than those in wild-type A. thaliana under salt stress. Accordingly, the salt-sensitive phenotype of overexpressing plants was recovered after the exogenous application of atractyloside due to the change of ATP content. Interestingly, Genevestigator survey and qRT-PCR analysis indicated a large number of genes, including those related to gibberellin synthesis could be regulated by the energy availability change under stress conditions in A. thaliana. Moreover, the exogenous application of uniconazole to overexpressing lines showed that gibberellin homeostasis was disturbed in the overexpressors. Our studies reveal a possible link between the ATP content mediated by AtMPTs and gibberellin metabolism in responses to high salinity stress in A. thaliana.

  10. The ABC transporter BcatrB from Botrytis cinerea exports camalexin and is a virulence factor on Arabidopsis thaliana.

    Science.gov (United States)

    Stefanato, Francesca L; Abou-Mansour, Eliane; Buchala, Antony; Kretschmer, Matthias; Mosbach, Andreas; Hahn, Matthias; Bochet, Christian G; Métraux, Jean-Pierre; Schoonbeek, Henk-jan

    2009-05-01

    Arabidopsis thaliana is known to produce the phytoalexin camalexin in response to abiotic and biotic stress. Here we studied the mechanisms of tolerance to camalexin in the fungus Botrytis cinerea, a necrotrophic pathogen of A. thaliana. Exposure of B. cinerea to camalexin induces expression of BcatrB, an ABC transporter that functions in the efflux of fungitoxic compounds. B. cinerea inoculated on wild-type A. thaliana plants yields smaller lesions than on camalexin-deficient A. thaliana mutants. A B. cinerea strain lacking functional BcatrB is more sensitive to camalexin in vitro and less virulent on wild-type plants, but is still fully virulent on camalexin-deficient mutants. Pre-treatment of A. thaliana with UV-C leads to increased camalexin accumulation and substantial resistance to B. cinerea. UV-C-induced resistance was not seen in the camalexin-deficient mutants cyp79B2/B3, cyp71A13, pad3 or pad2, and was strongly reduced in ups1. Here we demonstrate that an ABC transporter is a virulence factor that increases tolerance of the pathogen towards a phytoalexin, and the complete restoration of virulence on host plants lacking this phytoalexin.

  11. Geminiviruses Subvert Ubiquitination by Altering CSN-Mediated Derubylation of SCF E3 Ligase Complexes and Inhibit Jasmonate Signaling in Arabidopsis thaliana[C][W

    Science.gov (United States)

    Lozano-Durán, Rosa; Rosas-Díaz, Tabata; Gusmaroli, Giuliana; Luna, Ana P.; Taconnat, Ludivine; Deng, Xing Wang; Bejarano, Eduardo R.

    2011-01-01

    Viruses must create a suitable cell environment and elude defense mechanisms, which likely involves interactions with host proteins and subsequent interference with or usurpation of cellular machinery. Here, we describe a novel strategy used by plant DNA viruses (Geminiviruses) to redirect ubiquitination by interfering with the activity of the CSN (COP9 signalosome) complex. We show that geminiviral C2 protein interacts with CSN5, and its expression in transgenic plants compromises CSN activity on CUL1. Several responses regulated by the CUL1-based SCF ubiquitin E3 ligases (including responses to jasmonates, auxins, gibberellins, ethylene, and abscisic acid) are altered in these plants. Impairment of SCF function is confirmed by stabilization of yellow fluorescent protein–GAI, a substrate of the SCFSLY1. Transcriptomic analysis of these transgenic plants highlights the response to jasmonates as the main SCF-dependent process affected by C2. Exogenous jasmonate treatment of Arabidopsis thaliana plants disrupts geminivirus infection, suggesting that the suppression of the jasmonate response might be crucial for infection. Our findings suggest that C2 affects the activity of SCFs, most likely through interference with the CSN. As SCFs are key regulators of many cellular processes, the capability of viruses to selectively interfere with or hijack the activity of these complexes might define a novel and powerful strategy in viral infections. PMID:21441437

  12. Investigating uptake of water-dispersible CdSe/ZnS quantum dot nanoparticles by Arabidopsis thaliana plants

    International Nuclear Information System (INIS)

    Navarro, Divina A.; Bisson, Mary A.; Aga, Diana S.

    2012-01-01

    Graphical abstract: This study highlights the importance of quantum dot (QD) structural stability in preventing phytotoxicity. Overall, there is no evidence that Arabidopsis thaliana plants can internalize intact QDs within 1–7 days of exposure, with or without humic acids. Highlights: ► Potential uptake of water-dispersible CdSe/ZnS QDs by Arabidopsis was demonstrated. ► QDs were not internalized by Arabidopsis as intact particles. ► Plants exposed to Cd-, Se-, and QD + HA suspensions experienced oxidative stress. ► An effective LC–MS method proves detection of low levels of glutathione in plants. ► Uptake of Cd and/or Se leached from QDs is of major concern. - Abstract: Interest on the environmental impacts of engineered nanomaterials has rapidly increased over the past years because it is expected that these materials will eventually be released into the environment. The present work investigates the potential root uptake of water-dispersible CdSe/ZnS quantum dots (QDs) by the model plant species, Arabidopsis thaliana. Experiments revealed that Arabidopsis exposed to QDs that are dispersed in Hoagland's solution for 1–7 days did not internalize intact QDs. Analysis of Cd and Se concentrations in roots and leaves by inductively-coupled plasma mass spectrometry indicated that Cd and Se from QD-treated plants were not translocated into the leaves, and remained in the root system of Arabidopsis. Furthermore, fluorescence microscopy showed strong evidence that the QDs were generally on the outside surfaces of the roots, where the amount of QDs adsorbed is dependent on the stability of the QDs in suspension. Despite no evidence of nanoparticle internalization, the ratio of reduced glutathione levels (GSH) relative to the oxidized glutathione (GSSG) in plants decreased when plants were exposed to QD dispersions containing humic acids, suggesting that QDs caused oxidative stress on the plant at this condition.

  13. Effects of Intentionally Treated Water on Growth of Arabidopsis thaliana Seeds with Cryptochrome Mutations.

    Science.gov (United States)

    Shiah, Yung-Jong; Hsieh, Hsu-Liang; Chen, Huai-Ju; Radin, Dean I

    A previous experiment suggested that consumption of intentionally treated tea influenced subjective mood under double-blind, controlled conditions. To investigate that effect objectively, again under double-blind, controlled conditions, we studied whether Arabidopsis thaliana seeds hydrated with intentionally treated vs. untreated water would show differences in hypocotyl length, anthocyanin, and chlorophyll. Three Buddhist monks focused their intention on commercially bottled water with the goal of improving the growth of seeds; bottled water from the same source served as an untreated control. Seeds with the following three variations of cryptochrome (CRY) were used: the wild type Arabidopsis (Columbia-4), a gain-of-function mutation (His-CRY2), and a loss-of function mutation (cry1/2), where "gain" and "loss" refer to enhanced and reduced sensitivity to blue light, respectively. Seeds were hydrated with treated or untreated water under blinded conditions, and then placed in random positions in an incubator. The germination process was repeated three times in each experiment, each time using new seeds, and then the entire experiment was repeated four times. Data combined across the four experiments showed a significant decrease in hypocotyl length in the His-CRY2 seedlings (treated mean 1.31 ± 0.01mm, untreated mean 1.43 ± 0.01mm, P < 10 -13 ), a significant increase in anthocyanin with all three forms of cry, particularly His-CRY2 (treated mean 17.0 ± 0.31mg, untreated mean 14.5 ± 0.31mg, P < 10 -4 ), and a modest increase in chlorophyll in His-CRY2 (treated mean 247.6 ± 5.63mg, untreated mean 230.6 ± 5.63mg, P = .05). These outcomes conformed to the monks' intentions because a decrease in hypocotyl length and increase in anthocyanin and chlorophyll are associated with enhanced photomorphogenic growth. These experiments suggest that the His-CRY2 mutation of Arabidopsis may be an especially robust "detector" of intention. Copyright © 2017 Elsevier Inc. All

  14. Comparative transcriptomic characterization of aluminum, sodium chloride, cadmium and copper rhizotoxicities in Arabidopsis thaliana

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    Sakurai Nozomu

    2009-03-01

    Full Text Available Abstract Background Rhizotoxic ions in problem soils inhibit nutrient and water acquisition by roots, which in turn leads to reduced crop yields. Previous studies on the effects of rhizotoxic ions on root growth and physiological functions suggested that some mechanisms were common to all rhizotoxins, while others were more specific. To understand this complex system, we performed comparative transcriptomic analysis with various rhizotoxic ions, followed by bioinformatics analysis, in the model plant Arabidopsis thaliana. Results Roots of Arabidopsis were treated with the major rhizotoxic stressors, aluminum (Al ions, cadmium (Cd ions, copper (Cu ions and sodium (NaCl chloride, and the gene expression responses were analyzed by DNA array technology. The top 2.5% of genes whose expression was most increased by each stressor were compared with identify common and specific gene expression responses induced by these stressors. A number of genes encoding glutathione-S-transferases, peroxidases, Ca-binding proteins and a trehalose-synthesizing enzyme were induced by all stressors. In contrast, gene ontological categorization identified sets of genes uniquely induced by each stressor, with distinct patterns of biological processes and molecular function. These contained known resistance genes for each stressor, such as AtALMT1 (encoding Al-activated malate transporter in the Al-specific group and DREB (encoding dehydration responsive element binding protein in the NaCl-specific group. These gene groups are likely to reflect the common and differential cellular responses and the induction of defense systems in response to each ion. We also identified co-expressed gene groups specific to rhizotoxic ions, which might aid further detailed investigation of the response mechanisms. Conclusion In order to understand the complex responses of roots to rhizotoxic ions, we performed comparative transcriptomic analysis followed by bioinformatics characterization

  15. Mild salinity stimulates a stress-induced morphogenic response in Arabidopsis thaliana roots.

    Science.gov (United States)

    Zolla, Gaston; Heimer, Yair M; Barak, Simon

    2010-01-01

    Plant roots exhibit remarkable developmental plasticity in response to local soil conditions. It is shown here that mild salt stress stimulates a stress-induced morphogenic response (SIMR) in Arabidopsis thaliana roots characteristic of several other abiotic stresses: the proliferation of lateral roots (LRs) with a concomitant reduction in LR and primary root length. The LR proliferation component of the salt SIMR is dramatically enhanced by the transfer of seedlings from a low to a high NO3- medium, thereby compensating for the decreased LR length and maintaining overall LR surface area. Increased LR proliferation is specific to salt stress (osmotic stress alone has no stimulatory effect) and is due to the progression of more LR primordia from the pre-emergence to the emergence stage, in salt-stressed plants. In salt-stressed seedlings, greater numbers of LR primordia exhibit expression of a reporter gene driven by the auxin-sensitive DR5 promoter than in unstressed seedlings. Moreover, in the auxin transporter mutant aux1-7, the LR proliferation component of the salt SIMR is completely abrogated. The results suggest that salt stress promotes auxin accumulation in developing primordia thereby preventing their developmental arrest at the pre-emergence stage. Examination of ABA and ethylene mutants revealed that ABA synthesis and a factor involved in the ethylene signalling network also regulate the LR proliferation component of the salt SIMR.

  16. Statistical modeling of nitrogen-dependent modulation of root system architecture in Arabidopsis thaliana.

    Science.gov (United States)

    Araya, Takao; Kubo, Takuya; von Wirén, Nicolaus; Takahashi, Hideki

    2016-03-01

    Plant root development is strongly affected by nutrient availability. Despite the importance of structure and function of roots in nutrient acquisition, statistical modeling approaches to evaluate dynamic and temporal modulations of root system architecture in response to nutrient availability have remained as widely open and exploratory areas in root biology. In this study, we developed a statistical modeling approach to investigate modulations of root system architecture in response to nitrogen availability. Mathematical models were designed for quantitative assessment of root growth and root branching phenotypes and their dynamic relationships based on hierarchical configuration of primary and lateral roots formulating the fishbone-shaped root system architecture in Arabidopsis thaliana. Time-series datasets reporting dynamic changes in root developmental traits on different nitrate or ammonium concentrations were generated for statistical analyses. Regression analyses unraveled key parameters associated with: (i) inhibition of primary root growth under nitrogen limitation or on ammonium; (ii) rapid progression of lateral root emergence in response to ammonium; and (iii) inhibition of lateral root elongation in the presence of excess nitrate or ammonium. This study provides a statistical framework for interpreting dynamic modulation of root system architecture, supported by meta-analysis of datasets displaying morphological responses of roots to diverse nitrogen supplies. © 2015 Institute of Botany, Chinese Academy of Sciences.

  17. Autophagy induction upon reactive oxygen species in Cd-stressed Arabidopsis thaliana

    Science.gov (United States)

    Zhang, WeiNa; Chen, WenLi

    2010-02-01

    Autophagy is a protein degradation process in which cells recycle cytoplasmic contents when subjected to environmental stress conditions or during certain stages of development. Upon the induction of autophagy, a double membrane autophagosome forms around cytoplasmic components and delivers them to the vacuole for degradation. In plants, autophagy has been shown previously to be induced during abiotic stresses including oxidative stress. Cd, as a toxicity heavy metal, resulted in the production of reactive oxygen species (ROS). In this paper, we demonstrated that ROS contributed to the induction of autophagy in Cd-stressed Arabidopsis thaliana. However, pre-incubation with ascorbic acid (AsA, antioxidant molecule) and catalase (CAT, a H2O2-specific scavenger) decreased the ROS production and the number of autolysosomal-like structures. Together our results indicated that the oxidative condition was essential for autophagy, as treatment with AsA and CAT abolished the formation of autophagosomes, and ROS may function as signal molecules to induce autophagy in abiotic stress.

  18. Transcriptome Analysis of Induced Systemic Drought Tolerance Elicited by Pseudomonas chlororaphis O6 in Arabidopsis thaliana

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    Song-Mi Cho

    2013-06-01

    Full Text Available Root colonization by Pseudomonas chlororaphis O6 induces systemic drought tolerance in Arabidopsis thaliana. Microarray analysis was performed using the 22,800-gene Affymetrix GeneChips to identify differentially-expressed genes from plants colonized with or without P. chlororaphis O6 under drought stressed conditions or normal growth conditions. Root colonization in plants grown under regular irrigation condition increased transcript accumulation from genes associated with defense, response to reactive oxygen species, and auxin- and jasmonic acid-responsive genes, but decreased transcription factors associated with ethylene and abscisic acid signaling. The cluster of genes involved in plant disease resistance were up-regulated, but the set of drought signaling response genes were down-regulated in the P. chlororaphis O6-colonized under drought stress plants compared to those of the drought stressed plants without bacterial treatment. Transcripts of the jasmonic acid-marker genes, VSP1 and pdf-1.2, the salicylic acid regulated gene, PR-1, and the ethylene-response gene, HEL, also were up-regulated in plants colonized by P. chlororaphis O6, but differed in their responsiveness to drought stress. These data show how gene expression in plants lacking adequate water can be remarkably influenced by microbial colonization leading to plant protection, and the activation of the plant defense signal pathway induced by root colonization of P. chlororaphis O6 might be a key element for induced systemic tolerance by microbes.

  19. Genome-Wide Search for Translated Upstream Open Reading Frames in Arabidopsis Thaliana.

    Science.gov (United States)

    Hu, Qiwen; Merchante, Catharina; Stepanova, Anna N; Alonso, Jose M; Heber, Steffen

    2016-03-01

    Upstream open reading frames (uORFs) are open reading frames that occur within the 5' UTR of an mRNA. uORFs have been found in many organisms. They play an important role in gene regulation, cell development, and in various metabolic processes. It is believed that translated uORFs reduce the translational efficiency of the main coding region. However, only few uORFs are experimentally characterized. In this paper, we use ribosome footprinting together with a semi-supervised approach based on stacking classification models to identify translated uORFs in Arabidopsis thaliana. Our approach identified 5360 potentially translated uORFs in 2051 genes. GO terms enriched in genes with translated uORFs include catalytic activity, binding, transferase activity, phosphotransferase activity, kinase activity, and transcription regulator activity. The reported uORFs occur with a higher frequency in multi-isoform genes, and some uORFs are affected by alternative transcript start sites or alternative splicing events. Association rule mining revealed sequence features associated with the translation status of the uORFs. We hypothesize that uORF translation is a complex process that might be regulated by multiple factors. The identified uORFs are available online at:https://www.dropbox.com/sh/zdutupedxafhly8/AABFsdNR5zDfiozB7B4igFcja?dl=0. This paper is the extended version of our research presented at ISBRA 2015.

  20. Sample preparation for phosphoproteomic analysis of circadian time series in Arabidopsis thaliana.

    Science.gov (United States)

    Krahmer, Johanna; Hindle, Matthew M; Martin, Sarah F; Le Bihan, Thierry; Millar, Andrew J

    2015-01-01

    Systems biological approaches to study the Arabidopsis thaliana circadian clock have mainly focused on transcriptomics while little is known about the proteome, and even less about posttranslational modifications. Evidence has emerged that posttranslational protein modifications, in particular phosphorylation, play an important role for the clock and its output. Phosphoproteomics is the method of choice for a large-scale approach to gain more knowledge about rhythmic protein phosphorylation. Recent plant phosphoproteomics publications have identified several thousand phosphopeptides. However, the methods used in these studies are very labor-intensive and therefore not suitable to apply to a well-replicated circadian time series. To address this issue, we present and compare different strategies for sample preparation for phosphoproteomics that are compatible with large numbers of samples. Methods are compared regarding number of identifications, variability of quantitation, and functional categorization. We focus on the type of detergent used for protein extraction as well as methods for its removal. We also test a simple two-fraction separation of the protein extract. © 2015 Elsevier Inc. All rights reserved.

  1. Data integration for plant genomics--exemplars from the integration of Arabidopsis thaliana databases.

    Science.gov (United States)

    Lysenko, Artem; Lysenko, Atem; Hindle, Matthew Morritt; Taubert, Jan; Saqi, Mansoor; Rawlings, Christopher John

    2009-11-01

    The development of a systems based approach to problems in plant sciences requires integration of existing information resources. However, the available information is currently often incomplete and dispersed across many sources and the syntactic and semantic heterogeneity of the data is a challenge for integration. In this article, we discuss strategies for data integration and we use a graph based integration method (Ondex) to illustrate some of these challenges with reference to two example problems concerning integration of (i) metabolic pathway and (ii) protein interaction data for Arabidopsis thaliana. We quantify the degree of overlap for three commonly used pathway and protein interaction information sources. For pathways, we find that the AraCyc database contains the widest coverage of enzyme reactions and for protein interactions we find that the IntAct database provides the largest unique contribution to the integrated dataset. For both examples, however, we observe a relatively small amount of data common to all three sources. Analysis and visual exploration of the integrated networks was used to identify a number of practical issues relating to the interpretation of these datasets. We demonstrate the utility of these approaches to the analysis of groups of coexpressed genes from an individual microarray experiment, in the context of pathway information and for the combination of coexpression data with an integrated protein interaction network.

  2. The evolutionary response of plants to increased UV-B radiation: Field studies with Arabidopsis thaliana

    International Nuclear Information System (INIS)

    Trumbull, V.L.; Paige, K.N.

    1995-01-01

    The response of a species to any environmental change is determined by both phenotypic and evolutionary adjustments. To date, the majority of research concerning the response of terrestrial plants to increased UV-B radiation has focused on phenotypic adjustments. Recently we have initiated field studies aimed at assessing genetic variation for UV-B sensitivity within a natural population of Arabidopsis thaliana. This population consists of at least eight discrete genotypes that have been confirmed by RAPD analysis. We used an incomplete block design to assess the impact of UV-B (ambient and ambient + 6 kJ) and PAR (low and high) on these genotypes. The high UV-B treatment caused a significant reduction in fruit number and plant height while the high PAR treatment caused a significant increase in these variables. In addition, there was a marginally significant (p=0.1) UV-B x PAR x maternal line interaction for fruit number, indicating that genetic variation for UV-B sensitivity within this population depends on the PAR environment. The combination of high UV-B and high PAR caused a change in fruit number (relative to the ambient UV-B/high PAR treatment) ranging from an increase of 24% to a decrease of 47%. This range was much smaller in the low PAR treatment. These results indicate the potential for increased UV-B radiation to act as an agent of natural selection within this population

  3. A role for IAA in the infection of Arabidopsis thaliana by Orobanche aegyptiaca.

    Science.gov (United States)

    Bar-Nun, Nurit; Sachs, Tsvi; Mayer, Alfred M

    2008-01-01

    Vascular continuity is established between a host plant and the root parasite broomrape. It is generally accepted that the direction of vascular continuity results from polar flow of auxin. Our hypothesis was that chemical disruptions of auxin transport and activity could influence the infection of the host by the parasite. A sterile system for the routine infection of Arabidopsis thaliana seedlings in Nunc cell culture plates by germinated seeds of Orobanche aegyptiaca was developed. This method permitted a quantitative assay of the rate of host infection. The three-dimensional structure of the vascular contacts was followed in cleared tissue. IAA (indole acetic acid) or substances that influence its activity and transport were applied locally to the host root. The orientation of the xylem contacts showed that broomrape grafts itself upon the host by acting hormonally as a root rather than a shoot. Local applications of IAA, PCIB (p-chlorophenoxyisobutyric acid) or NPA (naphthylphthalamic acid) all resulted in drastic reductions of Orobanche infection Broomrape manipulates the host by acting as a sink for auxin. Disruption of auxin action or auxin flow at the contact site could be a novel basis for controlling infection by Orobanche.

  4. Mechano-chemical aspects of organ formation in Arabidopsis thaliana: the relationship between auxin and pectin.

    Directory of Open Access Journals (Sweden)

    Siobhan A Braybrook

    Full Text Available How instructive signals are translated into robust and predictable changes in growth is a central question in developmental biology. Recently, much interest has centered on the feedback between chemical instructions and mechanical changes for pattern formation in development. In plants, the patterned arrangement of aerial organs, or phyllotaxis, is instructed by the phytohormone auxin; however, it still remains to be seen how auxin is linked, at the apex, to the biochemical and mechanical changes of the cell wall required for organ outgrowth. Here, using Atomic Force Microscopy, we demonstrate that auxin reduces tissue rigidity prior to organ outgrowth in the shoot apex of Arabidopsis thaliana, and that the de-methyl-esterification of pectin is necessary for this reduction. We further show that development of functional organs produced by pectin-mediated ectopic wall softening requires auxin signaling. Lastly, we demonstrate that coordinated localization of the auxin transport protein, PIN1, is disrupted in a naked-apex produced by increasing cell wall rigidity. Our data indicates that a feedback loop between the instructive chemical auxin and cell wall mechanics may play a crucial role in phyllotactic patterning.

  5. Evaluation of genetic and metabolic role of SKIP11 in Arabidopsis thaliana

    Science.gov (United States)

    Hassan, Muhammad Naeem ul; Ismail, Ismanizan

    2015-09-01

    Most of the regulatory proteins are degraded by 26S proteasome complex, only when they are tagged by Ubiquitin. A complex of four proteins, SKP1-Cullin-Ring box-F box (SCF) catalyses the final step to link the Ubiquitin tag with the target proteins. SCF complex interacts with the target proteins through F-box proteins, which confer the overall substrate specificity to the complex. F-box proteins, one of the largest family of proteins in plants have an N-terminal F-box domain and variable C-terminal domains, like leucine-rich repeat, WD-40 repeat and the kelch-repeat domains. In this study, we analysed the role of SKIP11, a kelch containing F-box protein (KFB) from Arabidopsis thaliana, by using reverse genetics strategy. The results show that SKIP11 is involved in the down-regulation of oxylipin pathway, possibly through the degradation of enzymes or/ and the regulatory factors of the pathway.

  6. MODELO DE DIFERENCIACIÓN CELULAR EN LA FLORACIÓN DE Arabidopsis thaliana

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    José Roberto Romero-Arias

    2010-01-01

    Full Text Available Abordamos el problema de diferenciación celular suponiendo que las células reciben del medio en el que se encuentran información espacio-temporal que les permite cambiar la expresión de sus genes a través de la interacción entre campos físicos macroscópicos y sus redes genéticas. La idea fundamental es que la red genética de cada célula responda a la evolución dinámica de los campos macroscópicos, que rompen la simetría del espacio-tiempo, y de esa forma provean información a la red para expresar los genes de forma selectiva. Así, describimos un modelo de coevolución entre dos sistemas físicos que reaccionan químicamente para describir la floración de Arabidopsis thaliana, ya que esta planta ha sido uno de los organismos más estudiados y donde podemos usar una gran cantidad de datos, tanto de la evolución temporal de los órganos como de la actividad de la genética responsable.

  7. Structural determinants of Arabidopsis thaliana Hyponastic leaves 1 function in vivo.

    Directory of Open Access Journals (Sweden)

    Paula Burdisso

    Full Text Available MicroRNAs have turned out to be important regulators of gene expression. These molecules originate from longer transcripts that are processed by ribonuclease III (RNAse III enzymes. Dicer proteins are essential RNAse III enzymes that are involved in the generation of microRNAs (miRNAs and other small RNAs. The correct function of Dicer relies on the participation of accessory dsRNA binding proteins, the exact function of which is not well-understood so far. In plants, the double stranded RNA binding protein Hyponastic Leaves 1 (HYL1 helps Dicer Like protein (DCL1 to achieve an efficient and precise excision of the miRNAs from their primary precursors. Here we dissected the regions of HYL1 that are essential for its function in Arabidopsis thaliana plant model. We generated mutant forms of the protein that retain their structure but affect its RNA-binding properties. The mutant versions of HYL1 were studied both in vitro and in vivo, and we were able to identify essential aminoacids/residues for its activity. Remarkably, mutation and even ablation of one of the purportedly main RNA binding determinants does not give rise to any major disturbances in the function of the protein. We studied the function of the mutant forms in vivo, establishing a direct correlation between affinity for the pri-miRNA precursors and protein activity.

  8. Ethylene response factor AtERF72 negatively regulates Arabidopsis thaliana response to iron deficiency.

    Science.gov (United States)

    Liu, Wei; Li, Qiwei; Wang, Yi; Wu, Ting; Yang, Yafei; Zhang, Xinzhong; Han, Zhenhai; Xu, Xuefeng

    2017-09-23

    Ethylene regulates the plant's response to stress caused by iron (Fe) deficiency. However, specific roles of ERF proteins in response to Fe deficiency remain poorly understood. Here, we investigated the role of ERF72 in response to iron deficiency in Arabidopsis thaliana. In this study, the levels of the ethylene response factor AtERF72 increased in leaves and roots induced under the iron deficient conditions. erf72 mutant plants showed increased growth compared to wild type (WT) when grown in iron deficient medium for 5 d. erf72 mutants had increased root H + velocity and the ferric reductase activity, and increase in the expression of the iron deficiency response genes iron-regulated transporter 1 (IRT1) and H + -ATPase (HA2) levels in iron deficient conditions. Compared to WT plants, erf72 mutants retained healthy chloroplast structure with significantly higher Fe and Mg content, and decreased chlorophyll degradation gene pheophorbide a oxygenase (PAO) and chlorophyllase (CLH1) expression when grown in iron deficient media. Yeast one-hybrid analysis showed that ERF72 could directly bind to the promoter regions of iron deficiency responses genes IRT1, HA2 and CLH1. Based on our results, we suggest that ethylene released from plants under iron deficiency stress can activate the expression of ERF72, which responds to iron deficiency in the negative regulation. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. GWA Mapping of Anthocyanin Accumulation Reveals Balancing Selection of MYB90 in Arabidopsis thaliana

    Science.gov (United States)

    Bac-Molenaar, Johanna A.; Fradin, Emilie F.; Rienstra, Juriaan A.; Vreugdenhil, Dick; Keurentjes, Joost J. B.

    2015-01-01

    Induction of anthocyanin accumulation by osmotic stress was assessed in 360 accessions of Arabidopsis thaliana. A wide range of natural variation, with phenotypes ranging from green to completely red/purple rosettes, was observed. A genome wide association (GWA) mapping approach revealed that sequence diversity in a small 15 kb region on chromosome 1 explained 40% of the variation observed. Sequence and expression analyses of alleles of the candidate gene MYB90 identified a causal polymorphism at amino acid (AA) position 210 of this transcription factor of the anthocyanin biosynthesis pathway. This amino acid discriminates the two most frequent alleles of MYB90. Both alleles are present in a substantial part of the population, suggesting balancing selection between these two alleles. Analysis of the geographical origin of the studied accessions suggests that the macro climate is not the driving force behind positive or negative selection for anthocyanin accumulation. An important role for local climatic conditions is, therefore, suggested. This study emphasizes that GWA mapping is a powerful approach to identify alleles that are under balancing selection pressure in nature. PMID:26588092

  10. Dynamic subnuclear relocalisation of WRKY40 in response to Abscisic acid in Arabidopsis thaliana.

    Science.gov (United States)

    Geilen, Katja; Böhmer, Maik

    2015-08-21

    WRKY18, WRKY40 and WRKY60 are members of the WRKY transcription factor family and function as transcriptional regulators in ABA signal transduction in Arabidopsis thaliana. Here we show that WRKY18 and WRKY40, but not WRKY60, co-localise with PIF3, PIF4 and PHYB to Phytochrome B-containing nuclear bodies (PNBs). Localisation to the PNBs is phosphorylation-dependent and is inhibited by the general Ser/Thr-kinase inhibitor Staurosporine. Upon ABA treatment, WRKY40 relocalises from PNBs to the nucleoplasm in an OST1-dependent manner. This stimulus-induced relocalisation was not observed in response to other abiotic or biotic stimuli, including NaCl, MeJA or flg22 treatment. Bimolecular fluorescence complementation experiments indicate that while PIF3, PIF4 and PHYB physically interact in these bodies, PHYB, PIF3 and PIF4 do not interact with the two WRKY transcription factors, which may suggest a more general role for these bodies in regulation of transcriptional activity.

  11. Biodiversity of mineral nutrient and trace element accumulation in Arabidopsis thaliana.

    Science.gov (United States)

    Baxter, Ivan; Hermans, Christian; Lahner, Brett; Yakubova, Elena; Tikhonova, Marina; Verbruggen, Nathalie; Chao, Dai-Yin; Salt, David E

    2012-01-01

    In order to grow on soils that vary widely in chemical composition, plants have evolved mechanisms for regulating the elemental composition of their tissues to balance the mineral nutrient and trace element bioavailability in the soil with the requirements of the plant for growth and development. The biodiversity that exists within a species can be utilized to investigate how regulatory mechanisms of individual elements interact and to identify genes important for these processes. We analyzed the elemental composition (ionome) of a set of 96 wild accessions of the genetic model plant Arabidopsis thaliana grown in hydroponic culture and soil using inductively coupled plasma mass spectrometry (ICP-MS). The concentrations of 17-19 elements were analyzed in roots and leaves from plants grown hydroponically, and leaves and seeds from plants grown in artificial soil. Significant genetic effects were detected for almost every element analyzed. We observed very few correlations between the elemental composition of the leaves and either the roots or seeds. There were many pairs of elements that were significantly correlated with each other within a tissue, but almost none of these pairs were consistently correlated across tissues and growth conditions, a phenomenon observed in several previous studies. These results suggest that the ionome of a plant tissue is variable, yet tightly controlled by genes and gene × environment interactions. The dataset provides a valuable resource for mapping studies to identify genes regulating elemental accumulation. All of the ionomic data is available at www.ionomicshub.org.

  12. The genomic landscape of meiotic crossovers and gene conversions in Arabidopsis thaliana

    Science.gov (United States)

    Wijnker, Erik; Velikkakam James, Geo; Ding, Jia; Becker, Frank; Klasen, Jonas R; Rawat, Vimal; Rowan, Beth A; de Jong, Daniël F; de Snoo, C Bastiaan; Zapata, Luis; Huettel, Bruno; de Jong, Hans; Ossowski, Stephan; Weigel, Detlef; Koornneef, Maarten; Keurentjes, Joost JB; Schneeberger, Korbinian

    2013-01-01

    Knowledge of the exact distribution of meiotic crossovers (COs) and gene conversions (GCs) is essential for understanding many aspects of population genetics and evolution, from haplotype structure and long-distance genetic linkage to the generation of new allelic variants of genes. To this end, we resequenced the four products of 13 meiotic tetrads along with 10 doubled haploids derived from Arabidopsis thaliana hybrids. GC detection through short reads has previously been confounded by genomic rearrangements. Rigid filtering for misaligned reads allowed GC identification at high accuracy and revealed an ∼80-kb transposition, which undergoes copy-number changes mediated by meiotic recombination. Non-crossover associated GCs were extremely rare most likely due to their short average length of ∼25–50 bp, which is significantly shorter than the length of CO-associated GCs. Overall, recombination preferentially targeted non-methylated nucleosome-free regions at gene promoters, which showed significant enrichment of two sequence motifs. DOI: http://dx.doi.org/10.7554/eLife.01426.001 PMID:24347547

  13. SABRE is required for stabilization of root hair patterning in Arabidopsis thaliana.

    Science.gov (United States)

    Pietra, Stefano; Lang, Patricia; Grebe, Markus

    2015-03-01

    Patterned differentiation of distinct cell types is essential for the development of multicellular organisms. The root epidermis of Arabidopsis thaliana is composed of alternating files of root hair and non-hair cells and represents a model system for studying the control of cell-fate acquisition. Epidermal cell fate is regulated by a network of genes that translate positional information from the underlying cortical cell layer into a specific pattern of differentiated cells. While much is known about the genes of this network, new players continue to be discovered. Here we show that the SABRE (SAB) gene, known to mediate microtubule organization, anisotropic cell growth and planar polarity, has an effect on root epidermal hair cell patterning. Loss of SAB function results in ectopic root hair formation and destabilizes the expression of cell fate and differentiation markers in the root epidermis, including expression of the WEREWOLF (WER) and GLABRA2 (GL2) genes. Double mutant analysis reveal that wer and caprice (cpc) mutants, defective in core components of the epidermal patterning pathway, genetically interact with sab. This suggests that SAB may act on epidermal patterning upstream of WER and CPC. Hence, we provide evidence for a role of SAB in root epidermal patterning by affecting cell-fate stabilization. Our work opens the door for future studies addressing SAB-dependent functions of the cytoskeleton during root epidermal patterning. © 2014 The Authors. Physiologia Plantarum published by John Wiley & Sons Ltd on behalf of Scandinavian Plant Physiology Society.

  14. ANGUSTIFOLIA mediates one of the multiple SCRAMBLED signaling pathways regulating cell growth pattern in Arabidopsis thaliana.

    Science.gov (United States)

    Kwak, Su-Hwan; Song, Sang-Kee; Lee, Myeong Min; Schiefelbein, John

    2015-09-25

    In Arabidopsis thaliana, an atypical leucine-rich repeat receptor-like kinase, SCRAMBLED (SCM), is required for multiple developmental processes including root epidermal cell fate determination, silique dehiscence, inflorescence growth, ovule morphogenesis, and tissue morphology. Previous work suggested that SCM regulates these multiple pathways using distinct mechanisms via interactions with specific downstream factors. ANGUSTIFOLIA (AN) is known to regulate cell and tissue morphogenesis by influencing cortical microtubule arrangement, and recently, the AN protein was reported to interact with the SCM protein. Therefore, we examined whether AN might be responsible for mediating some of the SCM-dependent phenotypes. We discovered that both scm and an mutant lines cause an abnormal spiral or twisting growth of roots, but only the scm mutant affected root epidermal patterning. The siliques of the an and scm mutants also exhibited spiral growth, as previously reported, but only the scm mutant altered silique dehiscence. Interestingly, we discovered that the spiral growth of roots and siliques of the scm mutant is rescued by a truncated SCM protein that lacks its kinase domain, and that a juxtamembrane domain of SCM was sufficient for AN binding in the yeast two-hybrid analysis. These results suggest that the AN protein is one of the critical downstream factors of SCM pathways specifically responsible for mediating its effects on cell/tissue morphogenesis through cortical microtubule arrangement. Copyright © 2015 Elsevier Inc. All rights reserved.

  15. Natural variation in abiotic stress responsive gene expression and local adaptation to climate in Arabidopsis thaliana.

    Science.gov (United States)

    Lasky, Jesse R; Des Marais, David L; Lowry, David B; Povolotskaya, Inna; McKay, John K; Richards, James H; Keitt, Timothy H; Juenger, Thomas E

    2014-09-01

    Gene expression varies widely in natural populations, yet the proximate and ultimate causes of this variation are poorly known. Understanding how variation in gene expression affects abiotic stress tolerance, fitness, and adaptation is central to the field of evolutionary genetics. We tested the hypothesis that genes with natural genetic variation in their expression responses to abiotic stress are likely to be involved in local adaptation to climate in Arabidopsis thaliana. Specifically, we compared genes with consistent expression responses to environmental stress (expression stress responsive, "eSR") to genes with genetically variable responses to abiotic stress (expression genotype-by-environment interaction, "eGEI"). We found that on average genes that exhibited eGEI in response to drought or cold had greater polymorphism in promoter regions and stronger associations with climate than those of eSR genes or genomic controls. We also found that transcription factor binding sites known to respond to environmental stressors, especially abscisic acid responsive elements, showed significantly higher polymorphism in drought eGEI genes in comparison to eSR genes. By contrast, eSR genes tended to exhibit relatively greater pairwise haplotype sharing, lower promoter diversity, and fewer nonsynonymous polymorphisms, suggesting purifying selection or selective sweeps. Our results indicate that cis-regulatory evolution and genetic variation in stress responsive gene expression may be important mechanisms of local adaptation to climatic selective gradients. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  16. Reproductive, morphological, and phytochemical responses of Arabidopsis thaliana ecotypes to enhanced UV-B radiation

    Energy Technology Data Exchange (ETDEWEB)

    Trumbull, V.L.; McCloud, E.S.; Paige, K.N. (Univ. of Illinois, Urbana, IL (United States))

    1994-06-01

    Two ecotypes of Arabidopsis thaliana, collected from Libya and Norway, were grown in the greenhouse under. UV-B doses of 0 and 10.5 kJ m[sup [minus]2] UV-B[sub BE]. The high UV-B dose simulated midsummer ambient conditions over Libya and a 40% reduction in stratospheric ozone over Norway. The Libyan ectotype, which originated from latitudes where solar UV-B is high, showed no UV-B induced damage to plant growth. However the Norwegian ecotype, which originated from latitudes where solar UV-B is low, showed a significant reduction in plant height, inflorescence weight, and rosette weight in response to enhanced UV-B. Although fruit and seed number for both ecotypes were unaffected by enhanced UV-B radiation the germination success of the seeds harvested from the irradiated Norwegian plants were significantly reduced. The two ecotypes also differed with respect to their accumulation of kaempferol, a putative UV-B protective filter. The Libyan ecotype increased kaempferol concentration by 38% over the 0 kJ treatment whereas the Norwegian ecotype increased by only 15%. These data suggest that, for these ecotypes, variation in UV-B sensitivity may be explained by the differential induction of UV-absorbing leaf pigments.

  17. Gene network analysis of Arabidopsis thaliana flower development through dynamic gene perturbations.

    Science.gov (United States)

    Ó'Maoiléidigh, Diarmuid S; Thomson, Bennett; Raganelli, Andrea; Wuest, Samuel E; Ryan, Patrick T; Kwaśniewska, Kamila; Carles, Cristel C; Graciet, Emmanuelle; Wellmer, Frank

    2015-07-01

    Understanding how flowers develop from undifferentiated stem cells has occupied developmental biologists for decades. Key to unraveling this process is a detailed knowledge of the global regulatory hierarchies that control developmental transitions, cell differentiation and organ growth. These hierarchies may be deduced from gene perturbation experiments, which determine the effects on gene expression after specific disruption of a regulatory gene. Here, we tested experimental strategies for gene perturbation experiments during Arabidopsis thaliana flower development. We used artificial miRNAs (amiRNAs) to disrupt the functions of key floral regulators, and expressed them under the control of various inducible promoter systems that are widely used in the plant research community. To be able to perform genome-wide experiments with stage-specific resolution using the various inducible promoter systems for gene perturbation experiments, we also generated a series of floral induction systems that allow collection of hundreds of synchronized floral buds from a single plant. Based on our results, we propose strategies for performing dynamic gene perturbation experiments in flowers, and outline how they may be combined with versions of the floral induction system to dissect the gene regulatory network underlying flower development. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

  18. Evolutionary Rate Heterogeneity of Primary and Secondary Metabolic Pathway Genes in Arabidopsis thaliana.

    Science.gov (United States)

    Mukherjee, Dola; Mukherjee, Ashutosh; Ghosh, Tapash Chandra

    2015-11-10

    Primary metabolism is essential to plants for growth and development, and secondary metabolism helps plants to interact with the environment. Many plant metabolites are industrially important. These metabolites are produced by plants through complex metabolic pathways. Lack of knowledge about these pathways is hindering the successful breeding practices for these metabolites. For a better knowledge of the metabolism in plants as a whole, evolutionary rate variation of primary and secondary metabolic pathway genes is a prerequisite. In this study, evolutionary rate variation of primary and secondary metabolic pathway genes has been analyzed in the model plant Arabidopsis thaliana. Primary metabolic pathway genes were found to be more conserved than secondary metabolic pathway genes. Several factors such as gene structure, expression level, tissue specificity, multifunctionality, and domain number are the key factors behind this evolutionary rate variation. This study will help to better understand the evolutionary dynamics of plant metabolism. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  19. Multiple BiP genes of Arabidopsis thaliana are required for male gametogenesis and pollen competitiveness.

    Science.gov (United States)

    Maruyama, Daisuke; Sugiyama, Tomoyuki; Endo, Toshiya; Nishikawa, Shuh-Ichi

    2014-04-01

    Immunoglobulin-binding protein (BiP) is a molecular chaperone of the heat shock protein 70 (Hsp70) family. BiP is localized in the endoplasmic reticulum (ER) and plays key roles in protein translocation, protein folding and quality control in the ER. The genomes of flowering plants contain multiple BiP genes. Arabidopsis thaliana has three BiP genes. BIP1 and BIP2 are ubiquitously expressed. BIP3 encodes a less well conserved BiP paralog, and it is expressed only under ER stress conditions in the majority of organs. Here, we report that all BiP genes are expressed and functional in pollen and pollen tubes. Although the bip1 bip2 double mutation does not affect pollen viability, the bip1 bip2 bip3 triple mutation is lethal in pollen. This result indicates that lethality of the bip1 bip2 double mutation is rescued by BiP3 expression. A decrease in the copy number of the ubiquitously expressed BiP genes correlates well with a decrease in pollen tube growth, which leads to reduced fitness of mutant pollen during fertilization. Because an increased protein secretion activity is expected to increase the protein folding demand in the ER, the multiple BiP genes probably cooperate with each other to ensure ER homeostasis in cells with active secretion such as rapidly growing pollen tubes.

  20. On the Origin of De Novo Genes in Arabidopsis thaliana Populations.

    Science.gov (United States)

    Li, Zi-Wen; Chen, Xi; Wu, Qiong; Hagmann, Jörg; Han, Ting-Shen; Zou, Yu-Pan; Ge, Song; Guo, Ya-Long

    2016-08-03

    De novo genes, which originate from ancestral nongenic sequences, are one of the most important sources of protein-coding genes. This origination process is crucial for the adaptation of organisms. However, how de novo genes arise and become fixed in a population or species remains largely unknown. Here, we identified 782 de novo genes from the model plant Arabidopsis thaliana and divided them into three types based on the availability of translational evidence, transcriptional evidence, and neither transcriptional nor translational evidence for their origin. Importantly, by integrating multiple types of omics data, including data from genomes, epigenomes, transcriptomes, and translatomes, we found that epigenetic modifications (DNA methylation and histone modification) play an important role in the origination process of de novo genes. Intriguingly, using the transcriptomes and methylomes from the same population of 84 accessions, we found that de novo genes that are transcribed in approximately half of the total accessions within the population are highly methylated, with lower levels of transcription than those transcribed at other frequencies within the population. We hypothesized that, during the origin of de novo gene alleles, those neutralized to low expression states via DNA methylation have relatively high probabilities of spreading and becoming fixed in a population. Our results highlight the process underlying the origin of de novo genes at the population level, as well as the importance of DNA methylation in this process. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  1. Biodiversity of mineral nutrient and trace element accumulation in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Ivan Baxter

    Full Text Available In order to grow on soils that vary widely in chemical composition, plants have evolved mechanisms for regulating the elemental composition of their tissues to balance the mineral nutrient and trace element bioavailability in the soil with the requirements of the plant for growth and development. The biodiversity that exists within a species can be utilized to investigate how regulatory mechanisms of individual elements interact and to identify genes important for these processes. We analyzed the elemental composition (ionome of a set of 96 wild accessions of the genetic model plant Arabidopsis thaliana grown in hydroponic culture and soil using inductively coupled plasma mass spectrometry (ICP-MS. The concentrations of 17-19 elements were analyzed in roots and leaves from plants grown hydroponically, and leaves and seeds from plants grown in artificial soil. Significant genetic effects were detected for almost every element analyzed. We observed very few correlations between the elemental composition of the leaves and either the roots or seeds. There were many pairs of elements that were significantly correlated with each other within a tissue, but almost none of these pairs were consistently correlated across tissues and growth conditions, a phenomenon observed in several previous studies. These results suggest that the ionome of a plant tissue is variable, yet tightly controlled by genes and gene × environment interactions. The dataset provides a valuable resource for mapping studies to identify genes regulating elemental accumulation. All of the ionomic data is available at www.ionomicshub.org.

  2. A novel root gravitropism mutant of Arabidopsis thaliana exhibiting altered auxin physiology

    Science.gov (United States)

    Simmons, C.; Migliaccio, F.; Masson, P.; Caspar, T.; Soll, D.

    1995-01-01

    A root gravitropism mutant was isolated from the DuPont Arabidopsis thaliana T-DNA insertional mutagenesis collection. This mutant has reduced root gravitropism, hence the name rgr1. Roots of rgr1 are shorter than those of wild-type, and they have reduced lateral root formation. In addition, roots of rgr1 coil clockwise on inclined agar plates, unlike wild-type roots which grow in a wavy pattern. The rgr1 mutant has increased resistance, as measured by root elongation, to exogenously applied auxins (6-fold to indole-3-acetic acid, 3-fold to 2,4-dichlorophenoxyacetic acid, and 2-fold to napthyleneacetic acid). It is also resistant to polar auxin transport inhibitors (2-fold to triiodobenzoic acid and 3- to 5-fold to napthylphthalamic acid). The rgr1 mutant does not appear to be resistant to other plant hormone classes. When grown in the presence of 10(-7) M 2,4-dichlorophenoxyacetic acid, rgr1 roots have fewer root hairs than wild type. All these rgr1 phenotypes are Mendelian recessives. Complementation tests indicate that rgr1 is not allelic to previously characterized agravitropic or auxin-resistant mutants. The rgr1 locus was mapped using visible markers to 1.4 +/- 0.6 map units from the CH1 locus at 1-65.4. The rgr1 mutation and the T-DNA cosegregate, suggesting that rgr1 was caused by insertional gene inactivation.

  3. Root hydrotropism and thigmotropism in Arabidopsis thaliana are differentially controlled by redox status.

    Science.gov (United States)

    Ponce, Georgina; Corkidi, Gabriel; Eapen, Delfeena; Lledías, Fernando; Cárdenas, Luis; Cassab, Gladys

    2017-04-03

    Factors that affect the direction of root growth in response to environmental signals influence crop productivity. We analyzed the root tropic responses of thioredoxin (trxs), thigmotropic (wav2-1), and hydrotropic (ahr1 and nhr1) Arabidopsis thaliana mutants treated with low concentrations of paraquat (PQ), which induces mild oxidative stress, and established a new method for evaluating root waviness (root bending effort, RBE). This method estimates root bending by measuring and summing local curvature over the whole length of the root, regardless of the asymmetry of the wavy pattern under thigmostimulation. In roots of the wav2-1 mutant, but not in those of the trxs and ahr1 mutants, RBE was significantly inhibited under mild oxidative stress. Thigmotropic stimulation of wav2-1 mutant roots, with or without PQ treatment, showed high levels of reactive oxygen species fluorescence, in contrast to roots of the ahr1 mutant. Furthermore, PQ inhibited root growth in all genotypes tested, except in the wav2-1 mutant. In a hydrotropism assay of the trxs and wav2-1 mutants, root growth behavior was similar to the wild type with and without PQ, while the root growth of ahr1 and nhr1 mutants was diminished with PQ. These results indicate that hydrotropic and thigmotropic mutants respond differently to exogenous PQ, depending on the tropic stimulus perceived. Therefore, the mechanisms underlying hydrotropism and thigmotropism may differ.

  4. Genomic stability in response to high versus low linear energy transfer radiation in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Neil eHuefner

    2014-05-01

    Full Text Available Low linear energy transfer (LET gamma rays and high LET HZE (high atomic weight, high energy particles act as powerful mutagens in both plants and animals. DNA damage generated by HZE particles is more densely clustered than that generated by gamma rays. To understand the genetic requirements for resistance to high vs. low LET radiation, a series of Arabidopsis thaliana mutants were exposed to either 1GeV Fe nuclei or gamma radiation. A comparison of effects on the germination and subsequent growth of seedlings led us to conclude that the relative biological effectiveness (RBE of the two types of radiation (HZE vs. gamma are roughly 3:1. Similarly, in wild-type lines, loss of somatic heterozygosity was induced at an RBE of about a 2:1 (HZE vs. gamma. Checkpoint and repair defects, as expected, enhanced sensitivity to both agents. The replication fork checkpoint, governed by ATR, played a slightly more important role in resistance to HZE-induced mutagenesis than in resistance to gamma induced mutagenesis.

  5. A geographic cline in leaf salicylic acid with increasing elevation in Arabidopsis thaliana

    Science.gov (United States)

    Zhang, Nana; Tonsor, Stephen J; Traw, M Brian

    2015-01-01

    Salicylic acid (SA) occupies a key role as a hormone central to both plant resistance to bacterial pathogens and tolerance of abiotic stresses. Plants at high elevation experience colder temperatures and elevated UV levels. While it has been predicted that SA concentrations will be higher in plants from high elevation populations, few studies have addressed this question. Here, we asked how concentrations of SA vary in natural populations of Arabidopsis thaliana collected across an elevational gradient on the Iberian Peninsula. In a series of common garden experiments, we found that constitutive SA concentrations were highest in genotypes from the low elevation populations. This result was in the opposite direction from our prediction and is an exception to the general finding that phenolic compounds increase with increasing elevation. These data suggest that high constitutive SA is not associated with resistance to cold temperatures in these plants. Furthermore, we also found that leaf constitutive camalexin concentrations, an important defense against some bacterial and fungal enemies, were highest in the low elevation populations, suggesting that pathogen pressures may be important. Further examination of this elevational cline will likely provide additional insights into the interplay between phenolic compounds and biotic and abiotic stress. PMID:25875692

  6. Pollen tube and root-hair tip growth is disrupted in a mutant of Arabidopsis thaliana.

    Science.gov (United States)

    Schiefelbein, J; Galway, M; Masucci, J; Ford, S

    1993-11-01

    The expansion of both root hairs and pollen tubes occurs by a process known as tip growth. In this report, an Arabidopsis thaliana mutant (tip1) is described that displays defects in both root-hair and pollen-tube growth. The root hairs of the tip1 mutant plants are shorter than those of the wild-type plants and branched at their base. The tip1 pollen-tube growth defect was identified by the aberrant segregation ratio of phenotypically normal to mutant seeds in siliques from self-pollinated, heterozygous plants. Homozygous mutant seeds are not randomly distributed in the siliques, comprising only 14.4% of the total seeds, 5.3% of the seeds from the bottom half, and 2.2% of the seeds from the bottom quarter of the heterozygous siliques. Studies of pollen-tube growth in vivo showed that mutant pollen tubes grow more slowly than wild-type pollen through the transmitting tissue of wild-type flowers. Cosegregation studies indicate that the root-hair and pollen-tube defects are caused by the same genetic lesion. Based on these findings, the TIP1 gene is likely to encode a product involved in a fundamental aspect of tip growth in plant cells.

  7. Physiological responses of Arabidopsis thaliana to the interaction of iron deficiency and nitrogen form.

    Science.gov (United States)

    Karray-Bouraoui, Najoua; Attia, Houneida; Maghzaoui, Manel; Msilini, Najoua; Rabhi, M; Lachaâl, M

    2010-06-01

    Physiological responses of Arabidopsis thaliana to the interaction of iron deficiency and nitrogen form were studied using plants grown in hydroponics. Thirty-three-day-old seedlings were submitted to four treatments for 7 days: NO 3 + 5 microM Fe; NO 3 + 0.1 microM Fe; NH 4 + 5 microM Fe and NH 4 + 0.1 microM Fe. Leaf growth and chlorophyll content were highest in NO 3 -fed, Fe sufficient plants, but were strongly diminished by Fe deficiency under nitric nutrition, and by ammoniacal nutrition independently of Fe regime. However, the leaves of NH 4 -fed plants presented a higher Fe content than those of Fe sufficient, NO 3 -fed plants. Thus, leaf chlorosis of NH 4 -fed in plant did not depend on Fe availability, and seemed to be due to another factor. Root acidification capacity and Fe-chelate reductase (FCR) activity were also dependent on N form. The medium was acidified under ammoniacal regime and alkalinized under nitric regime regardless of Fe level. FCR activity stimulation in response to Fe deficiency was observed only in NO 3- fed plants. In addition, both N form and Fe level induced antioxidant responses in rosette leaves. Ammoniacal regime increased both peroxidase expression and anthocyanin accumulation, whereas Fe deficiency enhanced superoxide dismutase expression.

  8. Contrasted patterns of crossover and non-crossover at Arabidopsis thaliana meiotic recombination hotspots.

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    Jan Drouaud

    2013-11-01

    Full Text Available The vast majority of meiotic recombination events (crossovers (COs and non-crossovers (NCOs cluster in narrow hotspots surrounded by large regions devoid of recombinational activity. Here, using a new molecular approach in plants, called "pollen-typing", we detected and characterized hundreds of CO and NCO molecules in two different hotspot regions in Arabidopsis thaliana. This analysis revealed that COs are concentrated in regions of a few kilobases where their rates reach up to 50 times the genome average. The hotspots themselves tend to cluster in regions less than 8 kilobases in size with overlapping CO distribution. Non-crossover (NCO events also occurred in the two hotspots but at very different levels (local CO/NCO ratios of 1/1 and 30/1 and their track lengths were quite small (a few hundred base pairs. We also showed that the ZMM protein MSH4 plays a role in CO formation and somewhat unexpectedly we also found that it is involved in the generation of NCOs but with a different level of effect. Finally, factors acting in cis and in trans appear to shape the rate and distribution of COs at meiotic recombination hotspots.

  9. Jasmonate is involved in the induction of tyrosine aminotransferase and tocopherol biosynthesis in Arabidopsis thaliana.

    Science.gov (United States)

    Sandorf, Iris; Holländer-Czytko, Heike

    2002-11-01

    Coronatine-inducible tyrosine aminotransferase (TAT), which catalyses the transamination from tyrosine to p-hydroxyphenylpyruvate, is the first enzyme of a pathway leading via homogentisic acid to plastoquinone and tocopherols, the latter of which are known to be radical scavengers in plants. TAT can be also induced by the octadecanoids methyl jasmonate (MeJA) and methyl-12-oxophytodienoic acid (MeOPDA), as well as by wounding, high light, UV light and the herbicide oxyfluorfen. In order to elucidate the role of octadecanoids in the process of TAT induction in Arabidopsis thaliana (L.) Heynh., the jasmonate-deficient mutant delayed dehiscence (dde1) was used, in which the gene for 12-oxophytodienoic acid reductase 3 is disrupted. The amount of immunodetectable TAT was low. The enzyme was still fully induced by coronatine as well as by MeJA although induction by the latter was to a lesser extent and later than in the wild type. Treatment with MeOPDA, wounding and UV light, however, had hardly any effects. Tocopherol levels that showed considerable increases in the wild type after some treatments were much less affected in the mutant. However, starting levels of tocopherol were higher in non-induced dde1 than in the wild type. We conclude that jasmonate plays an important role in the signal transduction pathway regulating TAT activity and the biosynthesis of its product tocopherol.

  10. Gibberellic acid and cGMP-dependent transcriptional regulation in arabidopsis thaliana

    KAUST Repository

    Bastian, René

    2010-03-01

    An ever increasing amount of transcriptomic data and analysis tools provide novel insight into complex responses of biological systems. Given these resources we have undertaken to review aspects of transcriptional regulation in response to the plant hormone gibberellic acid (GA) and its second messenger guanosine 3\\',5\\'-cyclic monophosphate (cGMP) in Arabidopsis thaliana, both wild type and selected mutants. Evidence suggests enrichment of GA-responsive (GARE) elements in promoters of genes that are transcriptionally upregulated in response to cGMP but downregulated in a GA insensitive mutant (ga1-3). In contrast, in the genes upregulated in the mutant, no enrichment in the GARE is observed suggesting that GARE motifs are diagnostic for GA-induced and cGMP-dependent transcriptional upregulation. Further, we review how expression studies of GA-dependent transcription factors and transcriptional networks based on common promoter signatures derived from ab initio analyses can contribute to our understanding of plant responses at the systems level. © 2010 Landes Bioscience.

  11. ACA12 Is a Deregulated Isoform of Plasma Membrane Ca2+-ATPase of Arabidopsis thaliana

    Science.gov (United States)

    Limonta, Margherita; Romanowsky, Shawn; Olivari, Claudio; Bonza, Maria Cristina; Luoni, Laura; Rosenberg, Alexa; Harper, Jeffrey F.; De Michelis, Maria Ida

    2014-01-01

    Plant auto-inhibited Ca2+-ATPases (ACA) are crucial in defining the shape of calcium transients and therefore in eliciting plant responses to various stimuli. Arabidopsis thaliana genome encodes ten ACA isoforms that can be divided into four clusters based on gene structure and sequence homology. While isoforms from clusters 1, 2 and 4 have been characterized, virtually nothing is known about members of cluster 3 (ACA12 and ACA13). Here we show that a GFP-tagged ACA12 localizes at the plasma membrane and that expression of ACA12 rescues the phenotype of partial male sterility of a null mutant of the plasma membrane isoform ACA9, thus providing genetic evidence that ACA12 is a functional plasma membrane-resident Ca2+-ATPase. By ACA12 expression in yeast and purification by CaM-affinity chromatography, we show that, unlike other ACAs, the activity of ACA12 is not stimulated by CaM. Moreover, full length ACA12 is able to rescue a yeast mutant deficient in calcium pumps. Analysis of single point ACA12 mutants suggests that ACA12 loss of auto-inhibition can be ascribed to the lack of two acidic residues - highly conserved in other ACA isoforms - localized at the cytoplasmic edge of the second and third transmembrane segments. Together, these results support a model in which the calcium pump activity of ACA12 is primarily regulated by increasing or decreasing mRNA expression and/or protein translation and degradation. PMID:24101142

  12. A collection of target mimics for comprehensive analysis of microRNA function in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Marco Todesco

    2010-07-01

    Full Text Available Many targets of plant microRNAs (miRNAs are thought to play important roles in plant physiology and development. However, because plant miRNAs are typically encoded by medium-size gene families, it has often been difficult to assess their precise function. We report the generation of a large-scale collection of knockdowns for Arabidopsis thaliana miRNA families; this has been achieved using artificial miRNA target mimics, a recently developed technique fashioned on an endogenous mechanism of miRNA regulation. Morphological defects in the aerial part were observed for approximately 20% of analyzed families, all of which are deeply conserved in land plants. In addition, we find that non-cleavable mimic sites can confer translational regulation in cis. Phenotypes of plants expressing target mimics directed against miRNAs involved in development were in several cases consistent with previous reports on plants expressing miRNA-resistant forms of individual target genes, indicating that a limited number of targets mediates most effects of these miRNAs. That less conserved miRNAs rarely had obvious effects on plant morphology suggests that most of them do not affect fundamental aspects of development. In addition to insight into modes of miRNA action, this study provides an important resource for the study of miRNA function in plants.

  13. Proteomic signatures implicate cAMP in light and temperature responses in Arabidopsis thaliana

    KAUST Repository

    Thomas, Ludivine

    2013-05-01

    The second messenger 3\\'-5\\'-cyclic adenosine monophosphate (cAMP) and adenylyl cyclases (ACs), enzymes that catalyse the formation of cAMP from ATP, are increasingly recognized as important signaling molecules in a number of physiological responses in higher plants. Here we used proteomics to identify cAMP-dependent protein signatures in Arabidopsis thaliana and identify a number of differentially expressed proteins with a role in light- and temperature-dependent responses, notably photosystem II subunit P-1, plasma membrane associated cation-binding protein and chaperonin 60 β. Based on these proteomics results we conclude that, much like in cyanobacteria, algae and fungi, cAMP may have a role in light signaling and the regulation of photosynthesis as well as responses to temperature and we speculate that ACs could act as light and/or temperature sensors in higher plants. Biological significance: This current study is significant since it presents the first proteomic response to cAMP, a novel and key second messenger in plants. It will be relevant to researchers in plant physiology and in particular those with an interest in second messengers and their role in biotic and abiotic stress responses. © 2013 Elsevier B.V.

  14. Plasticity to simulated shade is associated with altitude in structured populations of Arabidopsis thaliana.

    Science.gov (United States)

    Botto, Javier F

    2015-07-01

    Plants compete for photosynthesis light and induce a shade avoidance syndrome (SAS) that confers an important advantage in asymmetric competition for light at high canopy densities. Shade plasticity was studied in a greenhouse experiment cultivating Arabidopsis thaliana plants from 15 populations spread across an altitudinal gradient in the northeast area of Spain that contain a high genetic variation into a reduced geographical range. Plants were exposed to sunlight or simulated shade to identify the range of shade plasticity. Fourteen vegetative, flowering and reproductive traits were measured throughout the life cycle. Shade plasticity in flowering time and dry mass was significantly associated with the altitude of population origin. Plants from coastal populations showed higher shade plasticity indexes than those from mountains. The altitudinal variation in flowering leaf plasticity adjusted negatively with average and minimum temperatures, whereas dry mass plasticity was better explained by negative regressions with the average, maximum and minimum temperatures, and by a positive regression with average precipitation of the population origin. The lack of an altitudinal gradient for the widest number of traits suggests that shade light could be a driver explaining the distribution pattern of individuals in smaller geographical scales than those explored here. © 2014 John Wiley & Sons Ltd.

  15. Modified cellulose synthase gene from 'Arabidopsis thaliana' confers herbicide resistance to plants

    Energy Technology Data Exchange (ETDEWEB)

    Somerville, Chris R.; Scieble, Wolf

    2000-10-11

    Cellulose synthase ('CS'), a key enzyme in the biosynthesis of cellulose in plants is inhibited by herbicides comprising thiazolidinones such as 5-tert-butyl-carbamoyloxy-3-(3-trifluromethyl) phenyl-4-thiazolidinone (TZ), isoxaben and 2,6-dichlorobenzonitrile (DCB). Two mutant genes encoding isoxaben and TZ-resistant cellulose synthase have been isolated from isoxaben and TZ-resistant Arabidopsis thaliana mutants. When compared with the gene coding for isoxaben or TZ-sensitive cellulose synthase, one of the resistant CS genes contains a point mutation, wherein glycine residue 998 is replaced by an aspartic acid. The other resistant mutation is due to a threonine to isoleucine change at amino acid residue 942. The mutant CS gene can be used to impart herbicide resistance to a plant; thereby permitting the utilization of the herbicide as a single application at a concentration which ensures the complete or substantially complete killing of weeds, while leaving the transgenic crop plant essentially undamaged.

  16. Nucleotide Binding Site Communication in Arabidopsis thaliana Adenosine 5′-Phosphosulfate Kinase*

    Science.gov (United States)

    Ravilious, Geoffrey E.; Jez, Joseph M.

    2012-01-01

    Adenosine 5′-phosphosulfate kinase (APSK) catalyzes the ATP-dependent synthesis of adenosine 3′-phosphate 5′-phosphosulfate (PAPS), which is an essential metabolite for sulfur assimilation in prokaryotes and eukaryotes. Using APSK from Arabidopsis thaliana, we examine the energetics of nucleotide binary and ternary complex formation and probe active site features that coordinate the order of ligand addition. Calorimetric analysis shows that binding can occur first at either nucleotide site, but that initial interaction at the ATP/ADP site was favored and enhanced affinity for APS in the second site by 50-fold. The thermodynamics of the two possible binding models (i.e. ATP first versus APS first) differs and implies that active site structural changes guide the order of nucleotide addition. The ligand binding analysis also supports an earlier suggestion of intermolecular interactions in the dimeric APSK structure. Crystallographic, site-directed mutagenesis, and energetic analyses of oxyanion recognition by the P-loop in the ATP/ADP binding site and the role of Asp136, which bridges the ATP/ADP and APS/PAPS binding sites, suggest how the ordered nucleotide binding sequence and structural changes are dynamically coordinated for catalysis. PMID:22810229

  17. Uptake and conversion of D-amino acids in Arabidopsis thaliana.

    Science.gov (United States)

    Gördes, Dirk; Kolukisaoglu, Üner; Thurow, Kerstin

    2011-02-01

    The D-enantiomers of proteinogenic amino acids fulfill essential functions in bacteria, fungi and animals. Just in the plant kingdom, the metabolism and role of D-amino acids (D-AAs) still remains unclear, although plants have to cope with significant amounts of these compounds from microbial decay in the rhizosphere. To fill this gap of knowledge, we tested the inhibitory effects of D-AAs on plant growth and established a method to quantitate 16 out of 19 proteinogenic amino acids and their D-enantiomers in plant tissue extracts. Therefore, the amino acids in the extracts were derivatized with Marfey's reagent and separated by HPLC-MS. We used two ecotypes (Col-0 and C24) and a mutant (lht1) of the model plant Arabidopsis thaliana to determine the influence and fate of exogenously applied D-AAs. All of them were found in high concentrations in the plant extracts after application, even in lht1, which points to additional transporters facilitating the import of D-AAs. The addition of particular amino acids (D-Trp, D-Phe, D-Met and D-His) led to the accumulation of the corresponding L-amino acid. In almost all cases, the application of a D-AA resulted in the accumulation of D-Ala and D-Glu. The presented results indicate that soil borne D-AAs can actively be taken up and metabolized via central metabolic routes.

  18. Post-translational Analysis of Arabidopsis thaliana Proteins in Response to Cyclic Guanosine Monophosphate Treatment

    KAUST Repository

    Parrott, Brian

    2011-12-12

    The introduction of mass spectrometry techniques to the field of biology has made possible the exploration of the proteome as a whole system as opposed to prior techniques, such as anti-body based assays or yeast two-hybrid studies, which were strictly limited to the study of a few proteins at a time. This practice has allowed for a systems biology approach of exploring the proteome, with the possibility of viewing entire pathways over increments of time. In this study, the effect of treating Arabidopsis thaliana suspension culture cells with 3’,5’-cyclic guanosine monophosphate (cGMP), which is a native second messenger, was examined. Samples were collected at four time points and proteins were extracted and enriched for both oxidation and phosphorylation before analysis via mass spectrometry. Preliminary results suggest a tendency towards an increased number of phosphorylated proteins as a result of cGMP treatment. The data also showed a sharp increase in methionine oxidation in response to the treatment, occurring within the first ten minutes. This finding suggests that cGMP may utilize methionine oxidation as a mechanism of signal transduction. As such, this study corroborates a growing body of evidence supporting the inclusion of methionine oxidation in intracellular signaling pathways.

  19. Root-level exposure reveals multiple physiological toxicity of triazine xenobiotics in Arabidopsis thaliana.

    Science.gov (United States)

    Alberto, Diana; Couée, Ivan; Sulmon, Cécile; Gouesbet, Gwenola

    2017-05-01

    Herbicides are pollutants of great concern due to environmental ubiquity resulting from extensive use in modern agriculture and persistence in soil and water. Studies at various spatial scales have also highlighted frequent occurrences of major herbicide breakdown products in the environment. Analysis of plant behavior toward such molecules and their metabolites under conditions of transient or persistent soil pollution is important for toxicity evaluation in the context of environmental risk assessment. In order to understand the mechanisms underlying the action of such environmental contaminants, the model plant Arabidopsis thaliana, which has been shown to be highly responsive to pesticides and other xenobiotics, was confronted with varying levels of the widely-used herbicide atrazine and of two of its metabolites, desethylatrazine and hydroxyatrazine, which are both frequently detected in water streams of agriculturally-intensive areas. After 24h of exposure to varying concentrations covering the range of triazine concentrations detected in the environment, root-level contaminations of atrazine, desethylatrazine and hydroxyatrazine were found to affect early growth and development in various dose-dependent and differential manners. Moreover, these differential effects of atrazine, desethylatrazine and hydroxyatrazine pointed to the involvement of distinct mechanisms directly affecting respiration and root development. The consequences of the identification of additional targets, in addition to the canonical photosystem II target, are discussed in relation with the ecotoxicological assessment of environmental xenobiotic contamination. Copyright © 2017 Elsevier GmbH. All rights reserved.

  20. Cryptic Genetic Variation for Arabidopsis thaliana Seed Germination Speed in a Novel Salt Stress Environment.

    Science.gov (United States)

    Yuan, Wei; Flowers, Jonathan M; Sahraie, Dustin J; Purugganan, Michael D

    2016-10-13

    The expansion of species ranges frequently necessitates responses to novel environments. In plants, the ability of seeds to disperse to marginal areas relies in part to its ability to germinate under stressful conditions. Here we examine the genetic architecture of Arabidopsis thaliana germination speed under a novel, saline environment, using an Extreme QTL (X-QTL) mapping platform we previously developed. We find that early germination in normal and salt conditions both rely on a QTL on the distal arm of chromosome 4, but we also find unique QTL on chromosomes 1, 2, 4, and 5 that are specific to salt stress environments. Moreover, different QTLs are responsible for early vs. late germination, suggesting a temporal component to the expression of life history under these stress conditions. Our results indicate that cryptic genetic variation exists for responses to a novel abiotic stress, which may suggest a role of such variation in adaptation to new climactic conditions or growth environments. Copyright © 2016 Yuan et al.

  1. Dynamics of vegetative cytoplasm during generative cell formation and pollen maturation in Arabidopsis thaliana

    Science.gov (United States)

    Kuang, A.; Musgrave, M. E.

    1996-01-01

    Ultrastructural changes of pollen cytoplasm during generative cell formation and pollen maturation in Arabidopsis thaliana were studied. The pollen cytoplasm develops a complicated ultrastructure and changes dramatically during these stages. Lipid droplets increase after generative cell formation and their organization and distribution change with the developmental stage. Starch grains in amyloplasts increase in number and size during generative and sperm cell formation and decrease at pollen maturity. The shape and membrane system of mitochondria change only slightly. Dictyosomes become very prominent, and numerous associated vesicles are observed during and after sperm cell formation. Endoplasmic reticulum appears extensively as stacks during sperm cell formation. Free and polyribosomes are abundant in the cytoplasm at all developmental stages although they appear denser at certain stages and in some areas. In mature pollen, all organelles are randomly distributed throughout the vegetative cytoplasm and numerous small particles appear. Organization and distribution of storage substances and appearance of these small particles during generative and sperm cell formation and pollen maturation are discussed.

  2. Investigation of the effect of phosphogypsum amendment on two Arabidopsis thaliana ecotype growth and development.

    Science.gov (United States)

    Ayadi, Amal; Chorriba, Amal; Fourati, Amine; Gargouri-Bouzid, Radhia

    2015-01-01

    The production of phosphoric acid from natural phosphate rock leads to an industrial waste called phosphogypsum (PG). About 5 tons of PG are generated per ton of phosphoric acid produced. This acidic waste (pH 2.2) is mostly disposed of by dumping into large stockpiles close to fertilizer production units, where they occupy large land areas that can cause serious environmental damages. Several attempts were made to test PG valorization via soil amendment because of its phosphate, sulphate and calcium content. The aim of the this study was to evaluate the potential use of PG as phosphate amendment in soil using two wild-type Arabidopsis thaliana ecotypes (Wassilewskija and Colombia) as model plants. Plants were grown in a greenhouse for 30 days, on substrates containing various PG concentrations (0%, 15%, 25%, 40% and 50%). The growth rate and physiological parameters (fresh weight, phosphate and chlorophyll content) were determined. The data revealed that 15% PG did not alter plant survival and leaf's dry weight, and the inorganic phosphate (Pi) uptake by plant seemed to be efficient. However, some alterations in Chlorophyll a/Chlorophyll b ratio were noticed. Higher PG concentrations (40 and 50% PG) exhibited an enhanced negative effect on plant growth, survival and Pi uptake. These inhibitory effects of the substrates may be related to the acidity of the medium in addition to its Cd content.

  3. Analysis of the transgenerational iron deficiency stress memory in Arabidopsis thaliana plants.

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    IRENE eMURGIA

    2015-09-01

    Full Text Available We investigated the existence of the transgenerational memory of iron (Fe deficiency stress, in Arabidopsis thaliana. Plants were grown under Fe deficiency/sufficiency, and so were their offspring. The frequency of Somatic Homologous Recombination (SHR events, of DNA strand breaks as well as the expression of the transcription elongation factor TFIIS-like gene increase when plants are grown under Fe deficiency. However, SHR frequency, DNA strand break events and TFIIS-like gene expression do not increase further when plants are grown for more than one generation under the same stress, and furthermore, they decrease back to control values within two succeeding generations grown under control conditions, regardless of the Fe deficiency stress history of the mother plants.Seedlings produced from plants grown under Fe deficiency evolve more oxygen than control seedlings, when grown under Fe sufficiency: however, this trait is not associated with any change in the protein profile of the photosynthetic apparatus and is not transmitted to more than one generation. Lastly, plants grown for multiple generations under Fe deficiency produce seeds with greater longevity: however this trait is not inherited in offspring generations unexposed to stress. These findings suggest the existence of multiple-step control of mechanisms to prevent a genuine and stable transgenerational transmission of Fe deficiency stress memory, with the tightest control on DNA integrity.

  4. Maternal environment affects the genetic basis of seed dormancy in Arabidopsis thaliana.

    Science.gov (United States)

    Postma, Froukje M; Ågren, Jon

    2015-02-01

    The genetic basis of seed dormancy, a key life history trait important for adaptive evolution in plant populations, has yet been studied only using seeds produced under controlled conditions in greenhouse environments. However, dormancy is strongly affected by maternal environmental conditions, and interactions between seed genotype and maternal environment have been reported. Consequently, the genetic basis of dormancy of seeds produced under natural field conditions remains unclear. We examined the effect of maternal environment on the genetic architecture of seed dormancy using a recombinant inbred line (RIL) population derived from a cross between two locally adapted populations of Arabidopsis thaliana from Italy and Sweden. We mapped quantitative trait loci (QTL) for dormancy of seeds produced in the greenhouse and at the native field sites of the parental genotypes. The Italian genotype produced seeds with stronger dormancy at fruit maturation than did the Swedish genotype in all three environments, and the maternal field environments induced higher dormancy levels compared to the greenhouse environment in both genotypes. Across the three maternal environments, a total of nine dormancy QTL were detected, three of which were only detected among seeds matured in the field, and six of which showed significant QTL × maternal environment interactions. One QTL had a large effect on dormancy across all three environments and colocalized with the candidate gene DOG1. Our results demonstrate the importance of studying the genetic basis of putatively adaptive traits under relevant conditions. © 2015 John Wiley & Sons Ltd.

  5. Metabolome analysis of Arabidopsis thaliana roots identifies a key metabolic pathway for iron acquisition.

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    Holger Schmidt

    Full Text Available Fe deficiency compromises both human health and plant productivity. Thus, it is important to understand plant Fe acquisition strategies for the development of crop plants which are more Fe-efficient under Fe-limited conditions, such as alkaline soils, and have higher Fe density in their edible tissues. Root secretion of phenolic compounds has long been hypothesized to be a component of the reduction strategy of Fe acquisition in non-graminaceous plants. We therefore subjected roots of Arabidopsis thaliana plants grown under Fe-replete and Fe-deplete conditions to comprehensive metabolome analysis by gas chromatography-mass spectrometry and ultra-pressure liquid chromatography electrospray ionization quadrupole time-of-flight mass spectrometry. Scopoletin and other coumarins were found among the metabolites showing the strongest response to two different Fe-limited conditions, the cultivation in Fe-free medium and in medium with an alkaline pH. A coumarin biosynthesis mutant defective in ortho-hydroxylation of cinnamic acids was unable to grow on alkaline soil in the absence of Fe fertilization. Co-cultivation with wild-type plants partially rescued the Fe deficiency phenotype indicating a contribution of extracellular coumarins to Fe solubilization. Indeed, coumarins were detected in root exudates of wild-type plants. Direct infusion mass spectrometry as well as UV/vis spectroscopy indicated that coumarins are acting both as reductants of Fe(III and as ligands of Fe(II.

  6. Identification of Adenyl Cyclase Activity in a Disease Resistance Protein in Arabidopsis thaliana

    KAUST Repository

    Hussein, Rana

    2012-11-01

    Cyclic nucleotide, cAMP, is an important signaling molecule in animals and plants. However, in plants the enzymes that synthesize this second messenger, adenyl cyclases (ACs), remain elusive. Given the physiological importance of cAMP in signaling, particularly in response to biotic and abiotic stresses, it is thus important to identify and characterize ACs in higher plants. Using computational approaches, a disease resistance protein from Arabidopsis thaliana, At3g04220 was found to have an AC catalytic center motif. In an attempt to prove that this candidate has adenyl cyclases activity in vitro, the coding sequence of the putative AC catalytic domain of this protein was cloned and expressed in E. coli and the recombinant protein was purified. The nucleotide cyclase activity of the recombinant protein was examined using cyclic nucleotide enzyme immunoassays. In parallel, the expression of At3g04220 was measured in leaves under three different stress conditions in order to determine under which conditions the disease resistance protein could function. Results show that the purified recombinant protein has Mn2+ dependent AC activity in vitro, and the expression analysis supports a role for At3g04220 and cAMP in plant defense.

  7. Structural characterization of the mechanosensitive channel candidate MCA2 from Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Hideki Shigematsu

    Full Text Available Mechanosensing in plants is thought to be governed by sensory complexes containing a Ca²⁺-permeable, mechanosensitive channel. The plasma membrane protein MCA1 and its paralog MCA2 from Arabidopsis thaliana are involved in mechanical stress-induced Ca²⁺ influx and are thus considered as candidates for such channels or their regulators. Both MCA1 and MCA2 were functionally expressed in Sf9 cells using a baculovirus system in order to elucidate their molecular natures. Because of the abundance of protein in these cells, MCA2 was chosen for purification. Purified MCA2 in a detergent-solubilized state formed a tetramer, which was confirmed by chemical cross-linking. Single-particle analysis of cryo-electron microscope images was performed to depict the overall shape of the purified protein. The three-dimensional structure of MCA2 was reconstructed at a resolution of 26 Å from 5,500 particles and appears to comprise a small transmembrane region and large cytoplasmic region.

  8. Intracellular Calcium Decreases Upon Hyper Gravity-Treatment of Arabidopsis Thaliana Cell Cultures

    Science.gov (United States)

    Neef, Maren; Denn, Tamara; Ecke, Margret; Hampp, Rüdiger

    2016-06-01

    Cell cultures of Arabidopsis thaliana ( A. t.) respond to changes in the gravitational field strength with fluctuations of the amount of cytosolic calcium (Ca2+). In parabolic flight experiments, where hyper- and μg phases follow each other, μg clearly increased Ca2+, while hyper-g caused a slight reduction. Since the latter observation had not been reported before, we studied this effect in more detail. Using a special centrifuge for heavy items (ZARM, Bremen, Germany), we determined the hyper-g-dependent intracellular Ca2+ level with transgenic cell lines expressing the Ca2+ sensor, cameleon. This sensor exhibits a shift in fluorescence from 480 to 530 nm in response to Ca2+ binding. The data show a drop in the intracellular Ca2+ concentration with a threshold gravity of around 3 g. This is above hypergravity levels achieved during parabolic flights (1.8 g). The use of mutants with different sub-cellular targets of cameleon expression (nucleus, tonoplast, plasma membrane) gave the same results, i.e. Ca2+ is obviously exported from several intracellular compartments.

  9. Crystal structure of the Epithiospecifier Protein, ESP from Arabidopsis thaliana provides insights into its product specificity.

    Science.gov (United States)

    Zhang, Weiwei; Wang, Wenhe; Liu, Zihe; Xie, Yongchao; Wang, Hao; Mu, Yajuan; Huang, Yao; Feng, Yue

    2016-09-16

    Specifier proteins are important components of the glucosinolate-myrosinase system, which mediate plant defense against herbivory and pathogen attacks. Upon tissue disruption, glucosinolates are hydrolyzed to instable aglucones by myrosinases, and then aglucones will rearrange to form defensive isothiocyanates. Specifier proteins can redirect this reaction to form other products, such as simple nitriles, epithionitriles and organic thiocyanates instead of isothiocyanates based on the side chain structure of glucosinolate and the type of the specifier proteins. Nevertheless, the molecular mechanism underlying the different product spectrums of various specifier proteins was not fully understood. Here in this study, we solved the crystal structure of the Epithiospecifier Protein, ESP from Arabidopsis thaliana (AtESP) at 2.3 Å resolution. Structural comparisons with the previously solved structure of thiocyanate forming protein, TFP from Thlaspi arvense (TaTFP) reveal that AtESP shows a dimerization pattern different from TaTFP. Moreover, AtESP harbors a slightly larger active site pocket than TaTFP and several residues around the active site are different between the two proteins, which might account for the different product spectrums of the two proteins. Together, our structural study provides important insights into the molecular mechanisms of specifier proteins and shed light on the basis of their different product spectrums. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. Sustained mitogen-activated protein kinase activation reprograms defense metabolism and phosphoprotein profile in Arabidopsis thaliana.

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    Ines eLassowskat

    2014-10-01

    Full Text Available Mitogen-activated protein kinases (MAPKs target a variety of protein substrates to regulate cellular signaling processes in eukaryotes. In plants, the number of identified MAPK substrates that control plant defense responses is still limited. Here, we generated transgenic Arabidopsis thaliana plants with an inducible system to simulate in vivo activation of two stress-activated MAPKs, MPK3 and MPK6. Metabolome analysis revealed that this artificial MPK3/6 activation (without any exposure to pathogens or other stresses is sufficient to drive the production of major defense-related metabolites, including various camalexin, indole glucosinolate and agmatine derivatives. An accompanying (phosphoproteome analysis led to detection of hundreds of potential phosphoproteins downstream of MPK3/6 activation. Besides known MAPK substrates, many candidates on this list possess typical MAPK-targeted phosphosites and in many cases, the corresponding phosphopeptides were detected by mass spectrometry. Notably, several of these putative phosphoproteins have been reported to be associated with the biosynthesis of antimicrobial defense substances (e.g. WRKY transcription factors and proteins encoded by the genes from the PEN pathway required for penetration resistance to filamentous pathogens. Thus, this work provides an inventory of candidate phosphoproteins, including putative direct MAPK substrates, for future analysis of MAPK-mediated defense control. (Proteomics data are available with the identifier PXD001252 via ProteomeXchange, http://proteomecentral.proteomexchange.org.

  11. Acclimation increases freezing stress response of Arabidopsis thaliana at proteome level

    KAUST Repository

    Fanucchi, Francesca

    2012-06-01

    This study used 2DE to investigate how Arabidopsis thaliana modulates protein levels in response to freezing stress after sub-lethal exposure at - 10 °C, both in cold-acclimated and in non-acclimated plants. A map was implemented in which 62 spots, corresponding to 44 proteins, were identified. Twenty-two spots were modulated upon treatments, and the corresponding proteins proved to be related to photosynthesis, energy metabolism, and stress response. Proteins demonstrated differences between control and acclimation conditions. Most of the acclimation-responsive proteins were either not further modulated or they were down-modulated by freezing treatment, indicating that the levels reached during acclimation were sufficient to deal with freezing. Anabolic metabolism appeared to be down-regulated in favor of catabolic metabolism. Acclimated plants and plants submitted to freezing after acclimation showed greater reciprocal similarity in protein profiles than either showed when compared both to control plants and to plants frozen without acclimation. The response of non-acclimated plants was aimed at re-modulating photosynthetic apparatus activity, and at increasing the levels of proteins with antioxidant-, molecular chaperone-, or post-transcriptional regulative functions. These changes, even less effective than the acclimation strategy, might allow the injured plastids to minimize the production of non-useful metabolites and might counteract photosynthetic apparatus injuries. © 2012 Elsevier B.V. All rights reserved.

  12. Microtubule Reorganization during Mitosis and Cytokinesis: Lessons Learned from Developing Microgametophytes in Arabidopsis thaliana

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    Bo eLiu

    2011-07-01

    Full Text Available In angiosperms, mitosis and cytokinesis take place in the absence of structurally defined microtubule-organizing centers and the underlying mechanisms are largely unknown. In the spindle and phragmoplast, microtubule reorganization depends on microtubule-interacting factors like the -tubulin complex. Because of their critical functions in cell division, loss-of-function mutations in the corresponding genes are often homozygous or sporophytic lethal. However, a number of mutations like gem1, gcp2, and nedd1 can be maintained in heterozygous mutants in Arabidopsis thaliana. When mutant microspores produced by a heterozygous parent undergo pollen mitosis I, they are amenable for phenotypic characterization by fluorescence microscopy. The results would allow us to pinpoint at specific functions of particular proteins in microtubule reorganization that are characteristic to specific stages of mitosis and cytokinesis. Conclusions made in the developing microgametophytes can be extrapolated to somatic cells regarding mechanisms that regulate nuclear migration, spindle pole formation, phragmoplast assembly, and cell division plane determination.

  13. Polyol specificity of recombinant Arabidopsis thaliana sorbitol dehydrogenase studied by enzyme kinetics and in silico modeling

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    María Francisca eAguayo

    2015-02-01

    Full Text Available Polyols are enzymatically-produced plant compounds which can act as compatible solutes during periods of abiotic stress. NAD+-dependent SORBITOL DEHYDROGENASE (SDH, E.C. 1.1.1.14 from Arabidopsis thaliana L. (AtSDH is capable of oxidizing several polyols including sorbitol, ribitol and xylitol. In the present study, enzymatic assays using recombinant AtSDH demonstrated a higher specificity constant for xylitol compared to sorbitol and ribitol, all of which are C2 (S and C4 (R polyols. Enzyme activity was reduced by preincubation with ethylenediaminetetraacetic acid (EDTA, indicating a requirement for zinc ions. In humans, it has been proposed that sorbitol becomes part of a pentahedric coordination sphere of the catalytic zinc during the reaction mechanism. In order to determine the validity of this pentahedric coordination model in a plant SDH, homology modeling and Molecular Dynamics simulations of AtSDH ternary complexes with the three polyols were performed using crystal structures of human and Bemisia argentifolii (Genn. (Hemiptera: Aleyrodidae SDHs as scaffolds. The results indicate that the differences in interaction with structural water molecules correlate very well with the observed enzymatic parameters, validate the proposed pentahedric coordination of the catalytic zinc ion in a plant SDH, and provide an explanation for why AtSDH shows a preference for polyols with a chirality of C2 (S and C4 (R.

  14. Induction of cell death by graphene in Arabidopsis thaliana (Columbia ecotype) T87 cell suspensions

    International Nuclear Information System (INIS)

    Begum, Parvin; Fugetsu, Bunshi

    2013-01-01

    Highlights: • This study was set up to explore potential influence of graphene on T87 cells. • Fragmented nuclei, membrane damage, mitochondrial dysfunction were observed. • ROS increased, ROS are key mediators in the cell death signaling pathway. • Translocation of graphene into cells and an endocytosis-like structure was observed. • Graphene entering into the cells by endocytosis. -- Abstract: The toxicity of graphene on suspensions of Arabidopsis thaliana (Columbia ecotype) T87 cells was investigated by examining the morphology, mitochondrial dysfunction, reactive oxygen species generation (ROS), and translocation of graphene as the toxicological endpoints. The cells were grown in Jouanneau and Péaud-Lenoel (JPL) media and exposed to graphene at concentrations 0–80 mg/L. Morphological changes were observed by scanning electron microscope and the adverse effects such as fragmented nuclei, membrane damage, mitochondrial dysfunction was observed with fluorescence microscopy by staining with Hoechst 33342/propidium iodide and succinate dehydrogenase (mitochondrial bioenergetic enzyme). Analysis of intracellular ROS by 2′,7′-dichlorofluorescein diacetate demonstrated that graphene induced a 3.3-fold increase in ROS, suggesting that ROS are key mediators in the cell death signaling pathway. Transmission electron microscopy verified the translocation of graphene into cells and an endocytosis-like structure was observed which suggested graphene entering into the cells by endocytosis. In conclusion, our results show that graphene induced cell death in T87 cells through mitochondrial damage mediated by ROS

  15. Rescue of syringyl lignin and sinapate ester biosynthesis in Arabidopsis thaliana by a coniferaldehyde 5-hydroxylase from Eucalyptus globulus.

    Science.gov (United States)

    García, José Renán; Anderson, Nickolas; Le-Feuvre, Regis; Iturra, Carolina; Elissetche, Juan; Chapple, Clint; Valenzuela, Sofía

    2014-08-01

    The gene coding for F5H from Eucalyptus globulus was cloned and used to transform an f5h -mutant of Arabidopsis thaliana , which was complemented, thus verifying the identity of the cloned gene. Coniferaldehyde 5-hydroxylase (F5H; EC 1.14.13) is a cytochrome P450-dependent monooxygenase that catalyzes the 5-hydroxylation step required for the production of syringyl units in lignin biosynthesis. The Eucalyptus globulus enzyme was characterized in vitro, and results showed that the preferred substrates were coniferaldehyde and coniferyl alcohol. Complementation experiments demonstrated that both cDNA and genomic constructs derived from F5H from E. globulus under the control of the cinnamate 4-hydroxylase promoter from Arabidopsis thaliana, or a partial F5H promoter from E. globulus, can rescue the inability of the A. thaliana fah1-2 mutant to accumulate sinapate esters and syringyl lignin. E. globulus is a species widely used to obtain products that require lignin removal, and the results suggest that EglF5H is a good candidate for engineering efforts aimed at increasing the lignin syringyl unit content, either for kraft pulping or biofuel production.

  16. Steroid-inducible BABY BOOM system for development of fertile Arabidopsis thaliana plants after prolonged tissue culture.

    Science.gov (United States)

    Lutz, Kerry A; Martin, Carla; Khairzada, Sahar; Maliga, Pal

    2015-10-01

    We describe a steroid-inducible BABY BOOM system that improves plant regeneration in Arabidopsis leaf cultures and yields fertile plants. Regeneration of Arabidopsis thaliana plants for extended periods of time in tissue culture may result in sterile plants. We report here a novel approach for A. thaliana regeneration using a regulated system to induce embryogenic cultures from leaf tissue. The system is based on BABY BOOM (BBM), a transcription factor that turns on genes involved in embryogenesis. We transformed the nucleus of A. thaliana plants with BBM:GR, a gene in which the BBM coding region is fused with the glucocorticoid receptor (GR) steroid-binding domain. In the absence of the synthetic steroid dexamethasone (DEX), the BBM:GR fusion protein is localized in the cytoplasm. Only when DEX is included in the culture medium does the BBM transcription factor enter the nucleus and turn on genes involved in embryogenesis. BBM:GR plant lines show prolific shoot regeneration from leaf pieces on media containing DEX. Removal of DEX from the culture media allowed for flowering and seed formation. Therefore, use of BBM:GR leaf tissue for regeneration of plants for extended periods of time in tissue culture will facilitate the recovery of fertile plants.

  17. The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Baumgarten Andrew

    2004-06-01

    Full Text Available Abstract Background Most genes in Arabidopsis thaliana are members of gene families. How do the members of gene families arise, and how are gene family copy numbers maintained? Some gene families may evolve primarily through tandem duplication and high rates of birth and death in clusters, and others through infrequent polyploidy or large-scale segmental duplications and subsequent losses. Results Our approach to understanding the mechanisms of gene family evolution was to construct phylogenies for 50 large gene families in Arabidopsis thaliana, identify large internal segmental duplications in Arabidopsis, map gene duplications onto the segmental duplications, and use this information to identify which nodes in each phylogeny arose due to segmental or tandem duplication. Examples of six gene families exemplifying characteristic modes are described. Distributions of gene family sizes and patterns of duplication by genomic distance are also described in order to characterize patterns of local duplication and copy number for large gene families. Both gene family size and duplication by distance closely follow power-law distributions. Conclusions Combining information about genomic segmental duplications, gene family phylogenies, and gene positions provides a method to evaluate contributions of tandem duplication and segmental genome duplication in the generation and maintenance of gene families. These differences appear to correspond meaningfully to differences in functional roles of the members of the gene families.

  18. The NADPH-oxidase AtRbohI plays a positive role in drought-stress response in Arabidopsis thaliana.

    Science.gov (United States)

    He, Huan; Yan, Jingwei; Yu, Xiaoyun; Liang, Yan; Fang, Lin; Scheller, Henrik Vibe; Zhang, Aying

    2017-09-23

    As the major resource of reactive oxygen species (ROS), the NADPH oxidases (Rbohs) have been shown to play important roles in plant cells under normal growth and stress conditions. Although many family members of Rbohs were studied, little is known about the function of RbohI in Arabidopsis thaliana. Here, we report that exogenous ABA application decreases RbohI expression and mannitol significantly increases RbohI expression at transcript level. The RbohI transcripts were strongly detected in dry seeds and roots. The loss-of-function mutant rbohI exhibited sensitivity to ABA and mannitol stress during germination. Furthermore, the lateral root growth of rbohI was severely inhibited after treatment with mannitol stress. Overexpression of RbohI in Arabidopsis significantly improves the drought tolerance. Moreover, more H 2 O 2 accumulated in RbohI overexpressors than in wild type plants in response to mannitol stress. Our conclusion is that AtRbohI functions in drought-stress response in Arabidopsis thaliana. Copyright © 2017. Published by Elsevier Inc.

  19. The NADPH-oxidase AtRbohI plays a positive role in drought-stress response in Arabidopsis thaliana

    Energy Technology Data Exchange (ETDEWEB)

    He, Huan [Nanjing Agricultural Univ. (China); Yan, Jingwei [Nanjing Agricultural Univ. (China); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Yu, Xiaoyun [Nanjing Agricultural Univ. (China); Liang, Yan [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Fang, Lin [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Scheller, Henrik Vibe [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Zhang, Aying [Nanjing Agricultural Univ. (China)

    2017-05-27

    As the major resource of reactive oxygen species (ROS), the NADPH oxidases (Rbohs) have been shown to play important roles in plant cells under normal growth and stress conditions. Although many family members of Rbohs were studied, little is known about the function of RbohI in Arabidopsis thaliana. Here, we report that exogenous ABA application decreases RbohI expression and mannitol significantly increases RbohI expression at transcript level. The RbohI transcripts were strongly detected in dry seeds and roots. The loss-of-function mutant rbohI exhibited sensitivity to ABA and mannitol stress during germination. Furthermore, the lateral root growth of rbohI was severely inhibited after treatment with mannitol stress. Overexpression of RbohI in Arabidopsis significantly improves the drought tolerance. Moreover, more H2O2 accumulated in RbohI overexpressors than in wild type plants in response to mannitol stress. Our conclusion is that AtRbohI functions in drought-stress response in Arabidopsis thaliana.

  20. The Opuntia streptacantha OpsHSP18 Gene Confers Salt and Osmotic Stress Tolerance in Arabidopsis thaliana

    Science.gov (United States)

    Salas-Muñoz, Silvia; Gómez-Anduro, Gracia; Delgado-Sánchez, Pablo; Rodríguez-Kessler, Margarita; Jiménez-Bremont, Juan Francisco

    2012-01-01

    Abiotic stress limits seed germination, plant growth, flowering and fruit quality, causing economic decrease. Small Heat Shock Proteins (sHSPs) are chaperons with roles in stress tolerance. Herein, we report the functional characterization of a cytosolic class CI sHSP (OpsHSP18) from Opuntia streptacantha during seed germination in Arabidopsis thaliana transgenic lines subjected to different stress and hormone treatments. The over-expression of the OpsHSP18 gene in A. thaliana increased the seed germination rate under salt (NaCl) and osmotic (glucose and mannitol) stress, and in ABA treatments, compared with WT. On the other hand, the over-expression of the OpsHSP18 gene enhanced tolerance to salt (150 mM NaCl) and osmotic (274 mM mannitol) stress in Arabidopsis seedlings treated during 14 and 21 days, respectively. These plants showed increased survival rates (52.00 and 73.33%, respectively) with respect to the WT (18.75 and 53.75%, respectively). Thus, our results show that OpsHSP18 gene might have an important role in abiotic stress tolerance, in particular in seed germination and survival rate of Arabidopsis plants under unfavorable conditions. PMID:22949853

  1. Naringenin inhibits seed germination and seedling root growth through a salicylic acid-independent mechanism in Arabidopsis thaliana.

    Science.gov (United States)

    Hernández, Iker; Munné-Bosch, Sergi

    2012-12-01

    Flavonoids fulfill an enormous range of biological functions in plants. In seeds, these compounds play several roles; for instance proanthocyanidins protect them from moisture, pathogen attacks, mechanical stress, UV radiation, etc., and flavonols have been suggested to protect the embryo from oxidative stress. The present study aimed at determining the role of flavonoids in Arabidopsis thaliana (L.) seed germination, and the involvement of salicylic acid (SA) and auxin (indole-3-acetic acid), two phytohormones with the same biosynthetic origin as flavonoids, the shikimate pathway, in such a putative role. We show that naringenin, a flavanone, strongly inhibits the germination of A. thaliana seeds in a dose-dependent and SA-independent manner. Altered auxin levels do not affect seed germination in Arabidopsis, but impaired auxin transport does, although to a minor extent. Naringenin and N-1-naphthylphthalamic acid (NPA) impair auxin transport through the same mechanisms, so the inhibition of germination by naringenin might involve impaired auxin transport among other mechanisms. From the present study it is concluded that naringenin inhibits the germination of Arabidopsis seeds in a dose-dependent and SA-independent manner, and the results also suggest that such effects are exerted, at least to some extent, through impaired auxin transport, although additional mechanisms seem to operate as well. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

  2. The application of Arabidopsis thaliana in studying tripartite interactions among plants, beneficial fungal endophytes and biotrophic plant-parasitic nematodes.

    Science.gov (United States)

    Martinuz, Alfonso; Zewdu, Getaneh; Ludwig, Nicole; Grundler, Florian; Sikora, Richard A; Schouten, Alexander

    2015-04-01

    The research demonstrated that Arabidopsis can be used as a model system for studying plant-nematode-endophyte tripartite interactions; thus, opening new possibilities for further characterizing the molecular mechanisms behind these interactions. Arabidopsis has been established as an important model system for studying plant biology and plant-microbe interactions. We show that this plant can also be used for studying the tripartite interactions among plants, the root-knot nematode Meloidogyne incognita and a beneficial endophytic isolate of Fusarium oxysporum, strain Fo162. In various plant species, Fo162 can systemically reduce M. incognita infection development and fecundity. Here it is shown that Fo162 can also colonize A. thaliana roots without causing disease symptoms, thus behaving as a typical endophyte. As observed for other plants, this endophyte could not migrate from the roots into the shoots and leaves. Direct inoculation of the leaves also did not result in colonization of the plant. A significant increase in plant fresh weight, root length and average root diameter was observed, suggesting the promotion of plant growth by the endophyte. The inoculation of A. thaliana with F. oxysporum strain Fo162 also resulted in a significant reduction in the number of M. incognita juveniles infecting the roots and ultimately the number of galls produced. This was also observed in a split-root experiment, in which the endophyte and nematode were spatially separated. The usefulness of Arabidopsis opens new possibilities for further dissecting complex tripartite interactions at the molecular and biochemical level.

  3. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.

    Science.gov (United States)

    Ding, Yong; Liu, Ning; Virlouvet, Laetitia; Riethoven, Jean-Jack; Fromm, Michael; Avramova, Zoya

    2013-12-30

    How plants respond to dehydration stress has been extensively researched. However, how plants respond to multiple consecutive stresses is virtually unknown. Pre-exposure to various abiotic stresses (including dehydration) may alter plants' subsequent responses by improving resistance to future exposures. These observations have led to the concept of 'stress memory' implying that during subsequent exposures plants provide responses that are different from those during their first encounter with the stress. Genes that provide altered responses in a subsequent stress define the 'memory genes' category; genes responding similarly to each stress form the 'non-memory' category. Using a genome-wide RNA-Seq approach we determine the transcriptional responses of Arabidopsis plants that have experienced multiple exposures to dehydration stress and compare them with the transcriptional behavior of plants encountering the stress for the first time. The major contribution of this study is the revealed existence of four distinct, previously unknown, transcription memory response patterns of dehydration stress genes in A.thaliana. The biological relevance for each of the four memory types is considered in the context of four overlapping strategies employed by a plant to improve its stress tolerance and/or survival: 1) increased synthesis of protective, damage-repairing, and detoxifying functions; 2) coordinating photosynthesis and growth under repetitive stress; 3) re-adjusting osmotic and ionic equilibrium to maintain homeostasis; and 4) re-adjusting interactions between dehydration and other stress/hormone regulated pathways. The results reveal the unknown, hitherto, existence of four distinct transcription memory response types in a plant and provide genome-wide characterization of memory and non-memory dehydration stress response genes in A.thaliana. The transcriptional responses during repeated exposures to stress are different from known responses occurring during a single

  4. Genetic and environmental control of the Verticillium syndrome in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Diederichsen Elke

    2010-11-01

    Full Text Available Abstract Background Verticillium spp. are major pathogens of dicotyledonous plants such as cotton, tomato, olive or oilseed rape. Verticillium symptoms are often ambiguous and influenced by development and environment. The aim of the present study was to define disease and resistance traits of the complex Verticillium longisporum syndrome in Arabidopsis thaliana (L. Heynh. A genetic approach was used to determine genetic, developmental and environmental factors controlling specific disease and resistance traits and to study their interrelations. Results A segregating F2/F3 population originating from ecotypes 'Burren' (Bur and 'Landsberg erecta' (Ler was established. Plants were root-dip inoculated and tested under greenhouse conditions. The Verticillium syndrome was dissected into components like systemic spread, stunting, development time and axillary branching. Systemic spread of V. longisporum via colonisation of the shoot was extensive in Ler; Bur showed a high degree of resistance against systemic spread. Fungal colonisation of the shoot apex was determined by (a determining the percentage of plants from which the fungus could be re-isolated and (b measuring fungal DNA content with quantitative real-time PCR (qPCR. Four quantitative trait loci (QTL controlling systemic spread were identified for the percentage of plants showing fungal outgrowth, two of these QTL were confirmed with qPCR data. The degree of colonisation by V. longisporum was negatively correlated with development time. QTL controlling development time showed some overlap with QTL for resistance to systemic spread. Stunting depended on host genotype, development time and seasonal effects. Five QTL controlling this trait were identified which did not co-localize with QTL controlling systemic spread. V. longisporum induced increased axillary branching in Bur; two QTL controlling this reaction were found. Conclusions Systemic spread of V. longisporum in the host as well as

  5. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana

    Science.gov (United States)

    2013-01-01

    Background How plants respond to dehydration stress has been extensively researched. However, how plants respond to multiple consecutive stresses is virtually unknown. Pre-exposure to various abiotic stresses (including dehydration) may alter plants’ subsequent responses by improving resistance to future exposures. These observations have led to the concept of ‘stress memory’ implying that during subsequent exposures plants provide responses that are different from those during their first encounter with the stress. Genes that provide altered responses in a subsequent stress define the ‘memory genes’ category; genes responding similarly to each stress form the ‘non-memory’ category. Results Using a genome-wide RNA-Seq approach we determine the transcriptional responses of Arabidopsis plants that have experienced multiple exposures to dehydration stress and compare them with the transcriptional behavior of plants encountering the stress for the first time. The major contribution of this study is the revealed existence of four distinct, previously unknown, transcription memory response patterns of dehydration stress genes in A.thaliana. The biological relevance for each of the four memory types is considered in the context of four overlapping strategies employed by a plant to improve its stress tolerance and/or survival: 1) increased synthesis of protective, damage-repairing, and detoxifying functions; 2) coordinating photosynthesis and growth under repetitive stress; 3) re-adjusting osmotic and ionic equilibrium to maintain homeostasis; and 4) re-adjusting interactions between dehydration and other stress/hormone regulated pathways. Conclusions The results reveal the unknown, hitherto, existence of four distinct transcription memory response types in a plant and provide genome-wide characterization of memory and non-memory dehydration stress response genes in A.thaliana. The transcriptional responses during repeated exposures to stress are different

  6. Dehydration stress memory genes of Zea mays; comparison with Arabidopsis thaliana

    Science.gov (United States)

    2014-01-01

    Background Pre-exposing plants to diverse abiotic stresses may alter their physiological and transcriptional responses to a subsequent stress, suggesting a form of “stress memory”. Arabidopsis thaliana plants that have experienced multiple exposures to dehydration stress display transcriptional behavior suggesting “memory” from an earlier stress. Genes that respond to a first stress by up-regulating or down-regulating their transcription but in a subsequent stress provide a significantly different response define the ‘memory genes’ category. Genes responding similarly to each stress form the ‘non-memory’ category. It is unknown whether such memory responses exists in other Angiosperm lineages and whether memory is an evolutionarily conserved response to repeated dehydration stresses. Results Here, we determine the transcriptional responses of maize (Zea mays L.) plants that have experienced repeated exposures to dehydration stress in comparison with plants encountering the stress for the first time. Four distinct transcription memory response patterns similar to those displayed by A. thaliana were revealed. The most important contribution is the evidence that monocot and eudicot plants, two lineages that have diverged 140 to 200 M years ago, display similar abilities to ‘remember’ a dehydration stress and to modify their transcriptional responses, accordingly. The highly sensitive RNA-Seq analyses allowed to identify genes that function similarly in the two lineages, as well as genes that function in species-specific ways. Memory transcription patterns indicate that the transcriptional behavior of responding genes under repeated stresses is different from the behavior during an initial dehydration stress, suggesting that stress memory is a complex phenotype resulting from coordinated responses of multiple signaling pathways. Conclusions Structurally related genes displaying the same memory responses in the two species would suggest conservation

  7. Bacillus subtilis Early Colonization of Arabidopsis thaliana Roots Involves Multiple Chemotaxis Receptors.

    Science.gov (United States)

    Allard-Massicotte, Rosalie; Tessier, Laurence; Lécuyer, Frédéric; Lakshmanan, Venkatachalam; Lucier, Jean-François; Garneau, Daniel; Caudwell, Larissa; Vlamakis, Hera; Bais, Harsh P; Beauregard, Pascale B

    2016-11-29

    Colonization of plant roots by Bacillus subtilis is mutually beneficial to plants and bacteria. Plants can secrete up to 30% of their fixed carbon via root exudates, thereby feeding the bacteria, and in return the associated B. subtilis bacteria provide the plant with many growth-promoting traits. Formation of a biofilm on the root by matrix-producing B. subtilis is a well-established requirement for long-term colonization. However, we observed that cells start forming a biofilm only several hours after motile cells first settle on the plant. We also found that intact chemotaxis machinery is required for early root colonization by B. subtilis and for plant protection. Arabidopsis thaliana root exudates attract B. subtilis in vitro, an activity mediated by the two characterized chemoreceptors, McpB and McpC, as well as by the orphan receptor TlpC. Nonetheless, bacteria lacking these chemoreceptors are still able to colonize the root, suggesting that other chemoreceptors might also play a role in this process. These observations suggest that A. thaliana actively recruits B. subtilis through root-secreted molecules, and our results stress the important roles of B. subtilis chemoreceptors for efficient colonization of plants in natural environments. These results demonstrate a remarkable strategy adapted by beneficial rhizobacteria to utilize carbon-rich root exudates, which may facilitate rhizobacterial colonization and a mutualistic association with the host. Bacillus subtilis is a plant growth-promoting rhizobacterium that establishes robust interactions with roots. Many studies have now demonstrated that biofilm formation is required for long-term colonization. However, we observed that motile B. subtilis mediates the first contact with the roots. These cells differentiate into biofilm-producing cells only several hours after the bacteria first contact the root. Our study reveals that intact chemotaxis machinery is required for the bacteria to reach the

  8. RNA interference in Agrobacterium rhizogenes-transformed roots of Arabidopsis and Medicago truncatula

    NARCIS (Netherlands)

    Limpens, E.H.M.; Ramos, J.; Franken, C.; Raz, V.; Compaan, B.; Franssen, H.; Bisseling, T.; Geurts, R.

    2004-01-01

    RNA interference (RNAi) is a powerful reverse genetic tool to study gene function. The data presented here show that Agrobacterium rhizogenes-mediated RNAi is a fast and effective tool to study genes involved in root biology. The Arabidopsis gene KOJAK, involved in root hair development, was

  9. Effect of BPA on the germination, root development, seedling growth and leaf differentiation under different light conditions in Arabidopsis thaliana.

    Science.gov (United States)

    Pan, Wen-Juan; Xiong, Can; Wua, Qiu-Ping; Liu, Jin-Xia; Liao, Hong-Mei; Chen, Wei; Liu, Yong-Sheng; Zheng, Lei

    2013-11-01

    Bisphenol A (BPA) is a well-known environmental toxic substance, which exerts unfavorable effects through endocrine disruptor (ER)-dependent and ER-independent mechanisms to threaten ecological systems seriously. BPA may also interact with other environmental factors, such as light and heavy metals, to have a synergetic effect in plants. However, there is little data concerning the toxic effect of BPA on the primary producers-plants and its possible interaction with light-dependent response. Here, the effects of BPA on germination, fresh weight, tap root length, and leaf differentiation were studied in Arabidopsis thaliana under different parts of light spectrum (dark, red, yellow, green, blue, and white light). Our results showed that low-dose BPA (1.0, 5.0 µM) caused an increase in the fresh weight, the tap root length and the lateral root formation of A. thaliana seedlings, while high-dose BPA (10.0, 25.0 µM) show an inhibition effect in a dose-dependent manner. Unlike karrikins, the effects of BPA on germination fresh weight and tap roots length under various light conditions are similar, which imply that BPA has no notable role in priming light response in germination and early seedling growth in A. thaliana. Meanwhile, BPA exposure influences the differentiation of A. thaliana leaf blade significantly in a light-dependent manner with little to no effect in dark and clear effect under red illumination.

  10. Yeast cell wall extract induces disease resistance against bacterial and fungal pathogens in Arabidopsis thaliana and Brassica crop.

    Directory of Open Access Journals (Sweden)

    Mari Narusaka

    Full Text Available Housaku Monogatari (HM is a plant activator prepared from a yeast cell wall extract. We examined the efficacy of HM application and observed that HM treatment increased the resistance of Arabidopsis thaliana and Brassica rapa leaves to bacterial and fungal infections. HM reduced the severity of bacterial leaf spot and anthracnose on A. thaliana and Brassica crop leaves with protective effects. In addition, gene expression analysis of A. thaliana plants after treatment with HM indicated increased expression of several plant defense-related genes. HM treatment appears to induce early activation of jasmonate/ethylene and late activation of salicylic acid (SA pathways. Analysis using signaling mutants revealed that HM required SA accumulation and SA signaling to facilitate resistance to the bacterial pathogen Pseudomonas syringae pv. maculicola and the fungal pathogen Colletotrichum higginsianum. In addition, HM-induced resistance conferred chitin-independent disease resistance to bacterial pathogens in A. thaliana. These results suggest that HM contains multiple microbe-associated molecular patterns that activate defense responses in plants. These findings suggest that the application of HM is a useful tool that may facilitate new disease control methods.

  11. Genome-wide analysis of mutations in mutant lineages selected following fast-neutron irradiation mutagenesis of Arabidopsis thaliana

    KAUST Repository

    Belfield, E.J.

    2012-04-12

    Ionizing radiation has long been known to induce heritable mutagenic change in DNA sequence. However, the genome-wide effect of radiation is not well understood. Here we report the molecular properties and frequency of mutations in phenotypically selected mutant lines isolated following exposure of the genetic model flowering plant Arabidopsis thaliana to fast neutrons (FNs). Previous studies suggested that FNs predominantly induce deletions longer than a kilobase in A. thaliana. However, we found a higher frequency of single base substitution than deletion mutations. While the overall frequency and molecular spectrum of fast-neutron (FN)-induced single base substitutions differed substantially from those of "background" mutations arising spontaneously in laboratory-grown plants, G:C>A:T transitions were favored in both. We found that FN-induced G:C>A:T transitions were concentrated at pyrimidine dinucleotide sites, suggesting that FNs promote the formation of mutational covalent linkages between adjacent pyrimidine residues. In addition, we found that FNs induced more single base than large deletions, and that these single base deletions were possibly caused by replication slippage. Our observations provide an initial picture of the genome-wide molecular profile of mutations induced in A. thaliana by FN irradiation and are particularly informative of the nature and extent of genome-wide mutation in lines selected on the basis of mutant phenotypes from FN-mutagenized A. thaliana populations.

  12. Quantitative dose-response of growth and development in Arabidopsis thaliana exposed to chronic gamma-radiation

    International Nuclear Information System (INIS)

    Daly, K.; Thompson, K.H.

    1975-01-01

    The response of Arabidopsis thaliana (L.) Heynh. (Cruciferae) to a gradient of chronic gamma-radiation was examined under field conditions. Plants that were initially introduced to the gamma field as dry seeds received exposures of 1.34 to 18 800R/20 hour day from the time of seed germination. Regression analysis demonstrated a significant, but non-linear, response for three variables, number of seedlings emerging, number of plants flowering, and plant volume; the response of a fourth variable, number of leaves per plant, was not related to daily exposure. LD 50 values ranged from 66R/20 hour day for plant volume to 1231R/20 hour day for seedling emergence. Flowering and plant volume were the most sensitive indicators of radiation exposure. The demonstration of a variable threshold at low levels of exposure indicates that in nature A. thaliana may be exposed to environmental radiation throughout its life-cycle without significant modification of growth or development. (author)

  13. Accumulation of the coumarin scopolin under abiotic stress conditions is mediated by the Arabidopsis thaliana THO/TREX complex

    KAUST Repository

    Döll, Stefanie

    2017-12-09

    Secondary metabolites are involved in the plant stress response. Among these are scopolin and its active form scopoletin, which are coumarin derivatives associated with reactive oxygen species scavenging and pathogen defence. Here we show that scopolin accumulation can be induced in the root by osmotic stress and in the leaf by low-temperature stress in Arabidopsis thaliana. A genetic screen for altered scopolin levels in A. thaliana revealed a mutant compromised in scopolin accumulation in response to stress; the lesion was present in a homologue of THO1 coding for a subunit of the THO/TREX complex. The THO/TREX complex contributes to RNA silencing, supposedly by trafficking precursors of small RNAs. Mutants defective in THO, AGO1, SDS3 and RDR6 were impaired with respect to scopolin accumulation in response to stress, suggesting a mechanism based on RNA silencing such as the trans-acting small interfering RNA pathway, which requires THO/TREX function.

  14. Biochemical characterization of Arabidopsis thaliana starch branching enzyme 2.2 reveals an enzymatic positive cooperativity.

    Science.gov (United States)

    Wychowski, A; Bompard, C; Grimaud, F; Potocki-Véronèse, G; D'Hulst, C; Wattebled, F; Roussel, X

    2017-09-01

    Starch Branching Enzymes (SBE) catalyze the formation of α(1 → 6) branching points on starch polymers: amylopectin and amylose. SBEs are classified in two groups named type 1 and 2. Both types are present in the entire plant kingdom except in some species such as Arabidopsis thaliana that expresses two type 2 SBEs: BE2.1 and BE2.2. The present work describes in vitro enzymatic characterization of the recombinant BE2.2. The function of recombinant BE2.2 was characterized in vitro using spectrophotometry assay, native PAGE and HPAEC-PAD analysis. Size Exclusion Chromatography separation and SAXS experiments were used to identify the oligomeric state and for structural analysis of this enzyme. Optimal pH and temperature for BE2.2 activity were determined to be pH 7 and 25 °C. A glucosyl donor of at least 12 residues is required for BE2.2 activity. The reaction results in the transfer in an α(1 → 6) position of a glucan preferentially composed of 6 glucosyl units. In addition, BE2.2, which has been shown to be monomeric in absence of substrate, is able to adopt different active forms in presence of branched substrates, which affect the kinetic parameters. BE2.2 has substrate specificity similar to those of the other type-2 BEs. We propose that the different conformations of the enzyme displaying more or less affinity toward its substrates would explain the adjustment of the kinetic data to the Hill equation. This work describes the enzymatic parameters of Arabidopsis BE2.2. It reveals for the first time conformational changes for a branching enzyme, leading to a positive cooperative binding process of this enzyme. Copyright © 2017 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

  15. Biochemical quantitation of the eIF5A hypusination in Arabidopsis thaliana uncovers ABA-dependent regulation

    Science.gov (United States)

    Belda-Palazón, Borja; Nohales, María A.; Rambla, José L.; Aceña, José L.; Delgado, Oscar; Fustero, Santos; Martínez, M. Carmen; Granell, Antonio; Carbonell, Juan; Ferrando, Alejandro

    2014-01-01

    The eukaryotic translation elongation factor eIF5A is the only protein known to contain the unusual amino acid hypusine which is essential for its biological activity. This post-translational modification is achieved by the sequential action of the enzymes deoxyhypusine synthase (DHS) and deoxyhypusine hydroxylase (DOHH). The crucial molecular function of eIF5A during translation has been recently elucidated in yeast and it is expected to be fully conserved in every eukaryotic cell, however the functional description of this pathway in plants is still sparse. The genetic approaches with transgenic plants for either eIF5A overexpression or antisense have revealed some activities related to the control of cell death processes but the molecular details remain to be characterized. One important aspect of fully understanding this pathway is the biochemical description of the hypusine modification system. Here we have used recombinant eIF5A proteins either modified by hypusination or non-modified to establish a bi-dimensional electrophoresis (2D-E) profile for the three eIF5A protein isoforms and their hypusinated or unmodified proteoforms present in Arabidopsis thaliana. The combined use of the recombinant 2D-E profile together with 2D-E/western blot analysis from whole plant extracts has provided a quantitative approach to measure the hypusination status of eIF5A. We have used this information to demonstrate that treatment with the hormone abscisic acid produces an alteration of the hypusine modification system in Arabidopsis thaliana. Overall this study presents the first biochemical description of the post-translational modification of eIF5A by hypusination which will be functionally relevant for future studies related to the characterization of this pathway in Arabidopsis thaliana. PMID:24904603

  16. Study on transfer and effects of radioactive materials into plants. Study on transfer and effects of radioactive materials into arabidopsis thaliana (L.) Heynh

    International Nuclear Information System (INIS)

    Tsurudome, Koji; Tokizawa, Takayuki

    2000-05-01

    The method of evaluating genetic effects and the measuring method of radiation dose distribution were studied. DNA was extracted from the arabidopsis thaliana (L.) Heynh (A. thaliana) grow in mine soil. The sequence of chalcone synthase gene and cinnamate-4-hydroxylase gene were analysed. No gene mutation was observed. Radiation dose distribution was studied by using x-ray films and imaging plates. No biologically concentrated region was observed in plants. (A. Yamamoto)

  17. NMR structure of the single QALGGH zinc finger domain from the Arabidopsis thaliana SUPERMAN protein.

    Science.gov (United States)

    Isernia, Carla; Bucci, Enrico; Leone, Marilisa; Zaccaro, Laura; Di Lello, Paola; Digilio, Giuseppe; Esposito, Sabrina; Saviano, Michele; Di Blasio, Benedetto; Pedone, Carlo; Pedone, Paolo V; Fattorusso, Roberto

    2003-03-03

    Zinc finger domains of the classical type represent the most abundant DNA binding domains in eukaryotic transcription factors. Plant proteins contain from one to four zinc finger domains, which are characterized by high conservation of the sequence QALGGH, shown to be critical for DNA-binding activity. The Arabidopsis thaliana SUPERMAN protein, which contains a single QALGGH zinc finger, is necessary for proper spatial development of reproductive floral tissues and has been shown to specifically bind to DNA. Here, we report the synthesis and UV and NMR spectroscopic structural characterization of a 37 amino acid SUPERMAN region complexed to a Zn(2+) ion (Zn-SUP37) and present the first high-resolution structure of a classical zinc finger domain from a plant protein. The NMR structure of the SUPERMAN zinc finger domain consists of a very well-defined betabetaalpha motif, typical of all other Cys(2)-His(2) zinc fingers structurally characterized. As a consequence, the highly conserved QALGGH sequence is located at the N terminus of the alpha helix. This region of the domain of animal zinc finger proteins consists of hypervariable residues that are responsible for recognizing the DNA bases. Therefore, we propose a peculiar DNA recognition code for the QALGGH zinc finger domain that includes all or some of the amino acid residues at positions -1, 2, and 3 (numbered relative to the N terminus of the helix) and possibly others at the C-terminal end of the recognition helix. This study further confirms that the zinc finger domain, though very simple, is an extremely versatile DNA binding motif.

  18. Differential tolerance to direct and indirect density-dependent costs of viral infection in Arabidopsis thaliana.

    Science.gov (United States)

    Pagán, Israel; Alonso-Blanco, Carlos; García-Arenal, Fernando

    2009-07-01

    Population density and costs of parasite infection may condition the capacity of organisms to grow, survive and reproduce, i.e. their competitive ability. In host-parasite systems there are different competitive interactions: among uninfected hosts, among infected hosts, and between uninfected and infected hosts. Consequently, parasite infection results in a direct cost, due to parasitism itself, and in an indirect cost, due to modification of the competitive ability of the infected host. Theory predicts that host fitness reduction will be higher under the combined effects of costs of parasitism and competition than under each factor separately. However, experimental support for this prediction is scarce, and derives mostly from animal-parasite systems. We have analysed the interaction between parasite infection and plant density using the plant-parasite system of Arabidopsis thaliana and the generalist virus Cucumber mosaic virus (CMV). Plants of three wild genotypes grown at different densities were infected by CMV at various prevalences, and the effects of infection on plant growth and reproduction were quantified. Results demonstrate that the combined effects of host density and parasite infection may result either in a reduction or in an increase of the competitive ability of the host. The two genotypes investing a higher proportion of resources to reproduction showed tolerance to the direct cost of infection, while the genotype investing a higher proportion of resources to growth showed tolerance to the indirect cost of infection. Our findings show that the outcome of the interaction between host density and parasitism depends on the host genotype, which determines the plasticity of life-history traits and consequently, the host capacity to develop different tolerance mechanisms to the direct or indirect costs of parasitism. These results indicate the high relevance of host density and parasitism in determining the competitive ability of a plant, and stress

  19. Differential tolerance to direct and indirect density-dependent costs of viral infection in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Israel Pagán

    2009-07-01

    Full Text Available Population density and costs of parasite infection may condition the capacity of organisms to grow, survive and reproduce, i.e. their competitive ability. In host-parasite systems there are different competitive interactions: among uninfected hosts, among infected hosts, and between uninfected and infected hosts. Consequently, parasite infection results in a direct cost, due to parasitism itself, and in an indirect cost, due to modification of the competitive ability of the infected host. Theory predicts that host fitness reduction will be higher under the combined effects of costs of parasitism and competition than under each factor separately. However, experimental support for this prediction is scarce, and derives mostly from animal-parasite systems. We have analysed the interaction between parasite infection and plant density using the plant-parasite system of Arabidopsis thaliana and the generalist virus Cucumber mosaic virus (CMV. Plants of three wild genotypes grown at different densities were infected by CMV at various prevalences, and the effects of infection on plant growth and reproduction were quantified. Results demonstrate that the combined effects of host density and parasite infection may result either in a reduction or in an increase of the competitive ability of the host. The two genotypes investing a higher proportion of resources to reproduction showed tolerance to the direct cost of infection, while the genotype investing a higher proportion of resources to growth showed tolerance to the indirect cost of infection. Our findings show that the outcome of the interaction between host density and parasitism depends on the host genotype, which determines the plasticity of life-history traits and consequently, the host capacity to develop different tolerance mechanisms to the direct or indirect costs of parasitism. These results indicate the high relevance of host density and parasitism in determining the competitive ability of a

  20. A novel approach for determining environment-specific protein costs: the case of Arabidopsis thaliana.

    Science.gov (United States)

    Sajitz-Hermstein, Max; Nikoloski, Zoran

    2010-09-15

    Comprehensive understanding of cellular processes requires development of approaches which consider the energetic balances in the cell. The existing approaches that address this problem are based on defining energy-equivalent costs which do not include the effects of a changing environment. By incorporating these effects, one could provide a framework for integrating 'omics' data from various levels of the system in order to provide interpretations with respect to the energy state and to elicit conclusions about putative global energy-related response mechanisms in the cell. Here we define a cost measure for amino acid synthesis based on flux balance analysis of a genome-scale metabolic network, and develop methods for its integration with proteomics and metabolomics data. This is a first measure which accounts for the effect of different environmental conditions. We applied this approach to a genome-scale network of Arabidopsis thaliana and calculated the costs for all amino acids and proteins present in the network under light and dark conditions. Integration of function and process ontology terms in the analysis of protein abundances and their costs indicates that, during the night, the cell favors cheaper proteins compared with the light environment. However, this does not imply that there is squandering of resources during the day. The results from the association analysis between the costs, levels and well-defined expenses of amino acid synthesis, indicate that our approach not only captures the adjustment made at the switch of conditions, but also could explain the anticipation of resource usage via a global energy-related regulatory mechanism of amino acid and protein synthesis.

  1. Functional dissection of sugar signals affecting gene expression in Arabidopsis thaliana.

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    Sabine Kunz

    Full Text Available BACKGROUND: Sugars modulate expression of hundreds of genes in plants. Previous studies on sugar signaling, using intact plants or plant tissues, were hampered by tissue heterogeneity, uneven sugar transport and/or inter-conversions of the applied sugars. This, in turn, could obscure the identity of a specific sugar that acts as a signal affecting expression of given gene in a given tissue or cell-type. METHODOLOGY/PRINCIPAL FINDINGS: To bypass those biases, we have developed a novel biological system, based on stem-cell-like Arabidopsis suspension culture. The cells were grown in a hormone-free medium and were sustained on xylose as the only carbon source. Using functional genomics we have identified 290 sugar responsive genes, responding rapidly (within 1 h and specifically to low concentration (1 mM of glucose, fructose and/or sucrose. For selected genes, the true nature of the signaling sugar molecules and sites of sugar perception were further clarified using non-metabolizable sugar analogues. Using both transgenic and wild-type A. thaliana seedlings, it was shown that the expression of selected sugar-responsive genes was not restricted to a specific tissue or cell type and responded to photoperiod-related changes in sugar availability. This suggested that sugar-responsiveness of genes identified in the cell culture system was not biased toward heterotrophic background and resembled that in whole plants. CONCLUSIONS: Altogether, our research strategy, using a combination of cell culture and whole plants, has provided an unequivocal evidence for the identity of sugar-responsive genes and the identity of the sugar signaling molecules, independently from their inter-conversions or use for energy metabolism.

  2. Cell size and growth regulation in the Arabidopsis thaliana apical stem cell niche

    Science.gov (United States)

    Willis, Lisa; Refahi, Yassin; Wightman, Raymond; Landrein, Benoit; Teles, José; Huang, Kerwyn Casey; Meyerowitz, Elliot M.

    2016-01-01

    Cell size and growth kinetics are fundamental cellular properties with important physiological implications. Classical studies on yeast, and recently on bacteria, have identified rules for cell size regulation in single cells, but in the more complex environment of multicellular tissues, data have been lacking. In this study, to characterize cell size and growth regulation in a multicellular context, we developed a 4D imaging pipeline and applied it to track and quantify epidermal cells over 3–4 d in Arabidopsis thaliana shoot apical meristems. We found that a cell size checkpoint is not the trigger for G2/M or cytokinesis, refuting the unexamined assumption that meristematic cells trigger cell cycle phases upon reaching a critical size. Our data also rule out models in which cells undergo G2/M at a fixed time after birth, or by adding a critical size increment between G2/M transitions. Rather, cell size regulation was intermediate between the critical size and critical increment paradigms, meaning that cell size fluctuations decay by ∼75% in one generation compared with 100% (critical size) and 50% (critical increment). Notably, this behavior was independent of local cell–cell contact topologies and of position within the tissue. Cells grew exponentially throughout the first >80% of the cell cycle, but following an asymmetrical division, the small daughter grew at a faster exponential rate than the large daughter, an observation that potentially challenges present models of growth regulation. These growth and division behaviors place strong constraints on quantitative mechanistic descriptions of the cell cycle and growth control. PMID:27930326

  3. A Multiparent Advanced Generation Inter-Cross to fine-map quantitative traits in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Paula X Kover

    2009-07-01

    Full Text Available Identifying natural allelic variation that underlies quantitative trait variation remains a fundamental problem in genetics. Most studies have employed either simple synthetic populations with restricted allelic variation or performed association mapping on a sample of naturally occurring haplotypes. Both of these approaches have some limitations, therefore alternative resources for the genetic dissection of complex traits continue to be sought. Here we describe one such alternative, the Multiparent Advanced Generation Inter-Cross (MAGIC. This approach is expected to improve the precision with which QTL can be mapped, improving the outlook for QTL cloning. Here, we present the first panel of MAGIC lines developed: a set of 527 recombinant inbred lines (RILs descended from a heterogeneous stock of 19 intermated accessions of the plant Arabidopsis thaliana. These lines and the 19 founders were genotyped with 1,260 single nucleotide polymorphisms and phenotyped for development-related traits. Analytical methods were developed to fine-map quantitative trait loci (QTL in the MAGIC lines by reconstructing the genome of each line as a mosaic of the founders. We show by simulation that QTL explaining 10% of the phenotypic variance will be detected in most situations with an average mapping error of about 300 kb, and that if the number of lines were doubled the mapping error would be under 200 kb. We also show how the power to detect a QTL and the mapping accuracy vary, depending on QTL location. We demonstrate the utility of this new mapping population by mapping several known QTL with high precision and by finding novel QTL for germination data and bolting time. Our results provide strong support for similar ongoing efforts to produce MAGIC lines in other organisms.

  4. Carbon and hydrogen isotopic effects of stomatal density in Arabidopsis thaliana

    Science.gov (United States)

    Lee, Hyejung; Feakins, Sarah J.; Sternberg, Leonel da S. L.

    2016-04-01

    Stomata are key gateways mediating carbon uptake and water loss from plants. Varied stomatal densities in fossil leaves raise the possibility that isotope effects associated with the openness of exchange may have mediated plant wax biomarker isotopic proxies for paleovegetation and paleoclimate in the geological record. Here we use Arabidopsis thaliana, a widely used model organism, to provide the first controlled tests of stomatal density on carbon and hydrogen isotopic compositions of cuticular waxes. Laboratory grown wildtype and mutants with suppressed and overexpressed stomatal densities allow us to directly test the isotope effects of stomatal densities independent of most other environmental or biological variables. Hydrogen isotope (D/H) measurements of both plant waters and plant wax n-alkanes allow us to directly constrain the isotopic effects of leaf water isotopic enrichment via transpiration and biosynthetic fractionations, which together determine the net fractionation between irrigation water and n-alkane hydrogen isotopic composition. We also measure carbon isotopic fractionations of n-alkanes and bulk leaf tissue associated with different stomatal densities. We find offsets of +15‰ for δD and -3‰ for δ13C for the overexpressed mutant compared to the suppressed mutant. Since the range of stomatal densities expressed is comparable to that found in extant plants and the Cenozoic fossil record, the results allow us to consider the magnitude of isotope effects that may be incurred by these plant adaptive responses. This study highlights the potential of genetic mutants to isolate individual isotope effects and add to our fundamental understanding of how genetics and physiology influence plant biochemicals including plant wax biomarkers.

  5. Studies on gene expressions analyses for Arabidopsis thaliana plants stimulated by space flight condition

    Science.gov (United States)

    Lu, Jinying; Liu, Min; Pan, Yi; Li, Huasheng

    We carried out whole-genome microarray to screen the transcript profile of Arabidopsis thaliana seedlings after three treatment: space microgravity condition( Seedlings grown in microgravity state of space flight of SIMBOX on Shenzhou-8), 1g centrifugal force in space(Seedlings grown in 1g centrifugal force state of space flight of SIMBOX on Shenzhou-8) and ground control. The result of microarray analysis is as followed: There were 368 genes significantly differentially expressed in space microgravity condition compared with that in 1g centrifuge space condition. Space radiation caused 246 genes significantly differentially expressed between seedlings in 1g centrifuge space condition and ground control. Space conditions (including microgravity and radiation) caused 621 genes significantly differentially expressed between seedlings in space microgravity condition and ground control. Microgravity and radiation as a single factor can cause plant gene expression change, but two factors synergism can produce some new effects on plant gene expression. The function of differential expression genes were analyst by bioinformatics, and we found the expression of genes related with stress were more different, such as the dehydration of protein (dehydrin Xero2) expression is up-regulated 57 times; low-temperature-induced protein expression is up-regulated in 49 times; heat shock protein expression is up-regulated 20 times; transcription factor DREB2A expression increase 25 times; protein phosphatase 2C expression is up-regulated 14 times; transcription factor NAM-like protein expression is up-regulated 13 times; cell wall metabolism related genes (xyloglucan, endo-1, 4-beta-D-glucanase) expression is down-regulated in 15 times. The results provide scientific data for the mechanism of space mutation.

  6. An extensive (co-expression analysis tool for the cytochrome P450 superfamily in Arabidopsis thaliana

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    Provart Nicholas J

    2008-04-01

    Full Text Available Abstract Background Sequencing of the first plant genomes has revealed that cytochromes P450 have evolved to become the largest family of enzymes in secondary metabolism. The proportion of P450 enzymes with characterized biochemical function(s is however very small. If P450 diversification mirrors evolution of chemical diversity, this points to an unexpectedly poor understanding of plant metabolism. We assumed that extensive analysis of gene expression might guide towards the function of P450 enzymes, and highlight overlooked aspects of plant metabolism. Results We have created a comprehensive database, 'CYPedia', describing P450 gene expression in four data sets: organs and tissues, stress response, hormone response, and mutants of Arabidopsis thaliana, based on public Affymetrix ATH1 microarray expression data. P450 expression was then combined with the expression of 4,130 re-annotated genes, predicted to act in plant metabolism, for co-expression analyses. Based on the annotation of co-expressed genes from diverse pathway annotation databases, co-expressed pathways were identified. Predictions were validated for most P450s with known functions. As examples, co-expression results for P450s related to plastidial functions/photosynthesis, and to phenylpropanoid, triterpenoid and jasmonate metabolism are highlighted here. Conclusion The large scale hypothesis generation tools presented here provide leads to new pathways, unexpected functions, and regulatory networks for many P450s in plant metabolism. These can now be exploited by the community to validate the proposed functions experimentally using reverse genetics, biochemistry, and metabolic profiling.

  7. Heat shock protein Hsp90-2 expression in the Arabidopsis thaliana seedlings under clinorotation

    Science.gov (United States)

    Kozeko, Liudmyla

    Heat shock proteins 90 kDa (Hsp90) are abundant under normal conditions and induced by stress. This family is distinguished from other chaperones in that most of its substrates are signal transduction proteins. Previously, we determined some time-dependent increase in the Hsp90 level in pea seedlings in response to simulated microgravity that indicated a stress-reaction. However, expression of the individual members of the Hsp90 family have specific pattern. The purpose of this study was to investigate possible alterations in the gene expression pattern of cytosolic Hsp90-2 in Arabidopsis thaliana seedlings under 2D-clinorotation. To obtain detailed expression pattern of the HSP90-2 genes we used seeds that provides a resource of loss-of-function mutations gene expression patterns via translational fusions with the reporter gene, GUS (a line N 166718, NASC). There were two variants of the experiment: 1) seedlings grew under clinorotation for 10, 12, 14 d; 2) seedlings grew in the stationary conditions for 10 d followed by clinorotation for 3 h -at 22o C and 16h light cycle. The seedlings grown in the stationary conditions were used as a control. GUS staining showed that HSP90-2 expression was regulated during seedling development and affected by clinorotation in the heterozygous mutant plants. In the homozygous for the mutation plants, HSP90-2 expression was stable during seedling development and not affected by clinorotation. GUS staining was observed in cotyledons, leaves and hypocotyls of the seedlings (especially intense in vascular bundles), indicating intensive cellular processes with participation of this chaperone. Possible pathways of influence of clinorotation on HSP90-2 expression are discussed.

  8. Regulation of anthocyanin biosynthesis in Arabidopsis thaliana red pap1-D cells metabolically programmed by auxins.

    Science.gov (United States)

    Liu, Zhong; Shi, Ming-Zhu; Xie, De-Yu

    2014-04-01

    Red pap1-D cells of Arabidopsis thaliana have been cloned from production of anthocyanin pigmentation 1-Dominant (pap1-D) plants. The red cells are metabolically programmed to produce high levels of anthocyanins by a WD40-bHLH-MYB complex that is composed of the TTG1, TT8/GL3 and PAP1 transcription factors. Here, we report that indole 3-acetic acid (IAA), naphthaleneacetic acid (NAA) and 2,4-dichlorophenoxyacetic acid (2,4-D) regulate anthocyanin biosynthesis in these red cells. Seven concentrations (0, 0.2, 0.4, 2.2, 9, 18 and 27 μM) were tested for the three auxins. IAA and 2,4-D at 2.2-27 μM reduced anthocyanin levels. NAA at 0-0.2 μM or above 9 μM also decreased anthocyanin levels, but from 0.4 to 9 μM, it increased them. HPLC-ESI-MS analysis identified seven cyanin molecules that were produced in red pap1-D cells, and their levels were affected by auxins. The expression levels of ten genes, including six transcription factors (TTG1, EGL3, MYBL2, TT8, GL3 and PAP1) and four pathway genes (PAL1, CHS, DFR and ANS) involved in anthocyanin biosynthesis were analyzed upon various auxin treatments. The resulting data showed that 2,4-D, NAA and IAA control anthocyanin biosynthesis by regulating the expression of TT8, GL3 and PAP1 as well as genes in the anthocyanin biosynthetic pathway, such as DFR and ANS. In addition, the expression of MYBL2, PAL1 and CHS in red pap1-D and wild-type cells differentially respond to the three auxins. Our data demonstrate that the three auxins regulate anthocyanin biosynthesis in metabolically programmed red cells via altering the expression of transcription factor genes and pathway genes.

  9. The induction of free proline accumulation by endogenous ABA in Arabidopsis thaliana during drought

    Energy Technology Data Exchange (ETDEWEB)

    Gottlieb, M.L.; Bray, E.A. (Univ. of California, Riverside (United States))

    1991-05-01

    Endogenous levels of abscisic acid (ABA) and free proline increase in response to drought stress. Exogenous ABA has been shown to induce proline accumulation, suggesting that ABA triggers the amino acid response. To determine if endogenous ABA induces free proline accumulation, increases in ABA and proline during drought stress were compared between wild type (WT), ABA-insensitive (abi) and ABA-deficient (aba) mutants of Arabidopsis thaliana. If elevated levels of endogenous ABA signal the proline response, then the mutants would not be expected to accumulate proline during stress. abi should be unable to respond to increased levels of endogenous ABA, while aba should be unable to accumulate sufficient ABA to elicit a proline response. Drought-stressed three week old shoots of WT, abi, and aba exhibited different patterns of endogenous ABA accumulation, but similar patterns of proline accumulation over 24 hours. Although the patterns of endogenous ABA accumulation differed, maximum levels were similar in WT and abi, but aba produced approximately 25% less. However, free proline accumulated in all three plant lines. abi exhibited a greater, more rapid increase in free proline over that in either WT or aba. aba, however, showed the same pattern and levels of accumulation as that in WT. Since free proline accumulated to at least similar levels in both WT and mutants, regardless of the levels of ABA accumulation, it may be that only a small endogenous ABA accumulation is required for proline accumulation. Alternatively, endogenous ABA may not be the direct signal for the proline response during drought stress.

  10. The effects of redox controls mediated by glutathione peroxidases on root architecture in Arabidopsis thaliana.

    Science.gov (United States)

    Passaia, Gisele; Queval, Guillaume; Bai, Juan; Margis-Pinheiro, Marcia; Foyer, Christine H

    2014-03-01

    Glutathione peroxidases (GPXs) fulfil important functions in oxidative signalling and protect against the adverse effects of excessive oxidation. However, there has been no systematic characterization of the functions of the different GPX isoforms in plants. The roles of the different members of the Arabidopsis thaliana GPX gene (AtGPX) family were therefore investigated using gpx1, gpx2, gpx3, gpx4, gpx6, gpx7, and gpx8 T-DNA insertion mutant lines. The shoot phenotypes were largely similar in all genotypes, with small differences from the wild type observed only in the gpx2, gpx3, gpx7, and gpx8 mutants. In contrast, all the mutants showed altered root phenotypes compared with the wild type. The gpx1, gpx4, gpx6, gpx7, and gpx8 mutants had a significantly greater lateral root density (LRD) than the wild type. Conversely, the gpx2 and gpx3 mutants had significantly lower LRD values than the wild type. Auxin increased the LRD in all genotypes, but the effect of auxin was significantly greater in the gpx1, gpx4, and gpx7 mutants than in the wild type. The application of auxin increased GPX4 and GPX7 transcripts, but not GPX1 mRNAs in the roots of wild-type plants. The synthetic strigolactone GR24 and abscisic acid (ABA) decreased LRD to a similar extent in all genotypes, except gpx6, which showed increased sensitivity to ABA. These data not only demonstrate the importance of redox controls mediated by AtGPXs in the control of root architecture but they also show that the plastid-localized GPX1 and GPX7 isoforms are required for the hormone-mediated control of lateral root development.

  11. Water stress and aphid feeding differentially influence metabolite composition in Arabidopsis thaliana (L..

    Directory of Open Access Journals (Sweden)

    Inga Mewis

    Full Text Available Little is known about how drought stress influences plant secondary metabolite accumulation and how this affects plant defense against different aphids. We therefore cultivated Arabidopsis thaliana (L. plants under well-watered, drought, and water-logged conditions. Two aphid species were selected for this study: the generalist Myzus persicae (Sulzer and the crucifer specialist Brevicoryne brassicae (L.. Metabolite concentrations in the phloem sap, which influence aphid growth, changed particularly under drought stress. Levels of sucrose and several amino acids, such as glutamic acid, proline, isoleucine, and lysine increased, while concentrations of 4-methoxyindol-3-ylmethyl glucosinolate decreased. M. persicae population growth was highest on plants under drought stress conditions. However, B. brassicae did not profit from improved phloem sap quality under drought stress and performed equally in all water treatments. Water stress and aphids generally had an opposite effect on the accumulation of secondary metabolites in the plant rosettes. Drought stress and water-logging led to increased aliphatic glucosinolate and flavonoid levels. Conversely, aphid feeding, especially of M. persicae, reduced levels of flavonoids and glucosinolates in the plants. Correspondingly, transcript levels of aliphatic biosynthetic genes decreased after feeding of both aphid species. Contrary to M. persicae, drought stress did not promote population growth of B. brassicae on these plants. The specialist aphid induced expression of CYP79B2, CYP79B3, and PAD3 with corresponding accumulation of indolyl glucosinolates and camalexin. This was distinct from M. persicae, which did not elicit similarly strong camalexin accumulation, which led to the hypothesis of a specific defense adaptations against the specialist aphid.

  12. Water stress and aphid feeding differentially influence metabolite composition in Arabidopsis thaliana (L.).

    Science.gov (United States)

    Mewis, Inga; Khan, Mohammed A M; Glawischnig, Erich; Schreiner, Monika; Ulrichs, Christian

    2012-01-01

    Little is known about how drought stress influences plant secondary metabolite accumulation and how this affects plant defense against different aphids. We therefore cultivated Arabidopsis thaliana (L.) plants under well-watered, drought, and water-logged conditions. Two aphid species were selected for this study: the generalist Myzus persicae (Sulzer) and the crucifer specialist Brevicoryne brassicae (L.). Metabolite concentrations in the phloem sap, which influence aphid growth, changed particularly under drought stress. Levels of sucrose and several amino acids, such as glutamic acid, proline, isoleucine, and lysine increased, while concentrations of 4-methoxyindol-3-ylmethyl glucosinolate decreased. M. persicae population growth was highest on plants under drought stress conditions. However, B. brassicae did not profit from improved phloem sap quality under drought stress and performed equally in all water treatments. Water stress and aphids generally had an opposite effect on the accumulation of secondary metabolites in the plant rosettes. Drought stress and water-logging led to increased aliphatic glucosinolate and flavonoid levels. Conversely, aphid feeding, especially of M. persicae, reduced levels of flavonoids and glucosinolates in the plants. Correspondingly, transcript levels of aliphatic biosynthetic genes decreased after feeding of both aphid species. Contrary to M. persicae, drought stress did not promote population growth of B. brassicae on these plants. The specialist aphid induced expression of CYP79B2, CYP79B3, and PAD3 with corresponding accumulation of indolyl glucosinolates and camalexin. This was distinct from M. persicae, which did not elicit similarly strong camalexin accumulation, which led to the hypothesis of a specific defense adaptations against the specialist aphid.

  13. Environmentally responsive genome-wide accumulation of de novo Arabidopsis thaliana mutations and epimutations

    KAUST Repository

    Jiang, Caifu

    2014-10-14

    Evolution is fueled by phenotypic diversity, which is in turn due to underlying heritable genetic (and potentially epigenetic) variation. While environmental factors are well known to influence the accumulation of novel variation in microorganisms and human cancer cells, the extent to which the natural environment influences the accumulation of novel variation in plants is relatively unknown. Here we use whole-genome and whole-methylome sequencing to test if a specific environmental stress (high-salinity soil) changes the frequency and molecular profile of accumulated mutations and epimutations (changes in cytosine methylation status) in mutation accumulation (MA) lineages of Arabidopsis thaliana. We first show that stressed lineages accumulate ∼100% more mutations, and that these mutations exhibit a distinctive molecular mutational spectrum (specific increases in relative frequency of transversion and insertion/deletion [indel] mutations). We next show that stressed lineages accumulate ∼45% more differentially methylated cytosine positions (DMPs) at CG sites (CG-DMPs) than controls, and also show that while many (∼75%) of these CG-DMPs are inherited, some can be lost in subsequent generations. Finally, we show that stress-associated CG-DMPs arise more frequently in genic than in nongenic regions of the genome. We suggest that commonly encountered natural environmental stresses can accelerate the accumulation and change the profiles of novel inherited variants in plants. Our findings are significant because stress exposure is common among plants in the wild, and they suggest that environmental factors may significantly alter the rates and patterns of incidence of the inherited novel variants that fuel plant evolution.

  14. Structural and functional characteristics of cGMP-dependent methionine oxidation in Arabidopsis thaliana proteins

    KAUST Repository

    Marondedze, Claudius

    2013-01-05

    Background: Increasing structural and biochemical evidence suggests that post-translational methionine oxidation of proteins is not just a result of cellular damage but may provide the cell with information on the cellular oxidative status. In addition, oxidation of methionine residues in key regulatory proteins, such as calmodulin, does influence cellular homeostasis. Previous findings also indicate that oxidation of methionine residues in signaling molecules may have a role in stress responses since these specific structural modifications can in turn change biological activities of proteins. Findings. Here we use tandem mass spectrometry-based proteomics to show that treatment of Arabidopsis thaliana cells with a non-oxidative signaling molecule, the cell-permeant second messenger analogue, 8-bromo-3,5-cyclic guanosine monophosphate (8-Br-cGMP), results in a time-dependent increase in the content of oxidised methionine residues. Interestingly, the group of proteins affected by cGMP-dependent methionine oxidation is functionally enriched for stress response proteins. Furthermore, we also noted distinct signatures in the frequency of amino acids flanking oxidised and un-oxidised methionine residues on both the C- and N-terminus. Conclusions: Given both a structural and functional bias in methionine oxidation events in response to a signaling molecule, we propose that these are indicative of a specific role of such post-translational modifications in the direct or indirect regulation of cellular responses. The mechanisms that determine the specificity of the modifications remain to be elucidated. 2013 Marondedze et al.; licensee BioMed Central Ltd.

  15. Water Stress and Aphid Feeding Differentially Influence Metabolite Composition in Arabidopsis thaliana (L.)

    Science.gov (United States)

    Mewis, Inga; Khan, Mohammed A. M.; Glawischnig, Erich; Schreiner, Monika; Ulrichs, Christian

    2012-01-01

    Little is known about how drought stress influences plant secondary metabolite accumulation and how this affects plant defense against different aphids. We therefore cultivated Arabidopsis thaliana (L.) plants under well-watered, drought, and water-logged conditions. Two aphid species were selected for this study: the generalist Myzus persicae (Sulzer) and the crucifer specialist Brevicoryne brassicae (L.). Metabolite concentrations in the phloem sap, which influence aphid growth, changed particularly under drought stress. Levels of sucrose and several amino acids, such as glutamic acid, proline, isoleucine, and lysine increased, while concentrations of 4-methoxyindol-3-ylmethyl glucosinolate decreased. M. persicae population growth was highest on plants under drought stress conditions. However, B. brassicae did not profit from improved phloem sap quality under drought stress and performed equally in all water treatments. Water stress and aphids generally had an opposite effect on the accumulation of secondary metabolites in the plant rosettes. Drought stress and water-logging led to increased aliphatic glucosinolate and flavonoid levels. Conversely, aphid feeding, especially of M. persicae, reduced levels of flavonoids and glucosinolates in the plants. Correspondingly, transcript levels of aliphatic biosynthetic genes decreased after feeding of both aphid species. Contrary to M. persicae, drought stress did not promote population growth of B. brassicae on these plants. The specialist aphid induced expression of CYP79B2, CYP79B3, and PAD3 with corresponding accumulation of indolyl glucosinolates and camalexin. This was distinct from M. persicae, which did not elicit similarly strong camalexin accumulation, which led to the hypothesis of a specific defense adaptations against the specialist aphid. PMID:23144921

  16. MicroRNA and tasiRNA diversity in mature pollen of Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Hafidh Said

    2009-12-01

    Full Text Available Abstract Background New generation sequencing technology has allowed investigation of the small RNA populations of flowering plants at great depth. However, little is known about small RNAs in their reproductive cells, especially in post-meiotic cells of the gametophyte generation. Pollen - the male gametophyte - is the specialised haploid structure that generates and delivers the sperm cells to the female gametes at fertilisation. Whether development and differentiation of the male gametophyte depends on the action of microRNAs and trans-acting siRNAs guiding changes in gene expression is largely unknown. Here we have used 454 sequencing to survey the various small RNA populations present in mature pollen of Arabidopsis thaliana. Results In this study we detected the presence of 33 different microRNA families in mature pollen and validated the expression levels of 17 selected miRNAs by Q-RT-PCR. The majority of the selected miRNAs showed pollen-enriched expression compared with leaves. Furthermore, we report for the first time the presence of trans-acting siRNAs in pollen. In addition to describing new patterns of expression for known small RNAs in each of these classes, we identified 7 putative novel microRNAs. One of these, ath-MIR2939, targets a pollen-specific F-box transcript and we demonstrate cleavage of its target mRNA in mature pollen. Conclusions Despite the apparent simplicity of the male gametophyte, comprising just two different cell types, pollen not only utilises many miRNAs and trans-acting siRNAs expressed in the somatic tissues but also expresses novel miRNAs.

  17. Bioinformatics analysis suggests base modifications of tRNAs and miRNAs in Arabidopsis thaliana

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    Jin Hailing

    2009-04-01

    Full Text Available Abstract Background Modifications of RNA bases have been found in some mRNAs and non-coding RNAs including rRNAs, tRNAs, and snRNAs, where modified bases are important for RNA function. Little is known about RNA base modifications in Arabidopsis thaliana. Results In the current work, we carried out a bioinformatics analysis of RNA base modifications in tRNAs and miRNAs using large numbers of cDNA sequences of small RNAs (sRNAs generated with the 454 technology and the massively parallel signature sequencing (MPSS method. We looked for sRNAs that map to the genome sequence with one-base mismatch (OMM, which indicate candidate modified nucleotides. We obtained 1,187 sites with possible RNA base modifications supported by both 454 and MPSS sequences. Seven hundred and three of these sites were within tRNA loci. Nucleotide substitutions were frequently located in the T arm (substitutions from A to U or G, upstream of the D arm (from G to C, U, or A, and downstream of the D arm (from G to U. The positions of major substitution sites corresponded with the following known RNA base modifications in tRNAs: N1-methyladenosine (m1A, N2-methylguanosine (m2G, and N2-N2-methylguanosine (m22G. Conclusion These results indicate that our bioinformatics method successfully detected modified nucleotides in tRNAs. Using this method, we also found 147 substitution sites in miRNA loci. As with tRNAs, substitutions from A to U or G and from G to C, U, or A were common, suggesting that base modifications might be similar in tRNAs and miRNAs. We suggest that miRNAs contain modified bases and such modifications might be important for miRNA maturation and/or function.

  18. Production of active human glucocerebrosidase in seeds of Arabidopsis thaliana complex-glycan-deficient (cgl) plants.

    Science.gov (United States)

    He, Xu; Galpin, Jason D; Tropak, Michael B; Mahuran, Don; Haselhorst, Thomas; von Itzstein, Mark; Kolarich, Daniel; Packer, Nicolle H; Miao, Yansong; Jiang, Liwen; Grabowski, Gregory A; Clarke, Lorne A; Kermode, Allison R

    2012-04-01

    There is a clear need for efficient methods to produce protein therapeutics requiring mannose-termination for therapeutic efficacy. Here we report on a unique system for production of active human lysosomal acid β-glucosidase (glucocerebrosidase, GCase, EC 3.2.1.45) using seeds of the Arabidopsis thaliana complex-glycan-deficient (cgl) mutant, which are deficient in the activity of N-acetylglucosaminyl transferase I (EC 2.4.1.101). Gaucher disease is a prevalent lysosomal storage disease in which affected individuals inherit mutations in the gene (GBA1) encoding GCase. A gene cassette optimized for seed expression was used to generate the human enzyme in seeds of the cgl (C5) mutant, and the recombinant GCase was mainly accumulated in the apoplast. Importantly, the enzymatic properties including kinetic parameters, half-maximal inhibitory concentration of isofagomine and thermal stability of the cgl-derived GCase were comparable with those of imiglucerase, a commercially available recombinant human GCase used for enzyme replacement therapy in Gaucher patients. N-glycan structural analyses of recombinant cgl-GCase showed that the majority of the N-glycans (97%) were mannose terminated. Additional purification was required to remove ∼15% of the plant-derived recombinant GCase that possessed potentially immunogenic (xylose- and/or fucose-containing) N-glycans. Uptake of cgl-derived GCase by mouse macrophages was similar to that of imiglucerase. The cgl seed system requires no addition of foreign (non-native) amino acids to the mature recombinant GCase protein, and the dry transgenic seeds represent a stable repository of the therapeutic protein. Other strategies that may completely prevent plant-like complex N-glycans are discussed, including the use of a null cgl mutant.

  19. Engineering the production of conjugated fatty acids in Arabidopsis thaliana leaves.

    Science.gov (United States)

    Yurchenko, Olga; Shockey, Jay M; Gidda, Satinder K; Silver, Maxwell I; Chapman, Kent D; Mullen, Robert T; Dyer, John M

    2017-08-01

    The seeds of many nondomesticated plant species synthesize oils containing high amounts of a single unusual fatty acid, many of which have potential usage in industry. Despite the identification of enzymes for unusual oxidized fatty acid synthesis, the production of these fatty acids in engineered seeds remains low and is often hampered by their inefficient exclusion from phospholipids. Recent studies have established the feasibility of increasing triacylglycerol content in plant leaves, which provides a novel approach for increasing energy density of biomass crops. Here, we determined whether the fatty acid composition of leaf oil could be engineered to accumulate unusual fatty acids. Eleostearic acid (ESA) is a conjugated fatty acid produced in seeds of the tung tree (Vernicia fordii) and has both industrial and nutritional end-uses. Arabidopsis thaliana lines with elevated leaf oil were first generated by transforming wild-type, cgi-58 or pxa1 mutants (the latter two of which contain mutations disrupting fatty acid breakdown) with the diacylglycerol acyltransferases (DGAT1 or DGAT2) and/or oleosin genes from tung. High-leaf-oil plant lines were then transformed with tung FADX, which encodes the fatty acid desaturase/conjugase responsible for ESA synthesis. Analysis of lipids in leaves revealed that ESA was efficiently excluded from phospholipids, and co-expression of tung FADX and DGAT2 promoted a synergistic increase in leaf oil content and ESA accumulation. Taken together, these results provide a new approach for increasing leaf oil content that is coupled with accumulation of unusual fatty acids. Implications for production of biofuels, bioproducts, and plant-pest interactions are discussed. © 2017 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

  20. Haemoglobin modulates NO emission and hyponasty under hypoxia-related stress in Arabidopsis thaliana

    Science.gov (United States)

    Hebelstrup, Kim H.

    2012-01-01

    Nitric oxide (NO) and ethylene are signalling molecules that are synthesized in response to oxygen depletion. Non-symbiotic plant haemoglobins (Hbs) have been demonstrated to act in roots under oxygen depletion to scavenge NO. Using Arabidopsis thaliana plants, the online emission of NO or ethylene was directly quantified under normoxia, hypoxia (0.1–1.0% O2), or full anoxia. The production of both gases was increased with reduced expression of either of the Hb genes GLB1 or GLB2, whereas NO emission decreased in plants overexpressing these genes. NO emission in plants with reduced Hb gene expression represented a major loss of nitrogen equivalent to 0.2mM nitrate per 24h under hypoxic conditions. Hb gene expression was greatly enhanced in flooded roots, suggesting induction by reduced oxygen diffusion. The function could be to limit loss of nitrogen under NO emission. NO reacts with thiols to form S-nitrosylated compounds, and it is demonstrated that hypoxia substantially increased the content of S-nitrosylated compounds. A parallel up-regulation of Hb gene expression in the normoxic shoots of the flooded plants may reflect signal transmission from root to shoot via ethylene and a role for Hb in the shoots. Hb gene expression was correlated with ethylene-induced upward leaf movement (hyponastic growth) but not with hypocotyl growth, which was Hb independent. Taken together the data suggest that Hb can influence flood-induced hyponasty via ethylene-dependent and, possibly, ethylene-independent pathways. PMID:22915746

  1. Chromium-Induced Ultrastructural Changes and Oxidative Stress in Roots of Arabidopsis thaliana

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    Eleftherios P. Eleftheriou

    2015-07-01

    Full Text Available Chromium (Cr is an abundant heavy metal in nature, toxic to living organisms. As it is widely used in industry and leather tanning, it may accumulate locally at high concentrations, raising concerns for human health hazards. Though Cr effects have extensively been investigated in animals and mammals, in plants they are poorly understood. The present study was then undertaken to determine the ultrastructural malformations induced by hexavalent chromium [Cr(VI], the most toxic form provided as 100 μM potassium dichromate (K2Cr2O7, in the root tip cells of the model plant Arabidopsis thaliana. A concentration-dependent decrease of root growth and a time-dependent increase of dead cells, callose deposition, hydrogen peroxide (H2O2 production and peroxidase activity were found in Cr(VI-treated seedlings, mostly at the transition root zone. In the same zone, nuclei remained ultrastructurally unaffected, but in the meristematic zone some nuclei displayed bulbous outgrowths or contained tubular structures. Endoplasmic reticulum (ER was less affected under Cr(VI stress, but Golgi bodies appeared severely disintegrated. Moreover, mitochondria and plastids became spherical and displayed translucent stroma with diminished internal membranes, but noteworthy is that their double-membrane envelopes remained structurally intact. Starch grains and electron dense deposits occurred in the plastids. Amorphous material was also deposited in the cell walls, the middle lamella and the vacuoles. Some vacuoles were collapsed, but the tonoplast appeared integral. The plasma membrane was structurally unaffected and the cytoplasm contained opaque lipid droplets and dense electron deposits. All electron dense deposits presumably consisted of Cr that is sequestered from sensitive sites, thus contributing to metal tolerance. It is concluded that the ultrastructural changes are reactive oxygen species (ROS-correlated and the malformations observed are organelle specific.

  2. TOR-Dependent and -Independent Pathways Regulate Autophagy in Arabidopsis thaliana.

    Science.gov (United States)

    Pu, Yunting; Luo, Xinjuan; Bassham, Diane C

    2017-01-01

    Autophagy is a critical process for recycling of cytoplasmic materials during environmental stress, senescence and cellular remodeling. It is upregulated under a wide range of abiotic stress conditions and is important for stress tolerance. Autophagy is repressed by the protein kinase target of rapamycin (TOR), which is activated in response to nutrients and in turn upregulates cell growth and translation and inhibits autophagy. Down-regulation of TOR in Arabidopsis thaliana leads to constitutive autophagy and to decreased growth, but the relationship to stress conditions is unclear. Here, we assess the extent to which TOR controls autophagy activation by abiotic stress. Overexpression of TOR inhibited autophagy activation by nutrient starvation, salt and osmotic stress, indicating that activation of autophagy under these conditions requires down-regulation of TOR activity. In contrast, TOR overexpression had no effect on autophagy induced by oxidative stress or ER stress, suggesting that activation of autophagy by these conditions is independent of TOR function. The plant hormone auxin has been shown previously to up-regulate TOR activity. To confirm the existence of two pathways for activation of autophagy, dependent on the stress conditions, auxin was added exogenously to activate TOR, and the effect on autophagy under different conditions was assessed. Consistent with the effect of TOR overexpression, the addition of the auxin NAA inhibited autophagy during nutrient deficiency, salt and osmotic stress, but not during oxidative or ER stress. NAA treatment was unable to block autophagy induced by a TOR inhibitor or by a mutation in the TOR complex component RAPTOR1B , indicating that auxin is upstream of TOR in the regulation of autophagy. We conclude that repression of auxin-regulated TOR activity is required for autophagy activation in response to a subset of abiotic stress conditions.

  3. Computational analysis of live cell images of the Arabidopsis thaliana plant.

    Science.gov (United States)

    Cunha, Alexandre; Tarr, Paul T; Roeder, Adrienne H K; Altinok, Alphan; Mjolsness, Eric; Meyerowitz, Elliot M

    2012-01-01

    Quantitative studies in plant developmental biology require monitoring and measuring the changes in cells and tissues as growth gives rise to intricate patterns. The success of these studies has been amplified by the combined strengths of two complementary techniques, namely live imaging and computational image analysis. Live imaging records time-lapse images showing the spatial-temporal progress of tissue growth with cells dividing and changing shape under controlled laboratory experiments. Image processing and analysis make sense of these data by providing computational ways to extract and interpret quantitative developmental information present in the acquired images. Manual labeling and qualitative interpretation of images are limited as they don't scale well to large data sets and cannot provide field measurements to feed into mathematical and computational models of growth and patterning. Computational analysis, when it can be made sufficiently accurate, is more efficient, complete, repeatable, and less biased. In this chapter, we present some guidelines for the acquisition and processing of images of sepals and the shoot apical meristem of Arabidopsis thaliana to serve as a basis for modeling. We discuss fluorescent markers and imaging using confocal laser scanning microscopy as well as present protocols for doing time-lapse live imaging and static imaging of living tissue. Image segmentation and tracking are discussed. Algorithms are presented and demonstrated together with low-level image processing methods that have proven to be essential in the detection of cell contours. We illustrate the application of these procedures in investigations aiming to unravel the mechanical and biochemical signaling mechanisms responsible for the coordinated growth and patterning in plants. Copyright © 2012 Elsevier Inc. All rights reserved.

  4. The response and recovery of the Arabidopsis thaliana transcriptome to phosphate starvation

    Directory of Open Access Journals (Sweden)

    Woo Jongchan

    2012-05-01

    Full Text Available Abstract Background Over application of phosphate fertilizers in modern agriculture contaminates waterways and disrupts natural ecosystems. Nevertheless, this is a common practice among farmers, especially in developing countries as abundant fertilizers are believed to boost crop yields. The study of plant phosphate metabolism and its underlying genetic pathways is key to discovering methods of efficient fertilizer usage. The work presented here describes a genome-wide resource on the molecular dynamics underpinning the response and recovery in roots and shoots of Arabidopsis thaliana to phosphate-starvation. Results Genome-wide profiling by micro- and tiling-arrays (accessible from GEO: GSE34004 revealed minimal overlap between root and shoot transcriptomes suggesting two independent phosphate-starvation regulons. Novel gene expression patterns were detected for over 1000 candidates and were classified as either initial, persistent, or latent responders. Comparative analysis to AtGenExpress identified cohorts of genes co-regulated across multiple stimuli. The hormone ABA displayed a dominant role in regulating many phosphate-responsive candidates. Analysis of co-regulation enabled the determination of specific versus generic members of closely related gene families with respect to phosphate-starvation. Thus, among others, we showed that PHR1-regulated members of closely related phosphate-responsive families (PHT1;1, PHT1;7–9, SPX1-3, and PHO1;H1 display greater specificity to phosphate-starvation than their more generic counterparts. Conclusion Our results uncover much larger, staged responses to phosphate-starvation than previously described. To our knowledge, this work describes the most complete genome-wide data on plant nutrient stress to-date.

  5. The Arabidopsis thaliana Cyclic-Nucleotide-Dependent Response – a Quantitative Proteomic and Phosphoproteomic Analysis

    KAUST Repository

    Alqurashi, May M.

    2013-11-01

    Protein phosphorylation governs many regulatory pathways and an increasing number of kinases, proteins that transfer phosphate groups, are in turn activated by cyclic nucleotides. One of the cyclic nucleotides, cyclic adenosine monophosphate (cAMP), has been shown to be a second messenger in abiotic and biotic stress responses. However, little is known about the precise role of cAMP in plants and in the down-stream activation of kinases, and hence cAMP-dependent phosphorylation. To increase our understanding of the role of cAMP, proteomic and phosphoproteomic profiles of Arabidopsis thaliana suspension culture cells were analyzed before and after treatment of cells with two different concentrations of 8-Bromo-cAMP (1 µM and 100 nM) and over a time-course of one hour. A comparative quantitative analysis was undertaken using two- dimensional gel electrophoresis and the Delta 2D software (DECODON) followed by protein spot identification by tandem mass spectrometry combined with Mascot and Scaffold. Differentially expressed proteins and regulated phosphoproteins were categorized according to their biological function using bioinformatics tools. The results revealed that the treatment with 1 µM and 100 nM 8-Bromo-cAMP was sufficient to induce specific concentration- and time-dependent changes at the proteome and phosphoproteome levels. In particular, different phosphorylation patterns were observed overtime preferentially affecting proteins in a number of functional categories, notably phosphatases, proteins that remove phosphate groups. This suggests that cAMP both transiently activates and deactivates proteins through specific phosphorylation events and provides new insight into biological mechanisms and functions at the systems level.

  6. Assessing the transcriptional regulation of L-CYSTEINE DESULFHYDRASE 1 in Arabidopsis thaliana

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    Ana M. Laureano-Marín

    2014-12-01

    Full Text Available Hydrogen sulfide is an important signaling molecule that functions as a physiological gasotransmitter of comparable importance to NO and CO in mammalian systems. In plants, numerous studies have shown that sulfide increases tolerance/resistance to stress conditions and regulates essential processes. The endogenous production of hydrogen sulfide in the cytosol of Arabidopsis thaliana occurs by the enzymatic desulfuration of L-cysteine, which is catalyzed by the L-cysteine desulfhydrase enzyme DES1. To define the functional role of DES1 and the role that the sulfide molecule may play in the regulation of physiological processes in plants, we studied the localization of the expression of this gene at the tissue level. Transcriptional data reveal that DES1 is expressed at all developmental stages and is more abundant at the seedling stage and in mature plants. At the tissue level, we analyzed the expression of a GFP reporter gene fused to promoter of DES1. The GFP fluorescent signal was detected in the cytosol of both epidermal and mesophyll cells, including the guard cells. GFP fluorescence was highly abundant around the hydathode pores and inside the trichomes. In mature plants, fluorescence was detected in floral tissues; a strong GFP signal was detected in sepals, petals and pistils. When siliques were examined, the highest GFP fluorescence was observed at the bases of the siliques and the seeds. The location of GFP expression, together with the identification of regulatory elements within the DES1 promoter, suggests that DES1 is hormonally regulated. An increase in DES1 expression in response to ABA was recently demonstrated; in the present work, we observe that in vitro auxin treatment significantly repressed the expression of DES1.

  7. The response and recovery of the Arabidopsis thaliana transcriptome to phosphate starvation

    KAUST Repository

    Woo, Jongchan

    2012-05-03

    Background: Over application of phosphate fertilizers in modern agriculture contaminates waterways and disrupts natural ecosystems. Nevertheless, this is a common practice among farmers, especially in developing countries as abundant fertilizers are believed to boost crop yields. The study of plant phosphate metabolism and its underlying genetic pathways is key to discovering methods of efficient fertilizer usage. The work presented here describes a genome-wide resource on the molecular dynamics underpinning the response and recovery in roots and shoots of Arabidopsis thaliana to phosphate-starvation.Results: Genome-wide profiling by micro- and tiling-arrays (accessible from GEO: GSE34004) revealed minimal overlap between root and shoot transcriptomes suggesting two independent phosphate-starvation regulons. Novel gene expression patterns were detected for over 1000 candidates and were classified as either initial, persistent, or latent responders. Comparative analysis to AtGenExpress identified cohorts of genes co-regulated across multiple stimuli. The hormone ABA displayed a dominant role in regulating many phosphate-responsive candidates. Analysis of co-regulation enabled the determination of specific versus generic members of closely related gene families with respect to phosphate-starvation. Thus, among others, we showed that PHR1-regulated members of closely related phosphate-responsive families (PHT1;1, PHT1;7-9, SPX1-3, and PHO1;H1) display greater specificity to phosphate-starvation than their more generic counterparts. Conclusion: Our results uncover much larger, staged responses to phosphate-starvation than previously described. To our knowledge, this work describes the most complete genome-wide data on plant nutrient stress to-date. 2012 Woo et al.; licensee BioMed Central Ltd.

  8. Real-time Recording of Cytosolic Calcium Levels in Arabidopsis thaliana Cell Cultures during Parabolic Flights

    Science.gov (United States)

    Neef, Maren; Ecke, Margret; Hampp, Rüdiger

    2015-07-01

    In plants, like in other organisms, calcium (Ca2+) is an important second messenger which participates in the conversion of environmental signals into molecular responses. There is increasing evidence, that sensing of changes in gravitation or reorientation of tissues is an example for such signaling cascades in which Ca2+ is involved. In order to determine g-dependent changes in the cytosolic calcium (Ca^{2+}_{ {cyt}}) concentration of plant cells, semisolid transgenic callus cell cultures of Arabidopsis thaliana (A.t.), expressing the calcium sensor YC3.6 (cameleon), were exposed to g-forces between 1.8 g and μ g during parabolic flights. Using such cells, intracellular calcium transients can be monitored by FRET in vivo and in real-time. Interestingly we observed a slight decrease of the Ca^{2+}_{ {cyt}} level during the hypergravity phases of a parabola but a significant increase of the Ca^{2+}_{ {cyt}} concentration during microgravity. Application of known Ca2+ inhibitors and antagonists yielded the following effects: nifedipine (Ca2+ channel blocker) showed no effect, whereas LaCl3, GdCl3 (both inhibitors of uptake at the plasma membrane), DPI (inhibitor of NADP oxidase), and DMSO (solvent) diminished the gravity-alteration-related Ca^{2+}_{ {cyt}} response. EGTA (binding of Ca2+) and eosin yellow (inhibitor of a plasma membrane-located Ca2+ pump) suppressed the respective Ca^{2+}_{ {cyt}} changes entirely. We thus conclude that the significant increase in Ca^{2+}_{ {cyt}} under microgravity is largely due to extracellular Ca2+ sources.

  9. Towards efficient photosynthesis: overexpression of Zea mays phosphoenolpyruvate carboxylase in Arabidopsis thaliana.

    Science.gov (United States)

    Kandoi, Deepika; Mohanty, Sasmita; Govindjee; Tripathy, Baishnab C

    2016-12-01

    Plants with C4 photosynthesis are efficient in carbon assimilation and have an advantage over C3 photosynthesis. In C4 photosynthesis, the primary CO 2 fixation is catalyzed by phosphoenolpyruvate carboxylase (PEPC). Here, we show that overexpression of Zea mays PEPC cDNA, under the control of 35 S promoter, in Arabidopsis thaliana resulted in ~7-10 fold higher protein abundance and ~7-10 fold increase in PEPC activity in the transgenic lines than that in the vector control. We suggest that overexpression of PEPC played an anaplerotic role to increase the supply of 4-carbon carboxylic acids, which provided carbon skeletons for