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Sample records for arabidopsis wrky2 transcription

  1. Isolation, Expression, and Promoter Analysis of GbWRKY2: A Novel Transcription Factor Gene from Ginkgo biloba

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    Yong-Ling Liao

    2015-01-01

    Full Text Available WRKY transcription factor is involved in multiple life activities including plant growth and development as well as biotic and abiotic responses. We identified 28 WRKY genes from transcriptome data of Ginkgo biloba according to conserved WRKY domains and zinc finger structure and selected three WRKY genes, which are GbWRKY2, GbWRKY16, and GbWRKY21, for expression pattern analysis. GbWRKY2 was preferentially expressed in flowers and strongly induced by methyl jasmonate. Here, we cloned the full-length cDNA and genomic DNA of GbWRKY2. The full-length cDNA of GbWRKY2 was 1,713 bp containing a 1,014 bp open reading frame encoding a polypeptide of 337 amino acids. The GbWRKY2 genomic DNA had one intron and two exons. The deduced GbWRKY2 contained one WRKY domain and one zinc finger motif. GbWRKY2 was classified into Group II WRKYs. Southern blot analysis revealed that GbWRKY2 was a single copy gene in G. biloba. Many cis-acting elements related to hormone and stress responses were identified in the 1,363 bp-length 5′-flanking sequence of GbWRKY2, including W-box, ABRE-motif, MYBCOREs, and PYRIMIDINE-boxes, revealing the molecular mechanism of upregulated expression of GbWRKY2 by hormone and stress treatments. Further functional characterizations in transiently transformed tobacco leaves allowed us to identify the region that can be considered as the minimal promoter.

  2. Isolation, Expression, and Promoter Analysis of GbWRKY2: A Novel Transcription Factor Gene from Ginkgo biloba

    Science.gov (United States)

    Liao, Yong-Ling; Shen, Yong-Bao; Chang, Jie; Zhang, Wei-Wei; Cheng, Shui-Yuan; Xu, Feng

    2015-01-01

    WRKY transcription factor is involved in multiple life activities including plant growth and development as well as biotic and abiotic responses. We identified 28 WRKY genes from transcriptome data of Ginkgo biloba according to conserved WRKY domains and zinc finger structure and selected three WRKY genes, which are GbWRKY2, GbWRKY16, and GbWRKY21, for expression pattern analysis. GbWRKY2 was preferentially expressed in flowers and strongly induced by methyl jasmonate. Here, we cloned the full-length cDNA and genomic DNA of GbWRKY2. The full-length cDNA of GbWRKY2 was 1,713 bp containing a 1,014 bp open reading frame encoding a polypeptide of 337 amino acids. The GbWRKY2 genomic DNA had one intron and two exons. The deduced GbWRKY2 contained one WRKY domain and one zinc finger motif. GbWRKY2 was classified into Group II WRKYs. Southern blot analysis revealed that GbWRKY2 was a single copy gene in G. biloba. Many cis-acting elements related to hormone and stress responses were identified in the 1,363 bp-length 5′-flanking sequence of GbWRKY2, including W-box, ABRE-motif, MYBCOREs, and PYRIMIDINE-boxes, revealing the molecular mechanism of upregulated expression of GbWRKY2 by hormone and stress treatments. Further functional characterizations in transiently transformed tobacco leaves allowed us to identify the region that can be considered as the minimal promoter. PMID:26351628

  3. 青花菜转录因子基因 BoWRKY2的克隆与表达分析%Cloning and expression analysis of a transcription factor gene BoWRKY2 from broccoli

    Institute of Scientific and Technical Information of China (English)

    蒋明; 陈贝贝; 管铭; 李金枝; 黄笑梅; 顾云吉

    2015-01-01

    Summary Broccoli ( Brassica oleracea var . italica) , which belongs to Cruciferae family , is a cash crop widely cultivated in China , and it is regarded as one of the most consumed vegetables in the world . The flower head of broccoli is rich in minerals , vitamins , fibers as well as anti‐oxidants , so it is recognized as a healthy vegetable with anti‐cancer properties . As a major broccoli production center in China , the average plantation areas reach to 8 000 hm2 in Taizhou of Zhejiang Province . However , broccoli cultivation suffered from plant diseases of downy mildew and stalk break which were caused by Hyaloperonospora parasitica and Sclerotinia sclerotiorum , respectively , resulting in yield and quality loss . WRKY transcription factors played important roles in plant stress responses , and WRKY domains were defined as an approximately 60‐amino acid motif named WRKYGQK as well as a zinc finger structure of C‐X4‐5‐C‐X2223‐H‐X1‐HattheirC‐terminus.TheWRKYdomainbindsspecificallytoDNAsequenceof(T)(T)TGAC(C/T) known as the W‐box which exists in defense‐related promoters . Enhanced disease resistance by overexpression of WRKY genes in different crop plants has been reported in recent years . Inthisstudy,aWRKYgenedesignatedasBoWRKY2,wasisolatedfromB.oleraceavar.italica.Basedon sequence analysis , expression patterns of BoWRKY2 were detected using reverse transcription‐polymerase chain reaction(RT‐PCR) methodwhilechallengedby H.parasiticaand S.sclerotiorum,respectively. The results showed that the genome DNA sequence was 1 507 bp in length with two introns and a complete coding sequence of 987 bp , and the length of two introns were 425 and 95 bp , respectively ; BoWRKY2 encoded 328 amino acids with a WRKYGQK residue and a zinc finger structure of C‐X5‐C‐X23‐H‐X1‐H . The WRKY domain located between 247 and 313 residues , and several DNA binding sites were found at sites of 66 , 67 , 69 , 71 , 74 , 281 , 282 , 283 and 317

  4. Cloning and expression pattern research under abiotic stress of theWRKY2 in potato%马铃薯WRKY2基因的克隆和非生物逆境下的表达模式

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    李立芹; 王西瑶

    2015-01-01

    Function of StWRKY2 has not been reported.Plant WRKY proteins are found as an important class of transcription factors in recent years,which are widely involved in biotic stress,abiotic stress and growth development regulation,and they are mainly divided into three groups.WRKY2 was cloned from potato by homology cloning, with length of the coding region 1 065 bp,encoding 355 amino acids by DNA sequencing.With the amino acid se-quence of StWRKY2 blasting in NCBI,19 homology amino acid sequences were selected to analysis conservative do-main.Amino acid analysis showed that the StWRKY2 contained 1 conserved WRKY domain (TTGACC)and be-longed to the second group of WRKY family members,and its zinc-finger structure was C-X5-C-X23 H-X-H.Phylog-eny tree results showed StWRKY2 was the most closest to SlWRKY7 (Solanum lycopersicum )with 96%similarity,and the similarity of a WRKY protein of tobacco was 86%.The protein-GST (glutathione-S-transferase) complex was obtained in Escherichia coli by using the method of prokaryotic expression.StWRKY2-GST could com-bine W-box in vivo by Electrophoretic Mobility Shift Assay analysis,but only GST protein could not combine W-box.StWRKY2-GST combination with W-box could be competed by cold probe(unlabeled probe).And the experi-ment results also showed that StWRKY2-GST could not combine mutation W-box,this suggested StWRKY2-GST combined W-box with specificity.Analysis of StWRKY2 expression level in the root,stem and leaf tissue through the real-time fluorescence quantitative PCR,the results showed that the gene was mainly expressed in the root.Next was leaf and stem.In order to further study the possible function of the gene,potato seeding from tissue culture were treated under 10 μmol/L low phosphorus,10 μmol/L low potassium,200 mmol/L NaCl,400 mmol/L PEG solution and 4 ℃ low-temperature treatment for 6 h,real-time fluorescence quantitative PCR showed that this gene expression level decreased significantly after low phosphorus

  5. Molecular screening tools to study Arabidopsis transcription factors

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    Nora eWehner

    2011-11-01

    Full Text Available In the model plant Arabidopsis thaliana, more than 2000 genes are estimated to encode transcription factors (TFs, which clearly emphasizes the importance of transcriptional control. Although genomic approaches have generated large TF Open Reading Frame (ORF collections, only a limited number of these genes is functionally characterized, yet. This review evaluates strategies and methods to identify TF functions. In particular, we focus on two recently developed TF screening platforms, which make use of publi-cally available GATEWAY® compatible ORF collections. (1 The Arabidopsis thaliana TF ORF over-Expression (AtTORF-Ex library provides pooled collections of transgenic lines over-expressing HA-tagged TF genes, which are suited for screening approaches to define TF functions in stress defense and development. (2 A high-throughput microtiter plate based Protoplast Trans Activation (PTA system has been established to screen for TFs which are regulating a given promoter:Luciferase construct in planta.

  6. Transcriptional Wiring of Cell Wall-Related Genes in Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    Marek Mutwil; Colin Ruprecht; Federico M. Giorgi; Martin Bringmann; Bj(o)rn Usadel; Staffan Persson

    2009-01-01

    Transcriptional coordination, or co-expression, of genes may signify functional relatedness of the correspond-ing proteins. For example, several genes involved in secondary cell wall cellulose biosynthesis are co-expressed with genes engaged in the synthesis of xylan, which is a major component of the secondary cell wall. To extend these types of anal-yses, we investigated the co-expression relationships of all Carbohydrate-Active enZYmes (CAZy)-related genes for Arabidopsis thaliana. Thus, the intention was to transcriptionally link different cell wall-related processes to each other, and also to other biological functions. To facilitate easy manual inspection, we have displayed these interactions as networks and matrices, and created a web-based interface (http://aranet.mpimp-golm.mpg.de/corecarb) containing downloadable files for all the transcriptional associations.

  7. Rethinking transcriptional activation in the Arabidopsis circadian clock.

    Science.gov (United States)

    Fogelmark, Karl; Troein, Carl

    2014-07-01

    Circadian clocks are biological timekeepers that allow living cells to time their activity in anticipation of predictable daily changes in light and other environmental factors. The complexity of the circadian clock in higher plants makes it difficult to understand the role of individual genes or molecular interactions, and mathematical modelling has been useful in guiding clock research in model organisms such as Arabidopsis thaliana. We present a model of the circadian clock in Arabidopsis, based on a large corpus of published time course data. It appears from experimental evidence in the literature that most interactions in the clock are repressive. Hence, we remove all transcriptional activation found in previous models of this system, and instead extend the system by including two new components, the morning-expressed activator RVE8 and the nightly repressor/activator NOX. Our modelling results demonstrate that the clock does not need a large number of activators in order to reproduce the observed gene expression patterns. For example, the sequential expression of the PRR genes does not require the genes to be connected as a series of activators. In the presented model, transcriptional activation is exclusively the task of RVE8. Predictions of how strongly RVE8 affects its targets are found to agree with earlier interpretations of the experimental data, but generally we find that the many negative feedbacks in the system should discourage intuitive interpretations of mutant phenotypes. The dynamics of the clock are difficult to predict without mathematical modelling, and the clock is better viewed as a tangled web than as a series of loops.

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

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    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.

  9. Arabidopsis transcriptional responses differentiating closely related chemicals (herbicides) and cross-species extrapolation to Brassica

    Science.gov (United States)

    Using whole genome Affymetrix ATH1 GeneChips we characterized the transcriptional response of Arabidopsis thaliana Columbia 24 hours after treatment with five different herbicides. Four of them (chloransulam, imazapyr, primisulfuron, sulfometuron) inhibit acetolactate synthase (A...

  10. Potential role of Arabidopsis PHP as an accessory subunit of the PAF1 transcriptional cofactor.

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    Park, Sunchung; Ek-Ramos, Maria Julissa; Oh, Sookyung; van Nocker, Steven

    2011-08-01

    Paf1C is a transcriptional cofactor that has been implicated in various transcription-associated mechanisms spanning initiation, elongation and RNA processing, and is important for multiple aspects of development in Arabidopsis. Our recent studies suggest Arabidopsis Paf1C is crucial for proper regulation of genes within H3K27me3-enriched chromatin, and that a protein named PHP may act as an accessory subunit of Paf1C that promotes this function.

  11. Subgroup-specific intrinsic disorder profiles of arabidopsis NAC transcription factors

    DEFF Research Database (Denmark)

    Stender, Emil G.; O'Shea, Charlotte; Skriver, Karen

    2015-01-01

    Protein intrinsic disorder (ID), referring to the lack of a fixed tertiary structure, is significant in signaling and transcription. We recently characterized ID in 6 phylogenetically representative Arabidopsis thaliana NAC transcription factors. Their transcription regulatory domains are mostly.......g. transcriptional activation and interactions. Based on our analysis, we suggest that ID profiling of regulatory proteins in general can be used to guide identification of interaction partners of network proteins....

  12. Analysis of a transcription factor using transient assay in Arabidopsis protoplasts.

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    Iwata, Yuji; Lee, Mi-Hyun; Koizumi, Nozomu

    2011-01-01

    Regulation of gene expression by transcription factors is a fundamental mechanism in essentially all aspects of cellular processes. Transient expression assay of a reporter plasmid containing a reporter gene driven by a promoter of interest and an effector plasmid expressing a transcription factor has been a powerful tool for analyzing transcription factors. Here we present a protocol for polyethylene glycol (PEG)-mediated transformation of Arabidopsis protoplasts. It details preparation of protoplasts from Arabidopsis suspension cultured cells or leaves of soil-grown Arabidopsis plants and subsequent PEG-mediated transformation with reporter and effector plasmids. This protocol can be completed within 24 h from protoplast preparation to reporter assay. As an example, analysis of the membrane-bound transcription factor AtbZIP60 and its target BiP3 promoter is shown.

  13. Exploring membrane-associated NAC transcription factors in Arabidopsis: implications for membrane biology in genome regulation

    OpenAIRE

    Kim, Sun-Young; Kim, Sang-Gyu; Kim, Youn-Sung; Seo, Pil Joon; Bae, Mikyoung; Yoon, Hye-Kyung; Park, Chung-Mo

    2006-01-01

    Controlled proteolytic cleavage of membrane-associated transcription factors (MTFs) is an intriguing activation strategy that ensures rapid transcriptional responses to incoming stimuli. Several MTFs are known to regulate diverse cellular functions in prokaryotes, yeast, and animals. In Arabidopsis, a few NAC MTFs mediate either cytokinin signaling during cell division or endoplasmic reticulum (ER) stress responses. Through genome-wide analysis, it was found that at least 13 members of the NA...

  14. Functional analysis of jasmonate-responsive transcription factors in Arabidopsis thaliana

    NARCIS (Netherlands)

    Zarei, Adel

    2007-01-01

    The aim of the studies described in this thesis was the functional analysis of JA-responsive transcription factors in Arabidopsis with an emphasis on the interaction with the promoters of their target genes. In short, the following new results were obtained. The promoter of the PDF1.2 gene contains

  15. Post-transcriptional gene silencing signal could move rapidly and bidirectionally in grafted Arabidopsis thaliana

    Institute of Scientific and Technical Information of China (English)

    LI Ming; JIANG Shiling; WANG Youqun; LIU Guoqin

    2006-01-01

    RNA interference (RNAi), one of the newly found ways for post-transcriptional gene silencing, has been widely used to investigate gene functions through transgenic methods for introducing an RNA silencing signal into plants. In the present study, we constructed a dexamethazone (DEX)-inducible RNAi binary vector harboring a specific sequence fragment (168-bp) homologous to KatB and KatC, two kinesin isoform genes of Arabidopsis, which were proved to result in the post-transcriptional gene silencing of KatB and KatC in DEX-induced transgenic plants. RT-PCR and Northern blot analysis on transgenic homozygous Arabidopsis (termed as RNAi-type plants) showed that DEX inducement causes KatB and KatC mRNA degradation. With a simplified method, Arabidopsis grafting was effectively performed between RNAi-type and wild-type lines. The target gene mRNA levels were tested based on semi-quantitative RT-PCR. Our results demonstrateed that DEX-induced gene silencing signals could result in a reduction in KatB and KatC mRNA in the wild-type rootstocks or scions, indicating that silencing signals of RNAi could be transmitted bidirectionally across the graft junction whether RNAi-plants were scions or stocks. In contrast to the previously reported results on grafted tobacco, the transmission of post- transcriptional gene silencing signals caused by RNAi in grafted Arabidopsis is more effective than that in tobacco.

  16. Control of trichome formation in Arabidopsis by poplar single-repeat R3 MYB transcription factors

    OpenAIRE

    Limei eZhou; Kaijie eZheng; Xiaoyu eWang; Hainan eTian; Xianling eWang; Shucai eWang

    2014-01-01

    In Arabidopsis, trichome formation is regulated by the interplay of R3 MYBs and several others transcription factors including the WD40-repeat protein TRANSPARENT TESTA GLABRA1 (TTG1), the R2R3 MYB transcription factor GLABRA1 (GL1), the bHLH transcription factor GLABRA3 (GL3) or ENHANCER OF GLABRA3 (EGL3), and the homeodomain protein GLABRA2 (GL2). R3 MYBs including TRICHOMELESS1 (TCL1), TRYPTICHON (TRY), CAPRICE (CPC), ENHANCER OF TRY AND CPC1 (ETC1), ETC2 and ETC3 negatively regulate trich...

  17. Transcript Abundance Explains mRNA Mobility Data in Arabidopsis thaliana.

    Science.gov (United States)

    Calderwood, Alexander; Kopriva, Stanislav; Morris, Richard J

    2016-03-01

    Recently, a large population of mRNA was shown to be able to travel between plant organs via sieve elements as a putative long-distance signaling molecule. However, a mechanistic basis by which transcripts are selected for transport has not yet been identified. Here, we show that experimental mRNA mobility data in Arabidopsis can be explained by transcript abundance and half-life. This suggests that the majority of identified mobile transcripts can be accounted for by non-sequence-specific movement of mRNA from companion cells into sieve elements. PMID:26952566

  18. A Genome-Scale Resource for the Functional Characterization of Arabidopsis Transcription Factors

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    Jose L. Pruneda-Paz

    2014-07-01

    Full Text Available Extensive transcriptional networks play major roles in cellular and organismal functions. Transcript levels are in part determined by the combinatorial and overlapping functions of multiple transcription factors (TFs bound to gene promoters. Thus, TF-promoter interactions provide the basic molecular wiring of transcriptional regulatory networks. In plants, discovery of the functional roles of TFs is limited by an increased complexity of network circuitry due to a significant expansion of TF families. Here, we present the construction of a comprehensive collection of Arabidopsis TFs clones created to provide a versatile resource for uncovering TF biological functions. We leveraged this collection by implementing a high-throughput DNA binding assay and identified direct regulators of a key clock gene (CCA1 that provide molecular links between different signaling modules and the circadian clock. The resources introduced in this work will significantly contribute to a better understanding of the transcriptional regulatory landscape of plant genomes.

  19. Transcription factor movement and tissue patterning in Arabidopsis root meristem

    NARCIS (Netherlands)

    Long, Y.

    2015-01-01

    Cell-cell communication is key to coordinated cellular functions in multicellular organisms. In addition to the signaling molecules found in animals, plants also frequently recruit mobile transcription factors to deliver positional information. The best studied example is SHORT-ROOT (SHR), a transcr

  20. 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.

  1. Deciphering the Molecular Mechanisms Underpinning the Transcriptional Control of Gene Expression by Master Transcriptional Regulators in Arabidopsis Seed.

    Science.gov (United States)

    Baud, Sébastien; Kelemen, Zsolt; Thévenin, Johanne; Boulard, Céline; Blanchet, Sandrine; To, Alexandra; Payre, Manon; Berger, Nathalie; Effroy-Cuzzi, Delphine; Franco-Zorrilla, Jose Manuel; Godoy, Marta; Solano, Roberto; Thevenon, Emmanuel; Parcy, François; Lepiniec, Loïc; Dubreucq, Bertrand

    2016-06-01

    In Arabidopsis (Arabidopsis thaliana), transcriptional control of seed maturation involves three related regulators with a B3 domain, namely LEAFY COTYLEDON2 (LEC2), ABSCISIC ACID INSENSITIVE3 (ABI3), and FUSCA3 (ABI3/FUS3/LEC2 [AFLs]). Although genetic analyses have demonstrated partially overlapping functions of these regulators, the underlying molecular mechanisms remained elusive. The results presented here confirmed that the three proteins bind RY DNA elements (with a 5'-CATG-3' core sequence) but with different specificities for flanking nucleotides. In planta as in the moss Physcomitrella patens protoplasts, the presence of RY-like (RYL) elements is necessary but not sufficient for the regulation of the OLEOSIN1 (OLE1) promoter by the B3 AFLs. G box-like domains, located in the vicinity of the RYL elements, also are required for proper activation of the promoter, suggesting that several proteins are involved. Consistent with this idea, LEC2 and ABI3 showed synergistic effects on the activation of the OLE1 promoter. What is more, LEC1 (a homolog of the NF-YB subunit of the CCAAT-binding complex) further enhanced the activation of this target promoter in the presence of LEC2 and ABI3. Finally, recombinant LEC1 and LEC2 proteins produced in Arabidopsis protoplasts could form a ternary complex with NF-YC2 in vitro, providing a molecular explanation for their functional interactions. Taken together, these results allow us to propose a molecular model for the transcriptional regulation of seed genes by the L-AFL proteins, based on the formation of regulatory multiprotein complexes between NF-YBs, which carry a specific aspartate-55 residue, and B3 transcription factors. PMID:27208266

  2. Protein intrinsic disorder in Arabidopsis NAC transcription factors

    DEFF Research Database (Denmark)

    O'Shea, Charlotte; Jensen, Mikael Kryger; Stender, Emil G.P.;

    2015-01-01

    transcription activation factor), cup-shaped cotyledon] TFs shows that the domains are present in similar average pre-molten or molten globule-like states, but have different patterns of order/disorder and MoRFs (molecular recognition features). ANAC046 (Arabidopsis NAC 046) was selected for further studies...... because of its simple MoRF pattern and its ability to interact with RCD1 (radical-induced cell death 1). Experiments in yeast and thermodynamic characterization suggest that its single MoRF region is sufficient for both transcriptional activation and interaction with RCD1. The remainder of the large...

  3. The role of transcriptional coactivator ADA2b in Arabidopsis abiotic stress responses.

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    Vlachonasios, Konstantinos E; Kaldis, Athanasios; Nikoloudi, Adriana; Tsementzi, Despoina

    2011-10-01

    Plant growth and crop production can be greatly affected by common environmental stresses such as drought, high salinity and low temperatures. Gene expression is affected by several abiotic stresses. Stress-inducible genes are regulated by transcription factors and epigenetic mechanisms such as histone modifications. In this Mini-Review, we have explored the role of transcriptional adaptor ADA2b in Arabidopsis responses to abiotic stress. ADA2b is required for the expression of genes involved in abiotic stress either by controlling H3 and H4 acetylation in the case of salt stress or affecting nucleosome occupancy in low temperatures response.

  4. The Transcriptional Coregulator LEUNIG_HOMOLOG Inhibits Light-Dependent Seed Germination in Arabidopsis.

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    Lee, Nayoung; Park, Jeongmoo; Kim, Keunhwa; Choi, Giltsu

    2015-08-01

    PHYTOCHROME-INTERACTING FACTOR1 (PIF1) is a basic helix-loop-helix transcription factor that inhibits light-dependent seed germination in Arabidopsis thaliana. However, it remains unclear whether PIF1 requires other factors to regulate its direct targets. Here, we demonstrate that LEUNIG_HOMOLOG (LUH), a Groucho family transcriptional corepressor, binds to PIF1 and coregulates its targets. Not only are the transcriptional profiles of the luh and pif1 mutants remarkably similar, more than 80% of the seeds of both genotypes germinate in the dark. We show by chromatin immunoprecipitation that LUH binds a subset of PIF1 targets in a partially PIF1-dependent manner. Unexpectedly, we found LUH binds and coregulates not only PIF1-activated targets but also PIF1-repressed targets. Together, our results indicate LUH functions with PIF1 as a transcriptional coregulator to inhibit seed germination.

  5. Identification of transcription-factor genes expressed in the Arabidopsis female gametophyte

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    Kang Il-Ho

    2010-06-01

    Full Text Available Abstract Background In flowering plants, the female gametophyte is typically a seven-celled structure with four cell types: the egg cell, the central cell, the synergid cells, and the antipodal cells. These cells perform essential functions required for double fertilization and early seed development. Differentiation of these distinct cell types likely involves coordinated changes in gene expression regulated by transcription factors. Therefore, understanding female gametophyte cell differentiation and function will require dissection of the gene regulatory networks operating in each of the cell types. These efforts have been hampered because few transcription factor genes expressed in the female gametophyte have been identified. To identify such genes, we undertook a large-scale differential expression screen followed by promoter-fusion analysis to detect transcription-factor genes transcribed in the Arabidopsis female gametophyte. Results Using quantitative reverse-transcriptase PCR, we analyzed 1,482 Arabidopsis transcription-factor genes and identified 26 genes exhibiting reduced mRNA levels in determinate infertile 1 mutant ovaries, which lack female gametophytes, relative to ovaries containing female gametophytes. Spatial patterns of gene transcription within the mature female gametophyte were identified for 17 transcription-factor genes using promoter-fusion analysis. Of these, ten genes were predominantly expressed in a single cell type of the female gametophyte including the egg cell, central cell and the antipodal cells whereas the remaining seven genes were expressed in two or more cell types. After fertilization, 12 genes were transcriptionally active in the developing embryo and/or endosperm. Conclusions We have shown that our quantitative reverse-transcriptase PCR differential-expression screen is sufficiently sensitive to detect transcription-factor genes transcribed in the female gametophyte. Most of the genes identified in this

  6. Transcriptional analysis of the Arabidopsis ovule by massively parallel signature sequencing.

    Science.gov (United States)

    Sánchez-León, Nidia; Arteaga-Vázquez, Mario; Alvarez-Mejía, César; Mendiola-Soto, Javier; Durán-Figueroa, Noé; Rodríguez-Leal, Daniel; Rodríguez-Arévalo, Isaac; García-Campayo, Vicenta; García-Aguilar, Marcelina; Olmedo-Monfil, Vianey; Arteaga-Sánchez, Mario; de la Vega, Octavio Martínez; Nobuta, Kan; Vemaraju, Kalyan; Meyers, Blake C; Vielle-Calzada, Jean-Philippe

    2012-06-01

    The life cycle of flowering plants alternates between a predominant sporophytic (diploid) and an ephemeral gametophytic (haploid) generation that only occurs in reproductive organs. In Arabidopsis thaliana, the female gametophyte is deeply embedded within the ovule, complicating the study of the genetic and molecular interactions involved in the sporophytic to gametophytic transition. Massively parallel signature sequencing (MPSS) was used to conduct a quantitative large-scale transcriptional analysis of the fully differentiated Arabidopsis ovule prior to fertilization. The expression of 9775 genes was quantified in wild-type ovules, additionally detecting >2200 new transcripts mapping to antisense or intergenic regions. A quantitative comparison of global expression in wild-type and sporocyteless (spl) individuals resulted in 1301 genes showing 25-fold reduced or null activity in ovules lacking a female gametophyte, including those encoding 92 signalling proteins, 75 transcription factors, and 72 RNA-binding proteins not reported in previous studies based on microarray profiling. A combination of independent genetic and molecular strategies confirmed the differential expression of 28 of them, showing that they are either preferentially active in the female gametophyte, or dependent on the presence of a female gametophyte to be expressed in sporophytic cells of the ovule. Among 18 genes encoding pentatricopeptide-repeat proteins (PPRs) that show transcriptional activity in wild-type but not spl ovules, CIHUATEOTL (At4g38150) is specifically expressed in the female gametophyte and necessary for female gametogenesis. These results expand the nature of the transcriptional universe present in the ovule of Arabidopsis, and offer a large-scale quantitative reference of global expression for future genomic and developmental studies.

  7. Transcriptional Regulation of Arabidopsis in Response to Salt Stress

    Institute of Scientific and Technical Information of China (English)

    Zhulong Chan

    2012-01-01

    Salt stress is a major factor limiting agricultural productivity worldwide.Adaptations to salt stress include avoidance by reduced sodium uptake,sequestration of toxic sodium ions away from the cytoplasm,or production of compatible solutes or osmoprotectants to reduce molecular disruption.Approaches to engineer salt stress resistance have included regulation of ion transport through introduction of Na+/H+ antiporter; synthesis of compatible solutes; or the introduction of transcription factors regulating expression of stress-responsive genes.On the other hand,naturally occurring variation among wild-type populations of plants also can be used to understand plant adaptive responses to their environments.In this study,we compared phenotypic and transcriptomic effects of constitutive expression of genes intended to confer salt stress tolerance by three different mechanisms:a transcription factor,CBF3/DREB1a; a metabolic gene,M6PR,for mannitol biosynthesis; and the Na+/H+ antiporter,SOS1.In the absence of salt,M6PR and SOS1 lines performed comparably with wild type; CBF3 lines exhibited dwarfing as reported previously.All three transgenes conferred fitness advantage when subjected to 100 mmol/L NaCI in the growth chamber.CBF3 and M6PR affected transcription of numerous abiotic stress-related genes as measured by Affymetrix microarray analysis.M6PR additionally modified expression of biotic stress and oxidative stress genes.Transcriptional effects of SOS1 were smaller and primarily limited to redox-related genes.In addition,we compared natural variations in salt tolerance between Ler and Sha ecotypes based on their responses to salt treatments and the results indicated that Ler was salt-sensitive,but Sha,which obtained a truncated RAS1 protein,was salt-tolerant.Transcriptome analysis revealed that many genes involved in secondary metabolism,photosynthesis,and protein synthesis were mainly down-regulated by salinity effects,while transposable element genes,microRNA and

  8. Evaluation of alternative RNA labeling protocols for transcript profiling with Arabidopsis AGRONOMICS1 tiling arrays

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    Müller Marlen

    2012-06-01

    Full Text Available Abstract Microarrays are routine tools for transcript profiling, and genomic tiling arrays such as the Arabidopsis AGRONOMICS1 arrays have been found to be highly suitable for such experiments because changes in genome annotation can be easily integrated at the data analysis level. In a transcript profiling experiment, RNA labeling is a critical step, most often initiated by oligo-dT-primed reverse transcription. Although this has been found to be a robust and reliable method, very long transcripts or non-polyadenylated transcripts might be labeled inefficiently. In this study, we first provide data handling methods to analyze AGRONOMICS1 tiling microarrays based on the TAIR10 genome annotation. Second, we describe methods to easily quantify antisense transcripts on such tiling arrays. Third, we test a random-primed RNA labeling method, and find that on AGRONOMICS1 arrays this method has similar general performance as the conventional oligo-dT-primed method. In contrast to the latter, however, the former works considerably better for long transcripts and for non-polyadenylated transcripts such as found in mitochondria and plastids. We propose that researchers interested in organelle function use the random-primed method to unleash the full potential of genomic tiling arrays.

  9. Ectopic expression of MYB46 identifies transcriptional regulatory genes involved in secondary wall biosynthesis in Arabidopsis.

    Science.gov (United States)

    Ko, Jae-Heung; Kim, Won-Chan; Han, Kyung-Hwan

    2009-11-01

    MYB46 functions as a transcriptional switch that turns on the genes necessary for secondary wall biosynthesis. Elucidating the transcriptional regulatory network immediately downstream of MYB46 is crucial to our understanding of the molecular and biochemical processes involved in the biosynthesis and deposition of secondary walls in plants. To gain insights into MYB46-mediated transcriptional regulation, we first established an inducible secondary wall thickening system in Arabidopsis by expressing MYB46 under the control of dexamethasone-inducible promoter. Then, we used an ATH1 GeneChip microarray and Illumina digital gene expression system to obtain a series of transcriptome profiles with regard to the induction of secondary wall development. These analyses allowed us to identify a group of transcription factors whose expression coincided with or preceded the induction of secondary wall biosynthetic genes. A transient transcriptional activation assay was used to confirm the hierarchical relationships among the transcription factors in the network. The in vivo assay showed that MYB46 transcriptionally activates downstream target transcription factors, three of which (AtC3H14, MYB52 and MYB63) were shown to be able to activate secondary wall biosynthesis genes. AtC3H14 activated the transcription of all of the secondary wall biosynthesis genes tested, suggesting that AtC3H14 may be another master regulator of secondary wall biosynthesis. The transcription factors identified here may include direct activators of secondary wall biosynthesis genes. The present study discovered novel hierarchical relationships among the transcription factors involved in the transcriptional regulation of secondary wall biosynthesis, and generated several testable hypotheses.

  10. Control of trichome formation in Arabidopsis by poplar single-repeat R3 MYB transcription factors

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    Limei eZhou

    2014-06-01

    Full Text Available In Arabidopsis, trichome formation is regulated by the interplay of R3 MYBs and several others transcription factors including the WD40-repeat protein TRANSPARENT TESTA GLABRA1 (TTG1, the R2R3 MYB transcription factor GLABRA1 (GL1, the bHLH transcription factor GLABRA3 (GL3 or ENHANCER OF GLABRA3 (EGL3, and the homeodomain protein GLABRA2 (GL2. R3 MYBs including TRICHOMELESS1 (TCL1, TRYPTICHON (TRY, CAPRICE (CPC, ENHANCER OF TRY AND CPC1 (ETC1, ETC2 and ETC3 negatively regulate trichome formation by competing with GL1 for binding GL3 or EGL3, thus blocking the formation of TTG1-GL3/EGL3-GL1, an activator complex required for the activation of the trichome positive regulator gene GL2. However, it is largely unknown if R3 MYBs in other plant species especially woody plants have similar functions. By BLASTing the Populus trichocarpa protein database using the entire amino acid sequence of TCL1, an Arabidopsis R3 MYB transcription factor, we identified a total of eight R3 MYB transcription factor genes in poplar, namely Populus trichocarpa TRICHOMELESS1through 8 (PtrTCL1-PtrTCL8. The amino acid signature required for interacting with bHLH transcription factors and the amino acids required for cell-to-cell movement of R3 MYBs are not fully conserved in all PtrTCLs. When tested in Arabidopsis protoplasts, however, all PtrTCL interacted with GL3. Expressing each of the eight PtrTCLs genes in Arabidopsis resulted in either glabrous phenotypes or plants with reduced trichome numbers, and expression levels of GL2 in all transgenic plants tested were greatly reduced. Expression of PtrTCL1 under the control of TCL1 native promoter almost completely complemented the mutant phenotype of tcl. In contrast, expression of PtrTCL1 under the control of TRY native promoter in the try mutant, or under the control of CPC native promoter in the cpc mutant resulted in glabrous phenotypes, suggesting that PtrTCL1 functions similarly to TCL1, but not TRY and CPC.

  11. Comprehensive transcriptional profiling of NaCl-stressed Arabidopsis roots reveals novel classes of responsive genes

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    Deyholos Michael K

    2006-10-01

    Full Text Available Abstract Background Roots are an attractive system for genomic and post-genomic studies of NaCl responses, due to their primary importance to agriculture, and because of their relative structural and biochemical simplicity. Excellent genomic resources have been established for the study of Arabidopsis roots, however, a comprehensive microarray analysis of the root transcriptome following NaCl exposure is required to further understand plant responses to abiotic stress and facilitate future, systems-based analyses of the underlying regulatory networks. Results We used microarrays of 70-mer oligonucleotide probes representing 23,686 Arabidopsis genes to identify root transcripts that changed in relative abundance following 6 h, 24 h, or 48 h of hydroponic exposure to 150 mM NaCl. Enrichment analysis identified groups of structurally or functionally related genes whose members were statistically over-represented among up- or down-regulated transcripts. Our results are consistent with generally observed stress response themes, and highlight potentially important roles for underappreciated gene families, including: several groups of transporters (e.g. MATE, LeOPT1-like; signalling molecules (e.g. PERK kinases, MLO-like receptors, carbohydrate active enzymes (e.g. XTH18, transcription factors (e.g. members of ZIM, WRKY, NAC, and other proteins (e.g. 4CL-like, COMT-like, LOB-Class 1. We verified the NaCl-inducible expression of selected transcription factors and other genes by qRT-PCR. Conclusion Micorarray profiling of NaCl-treated Arabidopsis roots revealed dynamic changes in transcript abundance for at least 20% of the genome, including hundreds of transcription factors, kinases/phosphatases, hormone-related genes, and effectors of homeostasis, all of which highlight the complexity of this stress response. Our identification of these transcriptional responses, and groups of evolutionarily related genes with either similar or divergent

  12. Overexpression of the Rap2.4f transcriptional factor in Arabidopsis promotes leaf senescence

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Senescence is a complex and highly regulated process. Leaf senescence is influenced by endogenous developmental and external environmental signals. In this work, we found that expression of an Ap2/DREB-type transcription factor gene, Arabidopsis Rap2.4f (At4g28140), was upregulated by salt, mannitol, and dark treatments. Constitutively overexpressing Rap2.4f under the control of the CaMV 35S promoter led to an increased chlorophyll degradation rate and upregulation of many senescence-associated genes in the transgenic Arabidopsis lines. Our results show that Rap2.4f is a positive regulator of senescence, promoting both developmental and dark-induced leaf senescence.

  13. Characterization and pilot functional study of a rootspecific MYB transcription factor of Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    An MYB transcription factor (AtMYB305) ofArabidopsis was structurally characterized. The biochemical activity of the protein was tested and its in vivo function was preliminarily analyzed. AtMYB305 contains two imperfect repeats (R2, R3) in its DNA binding domain. Gel mobility shift assay demonstrated that GST-AtMYB305 fusion protein bound specifically to the DNA fragment that included a consensus MYB recognition sequence (TAACTG). Overexpression of AtMYB305 in the fission yeast caused the formation of elongated cells with one condensed nucleus.Semi-quantitative RT-PCR analysis revealed that AtMYB305was expressed specifically in the roots of Arabidopsis.

  14. In Silico Identification of Co-transcribed Core Cell Cycle Regulators and Transcription Factors in Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Regulatory networks involving transcription factors and core cell cycle regulators are expected to play crucial roles in plant growth and development. In this report, we describe the identification of two groups of co-transcribed core cell cycle regulators and transcription factors via a two-step in silico screening. The core cell cycle regulators include TARDY ASYNCHRONOUS MEIOSIS (CYCA1;2), CYCB1;1, CYCB2;1, CDKB1;2, and CDKB2;2 while the transcription factors include CURLY LEAF, AINTEGUMENTA, a MYB protein, two Forkhead-associated domain proteins, and a SCARECROW family protein. Promoter analysis revealed a potential web of cross- and self-regulations among the identified proteins. Because one criterion for screening for these genes is that they are predominantly transcribed in young organs but not in mature organs, these genes are likely to be particularly involved in Arabidopsis organ growth.

  15. Genome-wide analysis of heat shock transcription factor families in rice and Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    Jingkang Guo; Jian Wu; Qian Ji; Chao Wang; Lei Luo; Yi Yuan; Yonghua Wang; Jian Wang

    2008-01-01

    The heat shock transcription factors (HSFs) are the major heat shock factors regulating the heat stress response. They participate in regulating the expression of heat shock proteins (HSPs), which are critical in the protection against stress damage and many other impor tant biological processes. Study of the HSF gene family is important for understanding the mechanism by which plants respond to stress. The completed genome sequences of rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana) constitute a valuable resource for comparative genomic analysis, as they are representatives of the two major evolutionary lineages within the angiosperms: the monocotyledons and the dicotyledons. The identification of phylogenetic relationships among HSF proteins in these species is a fundamental step to unravel the functionality of new and yet uncharacterized genes belonging to this family.In this study, the full complement of HSF genes in rice and Arabidopsis has probably been identified through the genome-wide scan. Phylogenetic analyses resulted in the identification of three major clusters of orthologous genes that contain members belonging to both species, which must have been represented in their common ancestor before the taxonomic splitting of the angiosperms. Further analysis of the phylogenetic tree reveals a possible dicot specific gene group. We also identified nine pairs of paralogs, as evidence for studies on the evolution history of rice HSF family and rice genome evolution. Expression data analysis indicates that HSF proteins are widely expressed in plants. These results provide a solid base for future functional genomic studies of the HSF gene family in rice and Arabidopsis.

  16. 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.

  17. Regulation of CAPRICE transcription by MYB proteins for root epidermis differentiation in Arabidopsis.

    Science.gov (United States)

    Koshino-Kimura, Yoshihiro; Wada, Takuji; Tachibana, Tatsuhiko; Tsugeki, Ryuji; Ishiguro, Sumie; Okada, Kiyotaka

    2005-06-01

    Epidermal cell differentiation in Arabidopsis root is studied as a model system for understanding cell fate specification. Two types of MYB-related transcription factors are involved in this cell differentiation. One of these, CAPRICE (CPC), encoding an R3-type MYB protein, is a positive regulator of hair cell differentiation and is preferentially transcribed in hairless cells. We analyzed the regulatory mechanism of CPC transcription. Deletion analyses of the CPC promoter revealed that hairless cell-specific transcription of the CPC gene required a 69 bp sequence, and a tandem repeat of this region was sufficient for its expression in epidermis. This region includes two MYB-binding sites, and the epidermis-specific transcription of CPC was abolished when base substitutions were introduced in these sites. We showed by gel mobility shift experiments and by yeast one-hybrid assay that WEREWOLF (WER), which is an R2R3-type MYB protein, directly binds to this region. We showed that WER also binds to the GL2 promoter region, indicating that WER directly regulates CPC and GL2 transcription by binding to their promoter regions.

  18. Calmodulin-binding transcription activator (CAMTA) 3 mediates biotic defense responses in Arabidopsis.

    Science.gov (United States)

    Galon, Yael; Nave, Roy; Boyce, Joy M; Nachmias, Dikla; Knight, Marc R; Fromm, Hillel

    2008-03-19

    Calmodulin-binding transcription activator (CAMTA) 3 (also called SR1) is a calmodulin-binding transcription factor in Arabidopsis. Two homozygous T-DNA insertion mutants (camta3-1, camta3-2) showed enhanced spontaneous lesions. Transcriptome analysis of both mutants revealed 6 genes with attenuated expression and 99 genes with elevated expression. Of the latter, 32 genes are related to defense against pathogens (e.g. WRKY33, PR1 and chitinase). Propagation of a virulent strain of the bacterial pathogen Pseudomonas syringae and the fungal pathogen Botrytis cinerea were attenuated in both mutants. Moreover, both mutants accumulated high levels of H2O2. We suggest that CAMTA3 regulates the expression of a set of genes involved in biotic defense responses.

  19. Differential Regulation of Strand-Specific Transcripts from Arabidopsis Centromeric Satellite Repeats.

    Directory of Open Access Journals (Sweden)

    2005-12-01

    Full Text Available Centromeres interact with the spindle apparatus to enable chromosome disjunction and typically contain thousands of tandemly arranged satellite repeats interspersed with retrotransposons. While their role has been obscure, centromeric repeats are epigenetically modified and centromere specification has a strong epigenetic component. In the yeast Schizosaccharomyces pombe, long heterochromatic repeats are transcribed and contribute to centromere function via RNA interference (RNAi. In the higher plant Arabidopsis thaliana, as in mammalian cells, centromeric satellite repeats are short (180 base pairs, are found in thousands of tandem copies, and are methylated. We have found transcripts from both strands of canonical, bulk Arabidopsis repeats. At least one subfamily of 180-base pair repeats is transcribed from only one strand and regulated by RNAi and histone modification. A second subfamily of repeats is also silenced, but silencing is lost on both strands in mutants in the CpG DNA methyltransferase MET1, the histone deacetylase HDA6/SIL1, or the chromatin remodeling ATPase DDM1. This regulation is due to transcription from Athila2 retrotransposons, which integrate in both orientations relative to the repeats, and differs between strains of Arabidopsis. Silencing lost in met1 or hda6 is reestablished in backcrosses to wild-type, but silencing lost in RNAi mutants and ddm1 is not. Twenty-four-nucleotide small interfering RNAs from centromeric repeats are retained in met1 and hda6, but not in ddm1, and may have a role in this epigenetic inheritance. Histone H3 lysine-9 dimethylation is associated with both classes of repeats. We propose roles for transcribed repeats in the epigenetic inheritance and evolution of centromeres.

  20. Two Arabidopsis orthologs of the transcriptional coactivator ADA2 have distinct biological functions.

    Science.gov (United States)

    Hark, Amy T; Vlachonasios, Konstantinos E; Pavangadkar, Kanchan A; Rao, Sumana; Gordon, Hillary; Adamakis, Ioannis-Dimosthenis; Kaldis, Athanasios; Thomashow, Michael F; Triezenberg, Steven J

    2009-02-01

    Histone acetylation is an example of covalent modification of chromatin structure that has the potential to regulate gene expression. Gcn5 is a prototypical histone acetyltransferase that associates with the transcriptional coactivator Ada2. In Arabidopsis, two genes encode proteins that resemble yeast ADA2 and share approximately 45% amino acid sequence identity. We previously reported that plants harboring a T-DNA insertion in the ADA2b gene display a dwarf phenotype with developmental defects in several organs. Here we describe T-DNA insertion alleles in the ADA2a gene, which result in no dramatic growth or developmental phenotype. Both ADA2a and ADA2b are expressed in a variety of plant tissues; moreover, expression of ADA2a from a constitutive promoter fails to complement the ada2b-1 mutant phenotype, consistent with the hypothesis that the two proteins have distinct biochemical roles. To further probe the cellular roles of ADA2a and ADA2b, we studied the response of the transcriptional coactivator mutants to abiotic stress. Although ada2b seedlings display hypersensitivity to salt and abscisic acid and altered responses to low temperature stress, the responses of ada2a seedlings to abiotic stress generally parallel those of wildtype plants. Intriguingly, ada2a;ada2b double mutant plants display an intermediate, gcn5-like phenotype, suggesting that ADA2a and ADA2b each work independently with GCN5 to affect genome function in Arabidopsis.

  1. Regulation of WRKY46 transcription factor function by mitogen-activated protein kinases in Arabidopsis thaliana.

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    Arsheed Hussain Sheikh

    2016-02-01

    Full Text Available AbstractMitogen-activated protein kinase (MAPK cascades are central signalling pathways activated in plants after sensing internal developmental and external stress cues. Knowledge about the downstream substrate proteins of MAPKs is still limited in plants. We screened Arabidopsis WRKY transcription factors as potential targets downstream of MAPKs, and concentrated on characterizing WRKY46 as a substrate of the MAPK, MPK3. Mass spectrometry revealed in vitro phosphorylation of WRKY46 at amino acid position S168 by MPK3. However, mutagenesis studies showed that a second phosphosite, S250, can also be phosphorylated. Elicitation with pathogen-associated molecular patterns (PAMPs, such as the bacterial flagellin-derived flg22 peptide led to in vivo destabilization of WRKY46 in Arabidopsis protoplasts. Mutation of either phosphorylation site reduced the PAMP-induced degradation of WRKY46. Furthermore, the protein for the double phosphosite mutant is expressed at higher levels compared to wild-type proteins or single phosphosite mutants. In line with its nuclear localization and predicted function as a transcriptional activator, overexpression of WRKY46 in protoplasts raised basal plant defence as reflected by the increase in promoter activity of the PAMP-responsive gene, NHL10, in a MAPK-dependent manner. Thus, MAPK-mediated regulation of WRKY46 is a mechanism to control plant defence.

  2. LATERAL ORGAN BOUNDARIES DOMAIN transcription factors direct callus formation in Arabidopsis regeneration

    Institute of Scientific and Technical Information of China (English)

    Mingzhu Fan; Chongyi Xu; Ke Xu; Yuxin Hu

    2012-01-01

    The remarkable regeneration capability of plant tissues or organs under culture conditions has underlain an extensive practice for decades.The initial step in plant in vitro regeneration often involves the induction of a pluripotent cell mass termed callus,which is driven by the phytohormone auxin and occurs via a root development pathway.However,the key molecules governing callus formation remain unknown.Here we demonstrate that Arabidopsis LATERAL ORGAN BOUNDARIES DOMAIN (LBD)/ASYMMETRIC LEAVES2-LIKE (ASL) transcription factors are involved in the control of callus formation program.The four LBD genes downstream of AUXIN RESPONSE FACTORs (ARFs),LBD16,LBD17,LBD18 and LBD29,are rapidly and dramatically induced by callus-inducing medium (CIM) in multiple organs.Ectopic expression of each of the four LBD genes in Arabidopsis is sufficient to trigger spontaneous callus formation without exogenous phytohormones,whereas suppression of LBD function inhibits the callus formation induced by CIM.Moreover,the callus triggered by LBD resembles that induced by CIM by characteristics of ectopically activated root meristem genes and efficient regeneration capacity.These findings define LBD transcription factors as key regulators in the callus induction process,thereby establishing a molecular link between auxin signaling and the plant regeneration program.

  3. Deciphering transcriptional and metabolic networks associated with lysine metabolism during Arabidopsis seed development.

    Science.gov (United States)

    Angelovici, Ruthie; Fait, Aaron; Zhu, Xiaohong; Szymanski, Jedrzej; Feldmesser, Ester; Fernie, Alisdair R; Galili, Gad

    2009-12-01

    In order to elucidate transcriptional and metabolic networks associated with lysine (Lys) metabolism, we utilized developing Arabidopsis (Arabidopsis thaliana) seeds as a system in which Lys synthesis could be stimulated developmentally without application of chemicals and coupled this to a T-DNA insertion knockout mutation impaired in Lys catabolism. This seed-specific metabolic perturbation stimulated Lys accumulation starting from the initiation of storage reserve accumulation. Our results revealed that the response of seed metabolism to the inducible alteration of Lys metabolism was relatively minor; however, that which was observable operated in a modular manner. They also demonstrated that Lys metabolism is strongly associated with the operation of the tricarboxylic acid cycle while largely disconnected from other metabolic networks. In contrast, the inducible alteration of Lys metabolism was strongly associated with gene networks, stimulating the expression of hundreds of genes controlling anabolic processes that are associated with plant performance and vigor while suppressing a small number of genes associated with plant stress interactions. The most pronounced effect of the developmentally inducible alteration of Lys metabolism was an induction of expression of a large set of genes encoding ribosomal proteins as well as genes encoding translation initiation and elongation factors, all of which are associated with protein synthesis. With respect to metabolic regulation, the inducible alteration of Lys metabolism was primarily associated with altered expression of genes belonging to networks of amino acids and sugar metabolism. The combined data are discussed within the context of network interactions both between and within metabolic and transcriptional control systems.

  4. Regulation of WRKY46 Transcription Factor Function by Mitogen-Activated Protein Kinases in Arabidopsis thaliana.

    Science.gov (United States)

    Sheikh, Arsheed H; Eschen-Lippold, Lennart; Pecher, Pascal; Hoehenwarter, Wolfgang; Sinha, Alok K; Scheel, Dierk; Lee, Justin

    2016-01-01

    Mitogen-activated protein kinase (MAPK) cascades are central signaling pathways activated in plants after sensing internal developmental and external stress cues. Knowledge about the downstream substrate proteins of MAPKs is still limited in plants. We screened Arabidopsis WRKY transcription factors as potential targets downstream of MAPKs, and concentrated on characterizing WRKY46 as a substrate of the MAPK, MPK3. Mass spectrometry revealed in vitro phosphorylation of WRKY46 at amino acid position S168 by MPK3. However, mutagenesis studies showed that a second phosphosite, S250, can also be phosphorylated. Elicitation with pathogen-associated molecular patterns (PAMPs), such as the bacterial flagellin-derived flg22 peptide led to in vivo destabilization of WRKY46 in Arabidopsis protoplasts. Mutation of either phosphorylation site reduced the PAMP-induced degradation of WRKY46. Furthermore, the protein for the double phosphosite mutant is expressed at higher levels compared to wild-type proteins or single phosphosite mutants. In line with its nuclear localization and predicted function as a transcriptional activator, overexpression of WRKY46 in protoplasts raised basal plant defense as reflected by the increase in promoter activity of the PAMP-responsive gene, NHL10, in a MAPK-dependent manner. Thus, MAPK-mediated regulation of WRKY46 is a mechanism to control plant defense. PMID:26870073

  5. DELLA-induced early transcriptional changes during etiolated development in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Javier Gallego-Bartolomé

    Full Text Available The hormones gibberellins (GAs control a wide variety of processes in plants, including stress and developmental responses. This task largely relies on the activity of the DELLA proteins, nuclear-localized transcriptional regulators that do not seem to have DNA binding capacity. The identification of early target genes of DELLA action is key not only to understand how GAs regulate physiological responses, but also to get clues about the molecular mechanisms by which DELLAs regulate gene expression. Here, we have investigated the global, early transcriptional response triggered by the Arabidopsis DELLA protein GAI during skotomorphogenesis, a developmental program tightly regulated by GAs. Our results show that the induction of GAI activity has an almost immediate effect on gene expression. Although this transcriptional regulation is largely mediated by the PIFs and HY5 transcription factors based on target meta-analysis, additional evidence points to other transcription factors that would be directly involved in DELLA regulation of gene expression. First, we have identified cis elements recognized by Dofs and type-B ARRs among the sequences enriched in the promoters of GAI targets; and second, an enrichment in additional cis elements appeared when this analysis was extended to a dataset of early targets of the DELLA protein RGA: CArG boxes, bound by MADS-box proteins, and the E-box CACATG that links the activity of DELLAs to circadian transcriptional regulation. Finally, Gene Ontology analysis highlights the impact of DELLA regulation upon the homeostasis of the GA, auxin, and ethylene pathways, as well as upon pre-existing transcriptional networks.

  6. A Protein Complex Required for Polymerase V Transcripts and RNA- Directed DNA Methylation in Arabidopsis

    KAUST Repository

    Law, Julie A.

    2010-05-01

    DNA methylation is an epigenetic modification associated with gene silencing. In Arabidopsis, DNA methylation is established by DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2), which is targeted by small interfering RNAs through a pathway termed RNA-directed DNA methylation (RdDM) [1, 2]. Recently, RdDM was shown to require intergenic noncoding (IGN) transcripts that are dependent on the Pol V polymerase. These transcripts are proposed to function as scaffolds for the recruitment of downstream RdDM proteins, including DRM2, to loci that produce both siRNAs and IGN transcripts [3]. However, the mechanism(s) through which Pol V is targeted to specific genomic loci remains largely unknown. Through affinity purification of two known RdDM components, DEFECTIVE IN RNA-DIRECTED DNA METHYLATION 1 (DRD1) [4] and DEFECTIVE IN MERISTEM SILENCING 3 (DMS3) [5, 6], we found that they copurify with each other and with a novel protein, RNA-DIRECTED DNA METHYLATION 1 (RDM1), forming a complex we term DDR. We also found that DRD1 copurified with Pol V subunits and that RDM1, like DRD1 [3] and DMS3 [7], is required for the production of Pol V-dependent transcripts. These results suggest that the DDR complex acts in RdDM at a step upstream of the recruitment or activation of Pol V. © 2010 Elsevier Ltd. All rights reserved.

  7. Arabidopsis NAC transcription factor JUB1 regulates GA/BR metabolism and signalling.

    Science.gov (United States)

    Shahnejat-Bushehri, Sara; Tarkowska, Danuse; Sakuraba, Yasuhito; Balazadeh, Salma

    2016-01-01

    Gibberellins (GAs) and brassinosteroids (BRs) are important phytohormones that control plant development and responses to environmental cues by involving DELLA proteins and BRASSINAZOLE-RESISTANT1 (BZR1) respectively as key transcription factors. Here, we reveal a new role for JUNGBRUNNEN1 (JUB1) as a transcriptional regulator of GA/BR signalling in Arabidopsis thaliana. JUB1 directly represses the hormone biosynthesis genes GA3ox1 and DWARF4 (DWF4), leading to reduced levels of GAs and BRs and typical GA/BR deficiency phenotypes exhibiting short hypocotyls, dwarfism, late flowering and male sterility. JUB1 also directly represses PHYTOCHROME INTERACTING FACTOR4 (PIF4), a transcription factor connecting hormonal and environmental stimuli. On the other hand, JUB1 activates the DELLA genes GA INSENSITIVE (GAI) and RGA-LIKE 1 (RGL1). In addition, BZR1 and PIF4 act as direct transcriptional repressors upstream of JUB1, establishing a negative feedback loop. Thus, JUB1 forms the core of a robust regulatory module that triggers DELLA accumulation, thereby restricting cell elongation while concomitantly enhancing stress tolerance. PMID:27249348

  8. A trihelix DNA binding protein counterbalances hypoxia-responsive transcriptional activation in Arabidopsis.

    Science.gov (United States)

    Giuntoli, Beatrice; Lee, Seung Cho; Licausi, Francesco; Kosmacz, Monika; Oosumi, Teruko; van Dongen, Joost T; Bailey-Serres, Julia; Perata, Pierdomenico

    2014-09-01

    Transcriptional activation in response to hypoxia in plants is orchestrated by ethylene-responsive factor group VII (ERF-VII) transcription factors, which are stable during hypoxia but destabilized during normoxia through their targeting to the N-end rule pathway of selective proteolysis. Whereas the conditionally expressed ERF-VII genes enable effective flooding survival strategies in rice, the constitutive accumulation of N-end-rule-insensitive versions of the Arabidopsis thaliana ERF-VII factor RAP2.12 is maladaptive. This suggests that transcriptional activation under hypoxia that leads to anaerobic metabolism may need to be fine-tuned. However, it is presently unknown whether a counterbalance of RAP2.12 exists. Genome-wide transcriptome analyses identified an uncharacterized trihelix transcription factor gene, which we named HYPOXIA RESPONSE ATTENUATOR1 (HRA1), as highly up-regulated by hypoxia. HRA1 counteracts the induction of core low oxygen-responsive genes and transcriptional activation of hypoxia-responsive promoters by RAP2.12. By yeast-two-hybrid assays and chromatin immunoprecipitation we demonstrated that HRA1 interacts with the RAP2.12 protein but with only a few genomic DNA regions from hypoxia-regulated genes, indicating that HRA1 modulates RAP2.12 through protein-protein interaction. Comparison of the low oxygen response of tissues characterized by different levels of metabolic hypoxia (i.e., the shoot apical zone versus mature rosette leaves) revealed that the antagonistic interplay between RAP2.12 and HRA1 enables a flexible response to fluctuating hypoxia and is of importance to stress survival. In Arabidopsis, an effective low oxygen-sensing response requires RAP2.12 stabilization followed by HRA1 induction to modulate the extent of the anaerobic response by negative feedback regulation of RAP2.12. This mechanism is crucial for plant survival under suboptimal oxygenation conditions. The discovery of the feedback loop regulating the oxygen

  9. A trihelix DNA binding protein counterbalances hypoxia-responsive transcriptional activation in Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Beatrice Giuntoli

    2014-09-01

    Full Text Available Transcriptional activation in response to hypoxia in plants is orchestrated by ethylene-responsive factor group VII (ERF-VII transcription factors, which are stable during hypoxia but destabilized during normoxia through their targeting to the N-end rule pathway of selective proteolysis. Whereas the conditionally expressed ERF-VII genes enable effective flooding survival strategies in rice, the constitutive accumulation of N-end-rule-insensitive versions of the Arabidopsis thaliana ERF-VII factor RAP2.12 is maladaptive. This suggests that transcriptional activation under hypoxia that leads to anaerobic metabolism may need to be fine-tuned. However, it is presently unknown whether a counterbalance of RAP2.12 exists. Genome-wide transcriptome analyses identified an uncharacterized trihelix transcription factor gene, which we named HYPOXIA RESPONSE ATTENUATOR1 (HRA1, as highly up-regulated by hypoxia. HRA1 counteracts the induction of core low oxygen-responsive genes and transcriptional activation of hypoxia-responsive promoters by RAP2.12. By yeast-two-hybrid assays and chromatin immunoprecipitation we demonstrated that HRA1 interacts with the RAP2.12 protein but with only a few genomic DNA regions from hypoxia-regulated genes, indicating that HRA1 modulates RAP2.12 through protein-protein interaction. Comparison of the low oxygen response of tissues characterized by different levels of metabolic hypoxia (i.e., the shoot apical zone versus mature rosette leaves revealed that the antagonistic interplay between RAP2.12 and HRA1 enables a flexible response to fluctuating hypoxia and is of importance to stress survival. In Arabidopsis, an effective low oxygen-sensing response requires RAP2.12 stabilization followed by HRA1 induction to modulate the extent of the anaerobic response by negative feedback regulation of RAP2.12. This mechanism is crucial for plant survival under suboptimal oxygenation conditions. The discovery of the feedback loop

  10. Fusarium oxysporum triggers tissue-specific transcriptional reprogramming in Arabidopsis thaliana.

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    Rebecca Lyons

    Full Text Available Some of the most devastating agricultural diseases are caused by root-infecting pathogens, yet the majority of studies on these interactions to date have focused on the host responses of aerial tissues rather than those belowground. Fusarium oxysporum is a root-infecting pathogen that causes wilt disease on several plant species including Arabidopsis thaliana. To investigate and compare transcriptional changes triggered by F. oxysporum in different Arabidopsis tissues, we infected soil-grown plants with F. oxysporum and subjected root and leaf tissue harvested at early and late timepoints to RNA-seq analyses. At least half of the genes induced or repressed by F. oxysporum showed tissue-specific regulation. Regulators of auxin and ABA signalling, mannose binding lectins and peroxidases showed strong differential expression in root tissue. We demonstrate that ARF2 and PRX33, two genes regulated in the roots, promote susceptibility to F. oxysporum. In the leaves, defensins and genes associated with the response to auxin, cold and senescence were strongly regulated while jasmonate biosynthesis and signalling genes were induced throughout the plant.

  11. DEWAX-mediated transcriptional repression of cuticular wax biosynthesis in Arabidopsis thaliana.

    Science.gov (United States)

    Suh, Mi Chung; Go, Young Sam

    2014-06-06

    The aerial parts of plants are covered with a cuticular wax layer, which is the first barrier between a plant and its environment. Although cuticular wax deposition increases more in the light than in the dark, little is known about the molecular mechanisms underlying the regulation of cuticular wax biosynthesis. Recently DEWAX (Decrease Wax Biosynthesis) encoding an AP2/ERF transcription factor was found to be preferentially expressed in the epidermis and induced by darkness. Wax analysis of the dewax knockout mutant, wild type, and DEWAX overexpression lines (OX) indicates that DEWAX is a negative regulator of cuticular wax biosynthesis. DEWAX represses the expression of wax biosynthetic genes CER1, LACS2, ACLA2, and ECR via direct interaction with their promoters. Cuticular wax biosynthesis is negatively regulated twice a day by the expression of DEWAX; throughout the night and another for stomata closing. Taken together, it is evident that DEWAX-mediated negative regulation of the wax biosynthetic genes plays role in determining the total wax loads produced in Arabidopsis during daily dark and light cycles. In addition, significantly higher levels of DEWAX transcripts in leaves than stems suggest that DEWAX-mediated transcriptional repression might be involved in the organ-specific regulation of total wax amounts on plant surfaces.

  12. A "Whirly" transcription factor is required for salicylic acid-dependent disease resistance in Arabidopsis.

    Science.gov (United States)

    Desveaux, Darrell; Subramaniam, Rajagopal; Després, Charles; Mess, Jean-Nicholas; Lévesque, Caroline; Fobert, Pierre R; Dangl, Jeffery L; Brisson, Normand

    2004-02-01

    Transcriptional reprogramming is critical for plant disease resistance responses; its global control is not well understood. Salicylic acid (SA) can induce plant defense gene expression and a long-lasting disease resistance state called systemic acquired resistance (SAR). Plant-specific "Whirly" DNA binding proteins were previously implicated in defense gene regulation. We demonstrate that the potato StWhy1 protein is a transcriptional activator of genes containing the PBF2 binding PB promoter element. DNA binding activity of AtWhy1, the Arabidopsis StWhy1 ortholog, is induced by SA and is required for both SA-dependent disease resistance and SA-induced expression of an SAR response gene. AtWhy1 is required for both full basal and specific disease resistance responses. The transcription factor-associated protein NPR1 is also required for SAR. Surprisingly, AtWhy1 activation by SA is NPR1 independent, suggesting that AtWhy1 works in conjunction with NPR1 to transduce the SA signal. Our analysis of AtWhy1 adds a critical component to the SA-dependent plant disease resistance response. PMID:14960277

  13. AthaMap-assisted transcription factor target gene identification in Arabidopsis thaliana.

    Science.gov (United States)

    Bülow, Lorenz; Brill, Yuri; Hehl, Reinhard

    2010-01-01

    The AthaMap database generates a map of potential transcription factor binding sites (TFBS) and small RNA target sites in the Arabidopsis thaliana genome. The database contains sites for 115 different transcription factors (TFs). TFBS were identified with positional weight matrices (PWMs) or with single binding sites. With the new web tool 'Gene Identification', it is possible to identify potential target genes for selected TFs. For these analyses, the user can define a region of interest of up to 6000 bp in all annotated genes. For TFBS determined with PWMs, the search can be restricted to high-quality TFBS. The results are displayed in tables that identify the gene, position of the TFBS and, if applicable, individual score of the TFBS. In addition, data files can be downloaded that harbour positional information of TFBS of all TFs in a region between -2000 and +2000 bp relative to the transcription or translation start site. Also, data content of AthaMap was increased and the database was updated to the TAIR8 genome release. Database URL: http://www.athamap.de/gene_ident.php. PMID:21177332

  14. Arabidopsis WRKY33 transcription factor is required for resistance to necrotrophic fungal pathogens.

    Science.gov (United States)

    Zheng, Zuyu; Qamar, Synan Abu; Chen, Zhixiang; Mengiste, Tesfaye

    2006-11-01

    Plant WRKY transcription factors are key regulatory components of plant responses to microbial infection. In addition to regulating the expression of defense-related genes, WRKY transcription factors have also been shown to regulate cross-talk between jasmonate- and salicylate-regulated disease response pathways. The two pathways mediate resistance against different types of microbial pathogens, and there are numerous reports of antagonistic interactions between them. Here we show that mutations of the Arabidopsis WRKY33 gene encoding a WRKY transcription factor cause enhanced susceptibility to the necrotrophic fungal pathogens Botrytis cinerea and Alternaria brassicicola concomitant with reduced expression of the jasmonate-regulated plant defensin PDF1.2 gene. Ectopic over-expression of WRKY33, on the other hand, increases resistance to the two necrotrophic fungal pathogens. The wrky33 mutants do not show altered responses to a virulent strain of the bacterial pathogen Pseudomonas syringae, although the ectopic expression of WRKY33 results in enhanced susceptibility to this pathogen. The susceptibility of WRKY33-over-expressing plants to P. syringae is associated with reduced expression of the salicylate-regulated PR-1 gene. The WRKY33 transcript is induced in response to pathogen infection, or treatment with salicylate or the paraquat herbicide that generates activated oxygen species in exposed cells. WRKY33 is localized to the nucleus of plant cells and recognizes DNA molecules containing the TTGACC W-box sequence. Together, these results indicate that pathogen-induced WRKY33 is an important transcription factor that regulates the antagonistic relationship between defense pathways mediating responses to P. syringae and necrotrophic pathogens.

  15. 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....

  16. Regulatory Network of Transcription Factors in Response to Drought in Arabidopsis and Crops

    Institute of Scientific and Technical Information of China (English)

    Chen Li-miao; Li Wen-bin; Zhou Xin-an

    2012-01-01

    Drought is one of the most important environmental constraints limiting plant growth, development and crop yield. Many drought-inducible genes have been identified by molecular and genomic analyses in Arabidopsis, rice and other crops. To better understand reaction mechanism of plant to drought tolerance, we mainly focused on introducing the research of transcription factors (TFs) in signal transduction and regulatory network of gene expression conferring drought. A TF could bind multiple target genes to increase one or more kinds of stress tolerance. Sometimes, several TFs might act together with a target gene. So drought-tolerance genes or TFs might respond to high-salinity, cold or other stresses. The crosstalk of multiple stresses signal pathways is a crucial aspect of understanding stress signaling.

  17. The Miscanthus NAC transcription factor MlNAC9 enhances abiotic stress tolerance in transgenic Arabidopsis.

    Science.gov (United States)

    Zhao, Xun; Yang, Xuanwen; Pei, Shengqiang; He, Guo; Wang, Xiaoyu; Tang, Qi; Jia, Chunlin; Lu, Ying; Hu, Ruibo; Zhou, Gongke

    2016-07-15

    NAC (NAM, ATAF1/2, and CUC2) transcription factors are known to play important roles in responses to abiotic stresses in plants. Currently, little information regarding the functional roles of NAC genes in stress tolerance is available in Miscanthus lutarioriparius, a promising bioenergy plant for cellulosic ethanol production. In this study, we carried out the functional characterization of MlNAC9 in abiotic stresses. MlNAC9 was shown to act as a nuclear localized transcription activator with the activation domain in its C-terminus. The overexpression of MlNAC9 in Arabidopsis conferred hypersensitivity to abscisic acid (ABA) at seed germination and root elongation stages. In addition, the overexpression of MlNAC9 led to increased seed germination rate and root growth under salt (NaCl) treatment. Meanwhile, the transgenic Arabidopsis overexpressing MlNAC9 showed enhanced tolerance to drought and cold stresses. The expression of stress-responsive marker genes was significantly increased in MlNAC9 overexpression lines compared to that of WT under ABA, drought, salt, and cold stresses. Correspondingly, the activities of antioxidant enzymes superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) were significantly increased and the malondialdehyde (MDA) content was lower accumulated in MlNAC9 overexpression lines under drought and salt treatments. These results indicated that the overexpression of MlNAC9 improved the tolerance to abiotic stresses via an ABA-dependent pathway, and the enhanced tolerance of transgenic plants was mainly attributed to the increased expression of stress-responsive genes and the enhanced scavenging capability of reactive oxygen species (ROS). PMID:27085481

  18. Arabidopsis Actin-Depolymerizing Factor-4 links pathogen perception, defense activation and transcription to cytoskeletal dynamics.

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    Katie Porter

    Full Text Available The primary role of Actin-Depolymerizing Factors (ADFs is to sever filamentous actin, generating pointed ends, which in turn are incorporated into newly formed filaments, thus supporting stochastic actin dynamics. Arabidopsis ADF4 was recently shown to be required for the activation of resistance in Arabidopsis following infection with the phytopathogenic bacterium Pseudomonas syringae pv. tomato DC3000 (Pst expressing the effector protein AvrPphB. Herein, we demonstrate that the expression of RPS5, the cognate resistance protein of AvrPphB, was dramatically reduced in the adf4 mutant, suggesting a link between actin cytoskeletal dynamics and the transcriptional regulation of R-protein activation. By examining the PTI (PAMP Triggered Immunity response in the adf4 mutant when challenged with Pst expressing AvrPphB, we observed a significant reduction in the expression of the PTI-specific target gene FRK1 (Flg22-Induced Receptor Kinase 1. These data are in agreement with recent observations demonstrating a requirement for RPS5 in PTI-signaling in the presence of AvrPphB. Furthermore, MAPK (Mitogen-Activated Protein Kinase-signaling was significantly reduced in the adf4 mutant, while no such reduction was observed in the rps5-1 point mutation under similar conditions. Isoelectric focusing confirmed phosphorylation of ADF4 at serine-6, and additional in planta analyses of ADF4's role in immune signaling demonstrates that nuclear localization is phosphorylation independent, while localization to the actin cytoskeleton is linked to ADF4 phosphorylation. Taken together, these data suggest a novel role for ADF4 in controlling gene-for-gene resistance activation, as well as MAPK-signaling, via the coordinated regulation of actin cytoskeletal dynamics and R-gene transcription.

  19. Structural diversity and transcription of class III peroxidases from Arabidopsis thaliana.

    Science.gov (United States)

    Welinder, Karen G; Justesen, Annemarie F; Kjaersgård, Inger V H; Jensen, Rikke B; Rasmussen, Søren K; Jespersen, Hans M; Duroux, Laurent

    2002-12-01

    Understanding peroxidase function in plants is complicated by the lack of substrate specificity, the high number of genes, their diversity in structure and our limited knowledge of peroxidase gene transcription and translation. In the present study we sequenced expressed sequence tags (ESTs) encoding novel heme-containing class III peroxidases from Arabidopsis thaliana and annotated 73 full-length genes identified in the genome. In total, transcripts of 58 of these genes have now been observed. The expression of individual peroxidase genes was assessed in organ-specific EST libraries and compared to the expression of 33 peroxidase genes which we analyzed in whole plants 3, 6, 15, 35 and 59 days after sowing. Expression was assessed in root, rosette leaf, stem, cauline leaf, flower bud and cell culture tissues using the gene-specific and highly sensitive reverse transcriptase-polymerase chain reaction (RT-PCR). We predicted that 71 genes could yield stable proteins folded similarly to horseradish peroxidase (HRP). The putative mature peroxidases derived from these genes showed 28-94% amino acid sequence identity and were all targeted to the endoplasmic reticulum by N-terminal signal peptides. In 20 peroxidases these signal peptides were followed by various N-terminal extensions of unknown function which are not present in HRP. Ten peroxidases showed a C-terminal extension indicating vacuolar targeting. We found that the majority of peroxidase genes were expressed in root. In total, class III peroxidases accounted for an impressive 2.2% of root ESTs. Rather few peroxidases showed organ specificity. Most importantly, genes expressed constitutively in all organs and genes with a preference for root represented structurally diverse peroxidases (< 70% sequence identity). Furthermore, genes appearing in tandem showed distinct expression profiles. The alignment of 73 Arabidopsis peroxidase sequences provides an easy access to the identification of orthologous peroxidases

  20. ATM-mediated transcriptional and developmental responses to gamma-rays in Arabidopsis.

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    Lilian Ricaud

    Full Text Available ATM (Ataxia Telangiectasia Mutated is an essential checkpoint kinase that signals DNA double-strand breaks in eukaryotes. Its depletion causes meiotic and somatic defects in Arabidopsis and progressive motor impairment accompanied by several cell deficiencies in patients with ataxia telangiectasia (AT. To obtain a comprehensive view of the ATM pathway in plants, we performed a time-course analysis of seedling responses by combining confocal laser scanning microscopy studies of root development and genome-wide expression profiling of wild-type (WT and homozygous ATM-deficient mutants challenged with a dose of gamma-rays (IR that is sublethal for WT plants. Early morphologic defects in meristematic stem cells indicated that AtATM, an Arabidopsis homolog of the human ATM gene, is essential for maintaining the quiescent center and controlling the differentiation of initial cells after exposure to IR. Results of several microarray experiments performed with whole seedlings and roots up to 5 h post-IR were compiled in a single table, which was used to import gene information and extract gene sets. Sequence and function homology searches; import of spatio-temporal, cell cycling, and mutant-constitutive expression characteristics; and a simplified functional classification system were used to identify novel genes in all functional classes. The hundreds of radiomodulated genes identified were not a random collection, but belonged to functional pathways such as those of the cell cycle; cell death and repair; DNA replication, repair, and recombination; and transcription; translation; and signaling, indicating the strong cell reprogramming and double-strand break abrogation functions of ATM checkpoints. Accordingly, genes in all functional classes were either down or up-regulated concomitantly with downregulation of chromatin deacetylases or upregulation of acetylases and methylases, respectively. Determining the early transcriptional indicators of

  1. Tissue-specific expression patterns of Arabidopsis NF-Y transcription factors suggest potential for extensive combinatorial complexity.

    Science.gov (United States)

    Siefers, Nicholas; Dang, Kristen K; Kumimoto, Roderick W; Bynum, William Edwards; Tayrose, Gregory; Holt, Ben F

    2009-02-01

    All aspects of plant and animal development are controlled by complex networks of transcription factors. Transcription factors are essential for converting signaling inputs, such as changes in daylength, into complex gene regulatory outputs. While some transcription factors control gene expression by binding to cis-regulatory elements as individual subunits, others function in a combinatorial fashion. How individual subunits of combinatorial transcription factors are spatially and temporally deployed (e.g. expression-level, posttranslational modifications and subcellular localization) has profound effects on their control of gene expression. In the model plant Arabidopsis (Arabidopsis thaliana), we have identified 36 Nuclear Factor Y (NF-Y) transcription factor subunits (10 NF-YA, 13 NF-YB, and 13 NF-YC subunits) that can theoretically combine to form 1,690 unique complexes. Individual plant subunits have functions in flowering time, embryo maturation, and meristem development, but how they combine to control these processes is unknown. To assist in the process of defining unique NF-Y complexes, we have created promoter:beta-glucuronidase fusion lines for all 36 Arabidopsis genes. Here, we show NF-Y expression patterns inferred from these promoter:beta-glucuronidase lines for roots, light- versus dark-grown seedlings, rosettes, and flowers. Additionally, we review the phylogenetic relationships and examine protein alignments for each NF-Y subunit family. The results are discussed with a special emphasis on potential roles for NF-Y subunits in photoperiod-controlled flowering time.

  2. In silico comparison of transcript abundances during Arabidopsis thaliana and Glycine max resistance to Fusarium virguliforme

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    Iqbal M Javed

    2008-09-01

    Full Text Available Abstract Background Sudden death syndrome (SDS of soybean (Glycine max L. Merr. is an economically important disease, caused by the semi-biotrophic fungus Fusarium solani f. sp. glycines, recently renamed Fusarium virguliforme (Fv. Due to the complexity and length of the soybean-Fusarium interaction, the molecular mechanisms underlying plant resistance and susceptibility to the pathogen are not fully understood. F. virguliforme has a very wide host range for the ability to cause root rot and a very narrow host range for the ability to cause a leaf scorch. Arabidopsis thaliana is a host for many types of phytopathogens including bacteria, fungi, viruses and nematodes. Deciphering the variations among transcript abundances (TAs of functional orthologous genes of soybean and A. thaliana involved in the interaction will provide insights into plant resistance to F. viguliforme. Results In this study, we reported the analyses of microarrays measuring TA in whole plants after A. thaliana cv 'Columbia' was challenged with fungal pathogen F. virguliforme. Infection caused significant variations in TAs. The total number of increased transcripts was nearly four times more than that of decreased transcripts in abundance. A putative resistance pathway involved in responding to the pathogen infection in A. thaliana was identified and compared to that reported in soybean. Conclusion Microarray experiments allow the interrogation of tens of thousands of transcripts simultaneously and thus, the identification of plant pathways is likely to be involved in plant resistance to Fusarial pathogens. Dissection of the set functional orthologous genes between soybean and A. thaliana enabled a broad view of the functional relationships and molecular interactions among plant genes involved in F. virguliforme resistance.

  3. DNA replication factor C1 mediates genomic stability and transcriptional gene silencing in Arabidopsis

    KAUST Repository

    Liu, Qian

    2010-07-01

    Genetic screening identified a suppressor of ros1-1, a mutant of REPRESSOR OF SILENCING1 (ROS1; encoding a DNA demethylation protein). The suppressor is a mutation in the gene encoding the largest subunit of replication factor C (RFC1). This mutation of RFC1 reactivates the unlinked 35S-NPTII transgene, which is silenced in ros1 and also increases expression of the pericentromeric Athila retrotransposons named transcriptional silent information in a DNA methylationindependent manner. rfc1 is more sensitive than the wild type to the DNA-damaging agent methylmethane sulphonate and to the DNA inter- and intra- cross-linking agent cisplatin. The rfc1 mutant constitutively expresses the G2/M-specific cyclin CycB1;1 and other DNA repair-related genes. Treatment with DNA-damaging agents mimics the rfc1 mutation in releasing the silenced 35S-NPTII, suggesting that spontaneously induced genomic instability caused by the rfc1 mutation might partially contribute to the released transcriptional gene silencing (TGS). The frequency of somatic homologous recombination is significantly increased in the rfc1 mutant. Interestingly, ros1 mutants show increased telomere length, but rfc1 mutants show decreased telomere length and reduced expression of telomerase. Our results suggest that RFC1 helps mediate genomic stability and TGS in Arabidopsis thaliana. © 2010 American Society of Plant Biologists.

  4. Soybean GmPHD-type transcription regulators improve stress tolerance in transgenic Arabidopsis plants.

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    Wei Wei

    Full Text Available BACKGROUND: Soybean [Glycine max (L. Merr.] is one of the most important crops for oil and protein resource. Improvement of stress tolerance will be beneficial for soybean seed production. PRINCIPAL FINDINGS: Six GmPHD genes encoding Alfin1-type PHD finger protein were identified and their expressions differentially responded to drought, salt, cold and ABA treatments. The six GmPHDs were nuclear proteins and showed ability to bind the cis-element "GTGGAG". The N-terminal domain of GmPHD played a major role in DNA binding. Using a protoplast assay system, we find that GmPHD1 to GmPHD5 had transcriptional suppression activity whereas GmPHD6 did not have. In yeast assay, the GmPHD6 can form homodimer and heterodimer with the other GmPHDs except GmPHD2. The N-terminal plus the variable regions but not the PHD-finger is required for the dimerization. Transgenic Arabidopsis plants overexpressing the GmPHD2 showed salt tolerance when compared with the wild type plants. This tolerance was likely achieved by diminishing the oxidative stress through regulation of downstream genes. SIGNIFICANCE: These results provide important clues for soybean stress tolerance through manipulation of PHD-type transcription regulator.

  5. Regulation of Arabidopsis Early Anther Development by Putative Cell-Cell Signaling Molecules and Transcriptional Regulators

    Institute of Scientific and Technical Information of China (English)

    Yu-Jin Sun; Carey LH Hord; Chang-Bin Chen; Hong Ma

    2007-01-01

    Anther development in flowering plants involves the formation of several cell types, including the tapetal and pollen mother cells. The use of genetic and molecular tools has led to the identification and characterization of genes that are critical for normal cell division and differentiation in Arabidopsis early anther development. We review here several recent studies on these genes, including the demonstration that the putative receptor protein kinases BAM1 and BAM2 together play essential roles in the control of early cell division and differentiation. In addition, we discuss the hypothesis that BAM1/2 may form a positive-negative feedback regulatory loop with a previously identified key regulator, SPOROCYTELESS (also called NOZZLE),to control the balance between sporogenous and somatic cell types in the anther. Furthermore, we summarize the isolation and functional analysis of the DYSFUNCTIONAL TAPETUM1 (DYT1) gene in promoting proper tapetal cell differentiation. Our finding that DYT1 encodes a putative transcription factor of the bHLH family, as well as relevant expression analyses, strongly supports a model that DYT1 serves as a critical link between upstream factors and downstream target genes that are critical for normal tapetum development and function. These studies, together with other recently published works, indicate that cell-cell communication and transcriptional control are key processes essential for cell fate specification in anther development.

  6. Arabidopsis MAP kinase 4 regulates gene expression through transcription factor release in the nucleus.

    Science.gov (United States)

    Qiu, Jin-Long; Fiil, Berthe Katrine; Petersen, Klaus; Nielsen, Henrik Bjørn; Botanga, Christopher J; Thorgrimsen, Stephan; Palma, Kristoffer; Suarez-Rodriguez, Maria Cristina; Sandbech-Clausen, Signe; Lichota, Jacek; Brodersen, Peter; Grasser, Klaus D; Mattsson, Ole; Glazebrook, Jane; Mundy, John; Petersen, Morten

    2008-08-20

    Plant and animal perception of microbes through pathogen surveillance proteins leads to MAP kinase signalling and the expression of defence genes. However, little is known about how plant MAP kinases regulate specific gene expression. We report that, in the absence of pathogens, Arabidopsis MAP kinase 4 (MPK4) exists in nuclear complexes with the WRKY33 transcription factor. This complex depends on the MPK4 substrate MKS1. Challenge with Pseudomonas syringae or flagellin leads to the activation of MPK4 and phosphorylation of MKS1. Subsequently, complexes with MKS1 and WRKY33 are released from MPK4, and WRKY33 targets the promoter of PHYTOALEXIN DEFICIENT3 (PAD3) encoding an enzyme required for the synthesis of antimicrobial camalexin. Hence, wrky33 mutants are impaired in the accumulation of PAD3 mRNA and camalexin production upon infection. That WRKY33 is an effector of MPK4 is further supported by the suppression of PAD3 expression in mpk4-wrky33 double mutant backgrounds. Our data establish direct links between MPK4 and innate immunity and provide an example of how a plant MAP kinase can regulate gene expression by releasing transcription factors in the nucleus upon activation.

  7. Unraveling the WRKY transcription factors network in Arabidopsis Thaliana by integrative approach

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    Mouna Choura

    2015-06-01

    Full Text Available The WRKY transcription factors superfamily are involved in diverse biological processes in plants including response to biotic and abiotic stresses and plant immunity. Protein-protein interaction network is a useful approach for understanding these complex processes. The availability of Arabidopsis Thaliana interactome offers a good opportunity to do get a global view of protein network. In this work, we have constructed the WRKY transcription factor network by combining different sources of evidence and we characterized its topological features using computational tools. We found that WRKY network is a hub-based network involving multifunctional proteins denoted as hubs such as WRKY 70, WRKY40, WRKY 53, WRKY 60, WRKY 33 and WRKY 51. Functional annotation showed seven functional modules particularly involved in biotic stress and defense responses. Furthermore, the gene ontology and pathway enrichment analysis revealed that WRKY proteins are mainly involved in plant-pathogen interaction pathways and their functions are directly related to the stress response and immune system process.

  8. The WEREWOLF MYB protein directly regulates CAPRICE transcription during cell fate specification in the Arabidopsis root epidermis.

    Science.gov (United States)

    Ryu, Kook Hui; Kang, Yeon Hee; Park, Young-hwan; Hwang, Ildoo; Schiefelbein, John; Lee, Myeong Min

    2005-11-01

    The Arabidopsis root epidermis is composed of two types of cells, hair cells and non-hair cells, and their fate is determined in a position-dependent manner. WEREWOLF (WER), a R2R3 MYB protein, has been shown genetically to function as a master regulator to control both of the epidermal cell fates. To directly test the proposed role of WER in this system, we examined its subcellular localization and defined its transcriptional activation properties. We show that a WER-GFP fusion protein is functional and accumulates in the nucleus of the N-position cells in the Arabidopsis root epidermis, as expected for a transcriptional regulator. We also find that a modified WER protein with a strong activation domain (WER-VP16) promotes the formation of both epidermal cell types, supporting the view that WER specifies both cell fates. In addition, we used the glucocorticoid receptor (GR) inducible system to show that CPC transcription is regulated directly by WER. Using EMSA, we found two WER-binding sites (WBSs; WBSI and WBSII) in the CPC promoter. WER-WBSI binding was confirmed in vivo using the yeast one-hybrid assay. Binding between the WER protein and both WBSs (WBSI and WBSII), and the importance of the two WBSs in CPC promoter activity were confirmed in Arabidopsis. These results provide experimental support for the proposed role of WER as an activator of gene transcription during the specification of both epidermal cell fates.

  9. The HIRA complex that deposits the histone H3.3 is conserved in Arabidopsis and facilitates transcriptional dynamics

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    Xin Nie

    2014-08-01

    Full Text Available In animals, replication-independent incorporation of nucleosomes containing the histone variant H3.3 enables global reprogramming of histone modifications and transcriptional profiles. H3.3 enrichment over gene bodies correlates with gene transcription in animals and plants. In animals, H3.3 is deposited into chromatin by specific protein complexes, including the HIRA complex. H3.3 variants evolved independently and acquired similar properties in animals and plants, questioning how the H3.3 deposition machinery evolved in plants and what are its biological functions. We performed phylogenetic analyses in the plant kingdom and identified in Arabidopsis all orthologs of human genes encoding members of the HIRA complex. Genetic analyses, biochemical data and protein localisation suggest that these proteins form a complex able to interact with H3.3 in Arabidopsis in a manner similar to that described in mammals. In contrast to animals, where HIRA is required for fertilization and early development, loss of function of HIRA in Arabidopsis causes mild phenotypes in the adult plant and does not perturb sexual reproduction and embryogenesis. Rather, HIRA function is required for transcriptional reprogramming during dedifferentiation of plant cells that precedes vegetative propagation and for the appropriate transcription of genes responsive to biotic and abiotic factors. We conclude that the molecular function of the HIRA complex is conserved between plants and animals. Yet plants diversified HIRA functions to enable asexual reproduction and responsiveness to the environment in response to the plant sessile lifestyle.

  10. CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes

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    Moreau Yves

    2007-10-01

    Full Text Available Abstract Background The Complete Arabidopsis Transcript MicroArray (CATMA initiative combines the efforts of laboratories in eight European countries 1 to deliver gene-specific sequence tags (GSTs for the Arabidopsis research community. The CATMA initiative offers the power and flexibility to regularly update the GST collection according to evolving knowledge about the gene repertoire. These GST amplicons can easily be reamplified and shared, subsets can be picked at will to print dedicated arrays, and the GSTs can be cloned and used for other functional studies. This ongoing initiative has already produced approximately 24,000 GSTs that have been made publicly available for spotted microarray printing and RNA interference. Results GSTs from the CATMA version 2 repertoire (CATMAv2, created in 2002 were mapped onto the gene models from two independent Arabidopsis nuclear genome annotation efforts, TIGR5 and PSB-EuGène, to consolidate a list of genes that were targeted by previously designed CATMA tags. A total of 9,027 gene models were not tagged by any amplified CATMAv2 GST, and 2,533 amplified GSTs were no longer predicted to tag an updated gene model. To validate the efficacy of GST mapping criteria and design rules, the predicted and experimentally observed hybridization characteristics associated to GST features were correlated in transcript profiling datasets obtained with the CATMAv2 microarray, confirming the reliability of this platform. To complete the CATMA repertoire, all 9,027 gene models for which no GST had yet been designed were processed with an adjusted version of the Specific Primer and Amplicon Design Software (SPADS. A total of 5,756 novel GSTs were designed and amplified by PCR from genomic DNA. Together with the pre-existing GST collection, this new addition constitutes the CATMAv3 repertoire. It comprises 30,343 unique amplified sequences that tag 24,202 and 23,009 protein-encoding nuclear gene models in the TAIR6 and Eu

  11. Transcription factor veracity: is GBF3 responsible for ABA-regulated expression of Arabidopsis Adh?

    Science.gov (United States)

    Lu, G; Paul, A L; McCarty, D R; Ferl, R J

    1996-01-01

    Assignment of particular transcription factors to specific roles in promoter elements can be problematic, especially in systems such as the G-box, where multiple factors of overlapping specificity exist. In the Arabidopsis alcohol dehydrogenase (Adh) promoter, the G-box regulates expression in response to cold and dehydration, presumably through the action of abscisic acid (ABA), and is bound by a nuclear protein complex in vivo during expression in cell cultures. In this report, we test the conventional wisdom of biochemical approaches used to identify DNA binding proteins and assess their specific interactions by using the G-box and a nearby half G-box element of the Arabidopsis Adh promoter as a model system. Typical in vitro assays demonstrated specific interaction of G-box factor 3 (GBF3) with both the G-box and the half G-box element. Dimethyl sulfate footprint analysis confirmed that the in vitro binding signature of GBF3 essentially matches the footprint signature detected in vivo at the G-box. Because RNA gel blot data indicated that GBF3 is itself induced by ABA, we might have concluded that GBF3 is indeed the GBF responsible in cell cultures for binding to the Adh G-box and is therefore responsible for ABA-regulated expression of Adh. Potential limitations of this conclusion are exposed by the fact that other GBFs bind the G-box with the same signature as GBF3, and subtle differences between in vivo and in vitro footprint signatures indicate that factors other than or in addition to GBF3 interact with the half G-box element. PMID:8672884

  12. Photosynthesis of root chloroplasts developed in Arabidopsis lines overexpressing GOLDEN2-LIKE transcription factors.

    Science.gov (United States)

    Kobayashi, Koichi; Sasaki, Daichi; Noguchi, Ko; Fujinuma, Daiki; Komatsu, Hirohisa; Kobayashi, Masami; Sato, Mayuko; Toyooka, Kiminori; Sugimoto, Keiko; Niyogi, Krishna K; Wada, Hajime; Masuda, Tatsuru

    2013-08-01

    In plants, genes involved in photosynthesis are encoded separately in nuclei and plastids, and tight cooperation between these two genomes is therefore required for the development of functional chloroplasts. Golden2-like (GLK) transcription factors are involved in chloroplast development, directly targeting photosynthesis-associated nuclear genes for up-regulation. Although overexpression of GLKs leads to chloroplast development in non-photosynthetic organs, the mechanisms of coordination between the nuclear gene expression influenced by GLKs and the photosynthetic processes inside chloroplasts are largely unknown. To elucidate the impact of GLK-induced expression of photosynthesis-associated nuclear genes on the construction of photosynthetic systems, chloroplast morphology and photosynthetic characteristics in greenish roots of Arabidopsis thaliana lines overexpressing GLKs were compared with those in wild-type roots and leaves. Overexpression of GLKs caused up-regulation of not only their direct targets but also non-target nuclear and plastid genes, leading to global induction of chloroplast biogenesis in the root. Large antennae relative to reaction centers were observed in wild-type roots and were further enhanced by GLK overexpression due to the increased expression of target genes associated with peripheral light-harvesting antennae. Photochemical efficiency was lower in the root chloroplasts than in leaf chloroplasts, suggesting that the imbalance in the photosynthetic machinery decreases the efficiency of light utilization in root chloroplasts. Despite the low photochemical efficiency, root photosynthesis contributed to carbon assimilation in Arabidopsis. Moreover, GLK overexpression increased CO₂ fixation and promoted phototrophic performance of the root, showing the potential of root photosynthesis to improve effective carbon utilization in plants.

  13. Structural and functional analysis of VQ motif-containing proteins in Arabidopsis as interacting proteins of WRKY transcription factors.

    Science.gov (United States)

    Cheng, Yuan; Zhou, Yuan; Yang, Yan; Chi, Ying-Jun; Zhou, Jie; Chen, Jian-Ye; Wang, Fei; Fan, Baofang; Shi, Kai; Zhou, Yan-Hong; Yu, Jing-Quan; Chen, Zhixiang

    2012-06-01

    WRKY transcription factors are encoded by a large gene superfamily with a broad range of roles in plants. Recently, several groups have reported that proteins containing a short VQ (FxxxVQxLTG) motif interact with WRKY proteins. We have recently discovered that two VQ proteins from Arabidopsis (Arabidopsis thaliana), SIGMA FACTOR-INTERACTING PROTEIN1 and SIGMA FACTOR-INTERACTING PROTEIN2, act as coactivators of WRKY33 in plant defense by specifically recognizing the C-terminal WRKY domain and stimulating the DNA-binding activity of WRKY33. In this study, we have analyzed the entire family of 34 structurally divergent VQ proteins from Arabidopsis. Yeast (Saccharomyces cerevisiae) two-hybrid assays showed that Arabidopsis VQ proteins interacted specifically with the C-terminal WRKY domains of group I and the sole WRKY domains of group IIc WRKY proteins. Using site-directed mutagenesis, we identified structural features of these two closely related groups of WRKY domains that are critical for interaction with VQ proteins. Quantitative reverse transcription polymerase chain reaction revealed that expression of a majority of Arabidopsis VQ genes was responsive to pathogen infection and salicylic acid treatment. Functional analysis using both knockout mutants and overexpression lines revealed strong phenotypes in growth, development, and susceptibility to pathogen infection. Altered phenotypes were substantially enhanced through cooverexpression of genes encoding interacting VQ and WRKY proteins. These findings indicate that VQ proteins play an important role in plant growth, development, and response to environmental conditions, most likely by acting as cofactors of group I and IIc WRKY transcription factors.

  14. ABSCISIC ACID-INSENSITIVE 4 negatively regulates flowering through directly promoting Arabidopsis FLOWERING LOCUS C transcription

    Science.gov (United States)

    Shu, Kai; Chen, Qian; Wu, Yaorong; Liu, Ruijun; Zhang, Huawei; Wang, Shengfu; Tang, Sanyuan; Yang, Wenyu; Xie, Qi

    2016-01-01

    During the life cycle of a plant, one of the major biological processes is the transition from the vegetative to the reproductive stage. In Arabidopsis, flowering time is precisely controlled by extensive environmental and internal cues. Gibberellins (GAs) promote flowering, while abscisic acid (ABA) is considered as a flowering suppressor. However, the detailed mechanism through which ABA inhibits the floral transition is poorly understood. Here, we report that ABSCISIC ACID-INSENSITIVE 4 (ABI4), a key component in the ABA signalling pathway, negatively regulates floral transition by directly promoting FLOWERING LOCUS C (FLC) transcription. The abi4 mutant showed the early flowering phenotype whereas ABI4-overexpressing (OE-ABI4) plants had delayed floral transition. Consistently, quantitative reverse transcription–PCR (qRT–PCR) assay revealed that the FLC transcription level was down-regulated in abi4, but up-regulated in OE-ABI4. The change in FT level was consistent with the pattern of FLC expression. Chromatin immunoprecipitation-qPCR (ChIP-qPCR), electrophoretic mobility shift assay (EMSA), and tobacco transient expression analysis showed that ABI4 promotes FLC expression by directly binding to its promoter. Genetic analysis demonstrated that OE-ABI4::flc-3 could not alter the flc-3 phenotype. OE-FLC::abi4 showed a markedly delayed flowering phenotype, which mimicked OE-FLC::WT, and suggested that ABI4 acts upstream of FLC in the same genetic pathway. Taken together, these findings suggest that ABA inhibits the floral transition by activating FLC transcription through ABI4. PMID:26507894

  15. Tomato Whole Genome Transcriptional Response to Tetranychus urticae Identifies Divergence of Spider Mite-Induced Responses Between Tomato and Arabidopsis.

    Science.gov (United States)

    Martel, Catherine; Zhurov, Vladimir; Navarro, Marie; Martinez, Manuel; Cazaux, Marc; Auger, Philippe; Migeon, Alain; Santamaria, M Estrella; Wybouw, Nicky; Diaz, Isabel; Van Leeuwen, Thomas; Navajas, Maria; Grbic, Miodrag; Grbic, Vojislava

    2015-03-01

    The two-spotted spider mite Tetranychus urticae is one of the most significant mite pests in agriculture, feeding on more than 1,100 plant hosts, including model plants Arabidopsis thaliana and tomato, Solanum lycopersicum. Here, we describe timecourse tomato transcriptional responses to spider mite feeding and compare them with Arabidopsis in order to determine conserved and divergent defense responses to this pest. To refine the involvement of jasmonic acid (JA) in mite-induced responses and to improve tomato Gene Ontology annotations, we analyzed transcriptional changes in the tomato JA-signaling mutant defenseless1 (def-1) upon JA treatment and spider mite herbivory. Overlay of differentially expressed genes (DEG) identified in def-1 onto those from the timecourse experiment established that JA controls expression of the majority of genes differentially regulated by herbivory. Comparison of defense responses between tomato and Arabidopsis highlighted 96 orthologous genes (of 2,133 DEG) that were recruited for defense against spider mites in both species. These genes, involved in biosynthesis of JA, phenylpropanoids, flavonoids, and terpenoids, represent the conserved core of induced defenses. The remaining tomato DEG support the establishment of tomato-specific defenses, indicating profound divergence of spider mite-induced responses between tomato and Arabidopsis.

  16. The Arabidopsis Transcription Factor NAC016 Promotes Drought Stress Responses by Repressing AREB1 Transcription through a Trifurcate Feed-Forward Regulatory Loop Involving NAP.

    Science.gov (United States)

    Sakuraba, Yasuhito; Kim, Ye-Sol; Han, Su-Hyun; Lee, Byoung-Doo; Paek, Nam-Chon

    2015-06-01

    Drought and other abiotic stresses negatively affect plant growth and development and thus reduce productivity. The plant-specific NAM/ATAF1/2/CUC2 (NAC) transcription factors have important roles in abiotic stress-responsive signaling. Here, we show that Arabidopsis thaliana NAC016 is involved in drought stress responses; nac016 mutants have high drought tolerance, and NAC016-overexpressing (NAC016-OX) plants have low drought tolerance. Using genome-wide gene expression microarray analysis and MEME motif searches, we identified the NAC016-specific binding motif (NAC16BM), GATTGGAT[AT]CA, in the promoters of genes downregulated in nac016-1 mutants. The NAC16BM sequence does not contain the core NAC binding motif CACG (or its reverse complement CGTG). NAC016 directly binds to the NAC16BM in the promoter of ABSCISIC ACID-RESPONSIVE ELEMENT BINDING PROTEIN1 (AREB1), which encodes a central transcription factor in the stress-responsive abscisic acid signaling pathway and represses AREB1 transcription. We found that knockout mutants of the NAC016 target gene NAC-LIKE, ACTIVATED BY AP3/PI (NAP) also exhibited strong drought tolerance; moreover, NAP binds to the AREB1 promoter and suppresses AREB1 transcription. Taking these results together, we propose that a trifurcate feed-forward pathway involving NAC016, NAP, and AREB1 functions in the drought stress response, in addition to affecting leaf senescence in Arabidopsis. PMID:26059204

  17. Dominant Repression by Arabidopsis Transcription Factor MYB44 Causes Oxidative Damage and Hypersensitivity to Abiotic Stress

    Directory of Open Access Journals (Sweden)

    Helene Persak

    2014-02-01

    Full Text Available In any living species, stress adaptation is closely linked with major changes of the gene expression profile. As a substrate protein of the rapidly stress-induced mitogen-activated protein kinase MPK3, Arabidopsis transcription factor MYB44 likely acts at the front line of stress-induced re-programming. We recently characterized MYB44 as phosphorylation-dependent positive regulator of salt stress signaling. Molecular events downstream of MYB44 are largely unknown. Although MYB44 binds to the MBSII element in vitro, it has no discernible effect on MBSII-driven reporter gene expression in plant co-transfection assays. This may suggest limited abundance of a synergistic co-regulator. MYB44 carries a putative transcriptional repression (Ethylene responsive element binding factor-associated Amphiphilic Repression, EAR motif. We employed a dominant repressor strategy to gain insights into MYB44-conferred stress resistance. Overexpression of a MYB44-REP fusion markedly compromised salt and drought stress tolerance—the opposite was seen in MYB44 overexpression lines. MYB44-mediated resistance likely results from induction of tolerance-enhancing, rather than from repression of tolerance-diminishing factors. Salt stress-induced accumulation of destructive reactive oxygen species is efficiently prevented in transgenic MYB44, but accelerated in MYB44-REP lines. Furthermore, heterologous overexpression of MYB44-REP caused tissue collapse in Nicotiana. A mechanistic model of MAPK-MYB-mediated enhancement in the antioxidative capacity and stress tolerance is proposed. Genetic engineering of MYB44 variants with higher trans-activating capacity may be a means to further raise stress resistance in crops.

  18. Quiescent center initiation in the Arabidopsis lateral root primordia is dependent on the SCARECROW transcription factor.

    Science.gov (United States)

    Goh, Tatsuaki; Toyokura, Koichi; Wells, Darren M; Swarup, Kamal; Yamamoto, Mayuko; Mimura, Tetsuro; Weijers, Dolf; Fukaki, Hidehiro; Laplaze, Laurent; Bennett, Malcolm J; Guyomarc'h, Soazig

    2016-09-15

    Lateral root formation is an important determinant of root system architecture. In Arabidopsis, lateral roots originate from pericycle cells, which undergo a program of morphogenesis to generate a new lateral root meristem. Despite its importance for root meristem organization, the onset of quiescent center (QC) formation during lateral root morphogenesis remains unclear. Here, we used live 3D confocal imaging to monitor cell organization and identity acquisition during lateral root development. Our dynamic observations revealed an early morphogenesis phase and a late meristem formation phase as proposed in the bi-phasic growth model. Establishment of lateral root QCs coincided with this developmental phase transition. QC precursor cells originated from the outer layer of stage II lateral root primordia, within which the SCARECROW (SCR) transcription factor was specifically expressed. Disrupting SCR function abolished periclinal divisions in this lateral root primordia cell layer and perturbed the formation of QC precursor cells. We conclude that de novo QC establishment in lateral root primordia operates via SCR-mediated formative cell division and coincides with the developmental phase transition. PMID:27510971

  19. AGO6 functions in RNA-mediated transcriptional gene silencing in shoot and root meristems in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Changho Eun

    Full Text Available RNA-directed DNA methylation (RdDM is a small interfering RNA (siRNA-mediated epigenetic modification that contributes to transposon silencing in plants. RdDM requires a complex transcriptional machinery that includes specialized RNA polymerases, named Pol IV and Pol V, as well as chromatin remodelling proteins, transcription factors, RNA binding proteins, and other plant-specific proteins whose functions are not yet clarified. In Arabidopsis thaliana, DICER-LIKE3 and members of the ARGONAUTE4 group of ARGONAUTE (AGO proteins are involved, respectively, in generating and using 24-nt siRNAs that trigger methylation and transcriptional gene silencing of homologous promoter sequences. AGO4 is the main AGO protein implicated in the RdDM pathway. Here we report the identification of the related AGO6 in a forward genetic screen for mutants defective in RdDM and transcriptional gene silencing in shoot and root apical meristems in Arabidopsis thaliana. The identification of AGO6, and not AGO4, in our screen is consistent with the primary expression of AGO6 in shoot and root growing points.

  20. Functional characterization of Arabidopsis NaCl-inducible WRKY25 and WRKY33 transcription factors in abiotic stresses.

    Science.gov (United States)

    Jiang, Yuanqing; Deyholos, Michael K

    2009-01-01

    Previous microarray analyses of Arabidopsis roots identified two closely related WRKY transcription factors (WRKY25 and WRKY33) among the transcripts that increased in abundance following treatment with NaCl. Here, we report further characterization of these genes, which we found to be inducible by a variety of abiotic stresses in an SOS-pathway independent manner, although WRKY33 induction was dependent on ABA signaling. Transcripts of both genes were detected in roots and leaves, while specific patterns of enrichment were observed in stems and floral buds for WRKY25 and WRKY33, respectively. We also identified upstream intergenic regions from each gene that were sufficient to confer stress-inducible expression on a reporter gene. However, the stress sensitivity of wrky25 null mutants did not differ from wild-type under any assay condition, while wrky33 null mutants and wrky25wrky33 double mutants showed only a moderate increase in NaCl-sensitivity, suggesting functional redundancy with other transcription factors. Nevertheless, overexpression of WRKY25 or WRKY33 was sufficient to increase Arabidopsis NaCl tolerance, while increasing sensitivity to ABA. Through microarray analyses of relevant genotypes, we identified 31 and 208 potential downstream targets of WRKY25 and WRKY33, respectively, most of which contained a W-box in their upstream regions.

  1. The sunflower transcription factor HaHB11 improves yield, biomass and tolerance to flooding in transgenic Arabidopsis plants.

    Science.gov (United States)

    Cabello, Julieta V; Giacomelli, Jorge I; Piattoni, Claudia V; Iglesias, Alberto A; Chan, Raquel L

    2016-03-20

    HaHB11 is a member of the sunflower homeodomain-leucine zipper I subfamily of transcription factors. The analysis of a sunflower microarray hybridized with RNA from HaHB11-transformed leaf-disks indicated the regulation of many genes encoding enzymes from glycolisis and fermentative pathways. A 1300bp promoter sequence, fused to the GUS reporter gene, was used to transform Arabidopsis plants showing an induction of expression after flooding treatments, concurrently with HaHB11 regulation by submergence in sunflower. Arabidopsis transgenic plants expressing HaHB11 under the control of the CaMV 35S promoter and its own promoter were obtained and these plants exhibited significant increases in rosette and stem biomass. All the lines produced more seeds than controls and particularly, those of high expression level doubled seeds yield. Transgenic plants also showed tolerance to flooding stress, both to submergence and waterlogging. Carbohydrates contents were higher in the transgenics compared to wild type and decreased less after submergence treatments. Finally, transcript levels of selected genes involved in glycolisis and fermentative pathways as well as the corresponding enzymatic activities were assessed both, in sunflower and transgenic Arabidopsis plants, before and after submergence. Altogether, the present work leads us to propose HaHB11 as a biotechnological tool to improve crops yield, biomass and flooding tolerance. PMID:26876611

  2. Transcriptional Gene Silencing Mediated by a Plastid Inner Envelope Phosphoenolpyruvate/Phosphate Translocator CUE1 in Arabidopsis1[OA

    Science.gov (United States)

    Shen, Jie; Ren, Xiaozhi; Cao, Rui; Liu, Jun; Gong, Zhizhong

    2009-01-01

    Mutations in REPRESSOR OF SILENCING1 (ROS1) lead to the transcriptional gene silencing (TGS) of ProRD29A:LUC (LUCIFERASE) and Pro35S:NPTII (Neomycin Phosphotransferase II) reporter genes. We performed a genetic screen to find suppressors of ros1 that identified two mutant alleles in the Arabidopsis (Arabidopsis thaliana) CHLOROPHYLL A/B BINDING PROTEIN UNDEREXPRESSED1 (CUE1) gene, which encodes a plastid inner envelope phosphoenolpyruvate/phosphate translocator. The cue1 mutations released the TGS of Pro35S:NPTII and the transcriptionally silent endogenous locus TRANSCRIPTIONAL SILENCING INFORMATION in a manner that was independent of DNA methylation but dependent on chromatin modification. The cue1 mutations did not affect the TGS of ProRD29A:LUC in ros1, which was dependent on RNA-directed DNA methylation. It is possible that signals from chloroplasts help to regulate the epigenetic status of a subset of genomic loci in the nucleus. PMID:19515789

  3. Arabidopsis WRKY33 is a key transcriptional regulator of hormonal and metabolic responses toward Botrytis cinerea infection.

    Science.gov (United States)

    Birkenbihl, Rainer P; Diezel, Celia; Somssich, Imre E

    2012-05-01

    The Arabidopsis (Arabidopsis thaliana) transcription factor WRKY33 is essential for defense toward the necrotrophic fungus Botrytis cinerea. Here, we aimed at identifying early transcriptional responses mediated by WRKY33. Global expression profiling on susceptible wrky33 and resistant wild-type plants uncovered massive differential transcriptional reprogramming upon B. cinerea infection. Subsequent detailed kinetic analyses revealed that loss of WRKY33 function results in inappropriate activation of the salicylic acid (SA)-related host response and elevated SA levels post infection and in the down-regulation of jasmonic acid (JA)-associated responses at later stages. This down-regulation appears to involve direct activation of several jasmonate ZIM-domain genes, encoding repressors of the JA-response pathway, by loss of WRKY33 function and by additional SA-dependent WRKY factors. Moreover, genes involved in redox homeostasis, SA signaling, ethylene-JA-mediated cross-communication, and camalexin biosynthesis were identified as direct targets of WRKY33. Genetic studies indicate that although SA-mediated repression of the JA pathway may contribute to the susceptibility of wrky33 plants to B. cinerea, it is insufficient for WRKY33-mediated resistance. Thus, WRKY33 apparently directly targets other still unidentified components that are also critical for establishing full resistance toward this necrotroph.

  4. EBE, an AP2/ERF transcription factor highly expressed in proliferating cells, affects shoot architecture in Arabidopsis.

    Science.gov (United States)

    Mehrnia, Mohammad; Balazadeh, Salma; Zanor, María-Inés; Mueller-Roeber, Bernd

    2013-06-01

    We report about ERF BUD ENHANCER (EBE; At5g61890), a transcription factor that affects cell proliferation as well as axillary bud outgrowth and shoot branching in Arabidopsis (Arabidopsis thaliana). EBE encodes a member of the APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) transcription factor superfamily; the gene is strongly expressed in proliferating cells and is rapidly and transiently up-regulated in axillary meristems upon main stem decapitation. Overexpression of EBE promotes cell proliferation in growing calli, while the opposite is observed in EBE-RNAi lines. EBE overexpression also stimulates axillary bud formation and outgrowth, while repressing it results in inhibition of bud growth. Global transcriptome analysis of estradiol-inducible EBE overexpression lines revealed 48 EBE early-responsive genes, of which 14 were up-regulated and 34 were down-regulated. EBE activates several genes involved in cell cycle regulation and dormancy breaking, including D-type cyclin CYCD3;3, transcription regulator DPa, and BRCA1-ASSOCIATED RING DOMAIN1. Among the down-regulated genes were DORMANCY-ASSOCIATED PROTEIN1 (AtDRM1), AtDRM1 homolog, MEDIATOR OF ABA-REGULATED DORMANCY1, and ZINC FINGER HOMEODOMAIN5. Our data indicate that the effect of EBE on shoot branching likely results from an activation of genes involved in cell cycle regulation and dormancy breaking.

  5. Protein intrinsic disorder in Arabidopsis NAC transcription factors: transcriptional activation by ANAC013 and ANAC046 and their interactions with RCD1.

    Science.gov (United States)

    O'Shea, Charlotte; Kryger, Mikael; Stender, Emil G P; Kragelund, Birthe B; Willemoës, Martin; Skriver, Karen

    2015-01-15

    Protein ID (intrinsic disorder) plays a significant, yet relatively unexplored role in transcription factors (TFs). In the present paper, analysis of the transcription regulatory domains (TRDs) of six phylogenetically representative, plant-specific NAC [no apical meristem, ATAF (Arabidopsis transcription activation factor), cup-shaped cotyledon] TFs shows that the domains are present in similar average pre-molten or molten globule-like states, but have different patterns of order/disorder and MoRFs (molecular recognition features). ANAC046 (Arabidopsis NAC 046) was selected for further studies because of its simple MoRF pattern and its ability to interact with RCD1 (radical-induced cell death 1). Experiments in yeast and thermodynamic characterization suggest that its single MoRF region is sufficient for both transcriptional activation and interaction with RCD1. The remainder of the large regulatory domain is unlikely to contribute to the interaction, since the domain and truncations thereof have similar affinities for RCD1, which are also similar for ANAC013-RCD1 interactions. However, different enthalpic and entropic contributions to binding were revealed for ANAC046 and ANAC013, suggestive of differences in binding mechanisms. Although substitution of both hydrophobic and acidic residues of the ANAC046 MoRF region abolished binding, substitution of other residues, even with α-helix-breaking proline, was less disruptive. Together, the biophysical analyses suggest that RCD1-ANAC046 complex formation does not involve folding-upon-binding, but rather fuzziness or an unknown structure in ANAC046. We suggest that the ANAC046 regulatory domain functions as an entropic chain with a terminal hot spot interacting with RCD1. RCD1, a cellular hub, may be able to interact with many different TFs by exploiting their ID-based flexibility, as demonstrated for its interactions with ANAC046 and ANAC013.

  6. Analysis of components of the mitochondrial transcription machinery in Arabidopsis thaliana

    OpenAIRE

    Kühn, Kristina

    2006-01-01

    In der vorliegenden Arbeit wurde die Transkription mitochondrialer Gene durch die kernkodierten Phagentyp-RNA-Polymerasen RpoTm und RpoTmp der Pflanze Arabidopsis untersucht. Im Mitochondriengenom von Arabidopsis wurden fr 12 Gene Promotoren bestimmt. Diese zeigten verschiedene Sequenzelemente und wichen meist von der fr Dikotyle publizierten Konsensussequenz ab. Fr die Mehrheit der Gene wurden multiple Promotoren identifiziert. Es wurden weiterhin Promotoren nachgewiesen, welche die Tran...

  7. Constitutive production of nitric oxide leads to enhanced drought stress resistance and extensive transcriptional reprogramming in Arabidopsis.

    Science.gov (United States)

    Shi, Haitao; Ye, Tiantian; Zhu, Jian-Kang; Chan, Zhulong

    2014-08-01

    Nitric oxide (NO) is involved in plant responses to many environmental stresses. Transgenic Arabidopsis lines that constitutively express rat neuronal NO synthase (nNOS) were described recently. In this study, it is reported that the nNOS transgenic Arabidopsis plants displayed high levels of osmolytes and increased antioxidant enzyme activities. Transcriptomic analysis identified 601 or 510 genes that were differentially expressed as a consequence of drought stress or nNOS transformation, respectively. Pathway and gene ontology (GO) term enrichment analyses revealed that genes involved in photosynthesis, redox, stress, and phytohormone and secondary metabolism were greatly affected by the nNOS transgene. Several CBF genes and members of zinc finger gene families, which are known to regulate transcription in the stress response, were changed by the nNOS transgene. Genes regulated by both the nNOS transgene and abscisic acid (ABA) treatments were compared and identified, including those for two ABA receptors (AtPYL4 and AtPYL5). Moreover, overexpression of AtPYL4 and AtPYL5 enhanced drought resistance, antioxidant enzyme activity, and osmolyte levels. These observations increase our understanding of the role of NO in drought stress response in Arabidopsis. PMID:24868034

  8. Phosphorylation of an ERF transcription factor by Arabidopsis MPK3/MPK6 regulates plant defense gene induction and fungal resistance.

    Science.gov (United States)

    Meng, Xiangzong; Xu, Juan; He, Yunxia; Yang, Kwang-Yeol; Mordorski, Breanne; Liu, Yidong; Zhang, Shuqun

    2013-03-01

    Arabidopsis thaliana MPK3 and MPK6, two mitogen-activated protein kinases (MAPKs or MPKs), play critical roles in plant disease resistance by regulating multiple defense responses. Previously, we characterized the regulation of phytoalexin biosynthesis by Arabidopsis MPK3/MPK6 cascade and its downstream WRKY33 transcription factor. Here, we report another substrate of MPK3/MPK6, ETHYLENE RESPONSE FACTOR6 (ERF6), in regulating Arabidopsis defense gene expression and resistance to the necrotrophic fungal pathogen Botrytis cinerea. Phosphorylation of ERF6 by MPK3/MPK6 in either the gain-of-function transgenic plants or in response to B. cinerea infection increases ERF6 protein stability in vivo. Phospho-mimicking ERF6 is able to constitutively activate defense-related genes, especially those related to fungal resistance, including PDF1.1 and PDF1.2, and confers enhanced resistance to B. cinerea. By contrast, expression of ERF6-EAR, in which ERF6 was fused to the ERF-associated amphiphilic repression (EAR) motif, strongly suppresses B. cinerea-induced defense gene expression, leading to hypersusceptibility of the ERF6-EAR transgenic plants to B. cinerea. Different from ERF1, the regulation and function of ERF6 in defensin gene activation is independent of ethylene. Based on these data, we conclude that ERF6, another substrate of MPK3 and MPK6, plays important roles downstream of the MPK3/MPK6 cascade in regulating plant defense against fungal pathogens.

  9. Genome-wide analysis of basic leucine zipper transcription factor families in Arabidopsis thaliana, Oryza saliva and Populus trichocarpa

    Institute of Scientific and Technical Information of China (English)

    JI Qian; ZHANG Liang-sheng; WANG Yi-fei; WANG Jian

    2009-01-01

    The basic leucine zipper (bZIP) transcription factors form a large gene family that is important in pathogen defense, light and stress signaling, etc. The Completed whole genome sequences of model plants Arabidopsis (Arabidopsis thaliana), rice (Oryza saliva) and poplar (Populus trichocarpa) constitute a valuable resource for genome-wide analysis and genomic comparative analysis, as they are representatives of the two major evolutionary lineages within the angiosperms: the monocotyledons and the dicotyledons. In this study, bioinformatics analysis identified 74, 89 and 88 bZIP genes respectively in Arabidopsis, rice and poplar. Moreover, a comprehensive overview of this gene family is presented, including the gene structure, phylogeny, chromosome distribution, conserved motifs. As a result, the plant bZIPs were organized into 10 subfamilies on basis of phylogenetic relationship. Gene duplication events during the family evolution history were also investigated. And it was further concluded that chromosomal/segmental duplication might have played a key role in gene expansion of bZIP gene family.

  10. An Arabidopsis F-box protein acts as a transcriptional co-factor to regulate floral development.

    Science.gov (United States)

    Chae, Eunyoung; Tan, Queenie K-G; Hill, Theresa A; Irish, Vivian F

    2008-04-01

    Plants flower in response to both environmental and endogenous signals. The Arabidopsis LEAFY (LFY) transcription factor is crucial in integrating these signals, and acts in part by activating the expression of multiple floral homeotic genes. LFY-dependent activation of the homeotic APETALA3 (AP3) gene requires the activity of UNUSUAL FLORAL ORGANS (UFO), an F-box component of an SCF ubiquitin ligase, yet how this regulation is effected has remained unclear. Here, we show that UFO physically interacts with LFY both in vitro and in vivo, and this interaction is necessary to recruit UFO to the AP3 promoter. Furthermore, a transcriptional repressor domain fused to UFO reduces endogenous LFY activity in plants, supporting the idea that UFO acts as part of a transcriptional complex at the AP3 promoter. Moreover, chemical or genetic disruption of proteasome activity compromises LFY-dependent AP3 activation, indicating that protein degradation is required to promote LFY activity. These results define an unexpected role for an F-box protein in functioning as a DNA-associated transcriptional co-factor in regulating floral homeotic gene expression. These results suggest a novel mechanism for promoting flower development via protein degradation and concomitant activation of the LFY transcription factor. This mechanism may be widely conserved, as homologs of UFO and LFY have been identified in a wide array of plant species. PMID:18287201

  11. An Arabidopsis F-box protein acts as a transcriptional co-factor to regulate floral development.

    Science.gov (United States)

    Chae, Eunyoung; Tan, Queenie K-G; Hill, Theresa A; Irish, Vivian F

    2008-04-01

    Plants flower in response to both environmental and endogenous signals. The Arabidopsis LEAFY (LFY) transcription factor is crucial in integrating these signals, and acts in part by activating the expression of multiple floral homeotic genes. LFY-dependent activation of the homeotic APETALA3 (AP3) gene requires the activity of UNUSUAL FLORAL ORGANS (UFO), an F-box component of an SCF ubiquitin ligase, yet how this regulation is effected has remained unclear. Here, we show that UFO physically interacts with LFY both in vitro and in vivo, and this interaction is necessary to recruit UFO to the AP3 promoter. Furthermore, a transcriptional repressor domain fused to UFO reduces endogenous LFY activity in plants, supporting the idea that UFO acts as part of a transcriptional complex at the AP3 promoter. Moreover, chemical or genetic disruption of proteasome activity compromises LFY-dependent AP3 activation, indicating that protein degradation is required to promote LFY activity. These results define an unexpected role for an F-box protein in functioning as a DNA-associated transcriptional co-factor in regulating floral homeotic gene expression. These results suggest a novel mechanism for promoting flower development via protein degradation and concomitant activation of the LFY transcription factor. This mechanism may be widely conserved, as homologs of UFO and LFY have been identified in a wide array of plant species.

  12. A single-repeat R3-MYB transcription factor MYBC1 negatively regulates freezing tolerance in Arabidopsis

    Energy Technology Data Exchange (ETDEWEB)

    Zhai, Hong, E-mail: Zhai.h@hotmail.com [Plant Bioengineering Laboratory, Northeast Agricultural University, Harbin 150030 (China); Bai, Xi, E-mail: baixi@neau.edu.cn [Plant Bioengineering Laboratory, Northeast Agricultural University, Harbin 150030 (China); Zhu, Yanming, E-mail: ymzhu2001@neau.edu.cn [Plant Bioengineering Laboratory, Northeast Agricultural University, Harbin 150030 (China); Li, Yong, E-mail: Yong@neau.edu.cn [Plant Bioengineering Laboratory, Northeast Agricultural University, Harbin 150030 (China); Cai, Hua, E-mail: small-big@sohu.com [Plant Bioengineering Laboratory, Northeast Agricultural University, Harbin 150030 (China); Ji, Wei, E-mail: iwei_j@hotmail.com [Plant Bioengineering Laboratory, Northeast Agricultural University, Harbin 150030 (China); Ji, Zuojun, E-mail: jizuojun_2001@163.com [Plant Bioengineering Laboratory, Northeast Agricultural University, Harbin 150030 (China); Liu, Xiaofei, E-mail: liuxfme@hotmail.com [Plant Bioengineering Laboratory, Northeast Agricultural University, Harbin 150030 (China); Liu, Xin, E-mail: fangfei6073@126.com [Plant Bioengineering Laboratory, Northeast Agricultural University, Harbin 150030 (China); Li, Jing, E-mail: lijing@neau.edu.cn [Plant Bioengineering Laboratory, Northeast Agricultural University, Harbin 150030 (China)

    2010-04-16

    We had previously identified the MYBC1 gene, which encodes a single-repeat R3-MYB protein, as a putative osmotic responding gene; however, no R3-MYB transcription factor has been reported to regulate osmotic stress tolerance. Thus, we sought to elucidate the function of MYBC1 in response to osmotic stresses. Real-time RT-PCR analysis indicated that MYBC1 expression responded to cold, dehydration, salinity and exogenous ABA at the transcript level. mybc1 mutants exhibited an increased tolerance to freezing stress, whereas 35S::MYBC1 transgenic plants exhibited decreased cold tolerance. Transcript levels of some cold-responsive genes, including CBF/DREB genes, KIN1, ADC1, ADC2 and ZAT12, though, were not altered in the mybc1 mutants or the 35S::MYBC1 transgenic plants in response to cold stress, as compared to the wild type. Microarray analysis results that are publically available were investigated and found transcript level of MYBC1 was not altered by overexpression of CBF1, CBF2, and CBF3, suggesting that MYBC1 is not down regulated by these CBF family members. Together, these results suggested that MYBC1is capable of negatively regulating the freezing tolerance of Arabidopsis in the CBF-independent pathway. In transgenic Arabidopsis carrying an MYBC1 promoter driven {beta}-glucuronidase (GUS) construct, GUS activity was observed in all tissues and was relatively stronger in the vascular tissues. Fused MYBC1 and GFP protein revealed that MYBC1 was localized exclusively in the nuclear compartment.

  13. Stress-and Pathogen-Induced Arabidopsis WRKY48 is a Transcriptional Activator that Represses Plant Basal Defense

    Institute of Scientific and Technical Information of China (English)

    Deng-Hui Xing; Zi-Bing Lai; Zu-Yu Zheng; K. M. Vinod; Bao-Fang Fan; Zhi-Xiang Chen

    2008-01-01

    Plant WRKY transcription factors can function as either positive or negative regulators of plant basal disease resistance. Arabidopsis WRKY48 is induced by mechanical and/or osmotic stress due to infiltration and pathogen infection and, therefore, may play a role in plant defense responses. WRKY48 is localized to the nucleus, recognizes the TrGACC Wbox sequence with a high affinity in vitro and functions in plant cells as a strong transcriptional activator. To determine the biological functions directly, we have isolated loss-of-function T-DNA insertion mutants and generated gain-of-function transgenic overexpression plants for WRKY48 in Arabidopsis. Growth of a virulent strain of the bacterial pathogen Pseudomonas syringae was decreased in the wrky48T-DNA insertion mutants. The enhanced resistance of the loss-of-function mutants was associated with increased induction of salicylic acid-regulated PR1 by the bacterial pathogen. By contrast, transgenic WRKY48-0verexpressing plants support enhanced growth of P syringae and the enhanced susceptibility was associated with reduced expression of defense-related PR genes. These results suggest that WRKY48 is a negative regulator of PR gene expression and basal resistance to the bacterial pathogen P syringae.

  14. Overexpression of Arabidopsis and rice stress genes' inducible transcription factor confers drought and salinity tolerance to rice.

    Science.gov (United States)

    Datta, Karabi; Baisakh, Niranjan; Ganguly, Moumita; Krishnan, Sellapan; Yamaguchi Shinozaki, Kazuko; Datta, Swapan K

    2012-06-01

    Rice yield is greatly affected by environmental stresses such as drought and salinity. In response to the challenge of producing rice plants tolerant to these stresses, we introduced cDNA encoding the transcription factors DREB1A and DREB1B under the control of the stress inducible rd29 promoter. Two different indica rice cultivars were used, BR29, an improved commercially cultivated variety from Bangladesh and IR68899B, an IRRI bred maintainer line for hybrid rice. Agrobacterium mediated transformation of BR29 was done independently with DREB1A isolated from rice and Arabidopsis and DREB1B isolated from rice, whereas biolistic transformation was done with rice- DREB1B in the case of IR68899B. Initial genetic integration was confirmed by PCR and Southern blot analysis. Salinity tolerance was assayed in very young seedlings. Drought stress tests were found to be more reliable when they were carried out at the pre-flowering booting stage. RNA gel blot analysis as well as quantitative PCR analysis was performed to estimate the transcription level under stressed and unstressed conditions. Agronomic performance studies were done with stressed and unstressed plants to compare the yield losses due to dehydration and salt loading stresses. Noticeably enhanced tolerance to dehydration was observed in the plants transformed with DREB1A isolated from Arabidopsis while DREB1B was found to be more effective for salt tolerance.

  15. Phosphorylation of a WRKY transcription factor by two pathogen-responsive MAPKs drives phytoalexin biosynthesis in Arabidopsis.

    Science.gov (United States)

    Mao, Guohong; Meng, Xiangzong; Liu, Yidong; Zheng, Zuyu; Chen, Zhixiang; Zhang, Shuqun

    2011-04-01

    Plant sensing of invading pathogens triggers massive metabolic reprogramming, including the induction of secondary antimicrobial compounds known as phytoalexins. We recently reported that MPK3 and MPK6, two pathogen-responsive mitogen-activated protein kinases, play essential roles in the induction of camalexin, the major phytoalexin in Arabidopsis thaliana. In search of the transcription factors downstream of MPK3/MPK6, we found that WRKY33 is required for MPK3/MPK6-induced camalexin biosynthesis. In wrky33 mutants, both gain-of-function MPK3/MPK6- and pathogen-induced camalexin production are compromised, which is associated with the loss of camalexin biosynthetic gene activation. WRKY33 is a pathogen-inducible transcription factor, whose expression is regulated by the MPK3/MPK6 cascade. Chromatin immunoprecipitation assays reveal that WRKY33 binds to its own promoter in vivo, suggesting a potential positive feedback regulatory loop. Furthermore, WRKY33 is a substrate of MPK3/MPK6. Mutation of MPK3/MPK6 phosphorylation sites in WRKY33 compromises its ability to complement the camalexin induction in the wrky33 mutant. Using a phospho-protein mobility shift assay, we demonstrate that WRKY33 is phosphorylated by MPK3/MPK6 in vivo in response to Botrytis cinerea infection. Based on these data, we conclude that WRKY33 functions downstream of MPK3/MPK6 in reprogramming the expression of camalexin biosynthetic genes, which drives the metabolic flow to camalexin production in Arabidopsis challenged by pathogens.

  16. Comprehensive analysis of single-repeat R3 MYB proteins in epidermal cell patterning and their transcriptional regulation in Arabidopsis

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    Schiefelbein John

    2008-07-01

    Full Text Available Abstract Background Single-repeat R3 MYB transcription factors are critical components of the lateral inhibition machinery that mediates epidermal cell patterning in plants. Sequence analysis of the Arabidopsis genome using the BLAST program reveals that there are a total of six genes, including TRIPTYCHON (TRY, CAPRICE (CPC, TRICHOMELESS1 (TCL1, and ENHANCER of TRY and CPC 1, 2, and 3 (ETC1, ETC2 and ETC3 encoding single-repeat R3 MYB transcription factors that are approximately 50% identical to one another at the amino acid level. Previous studies indicate that these single-repeat R3 MYBs regulate epidermal cell patterning. However, each of the previous studies of these single-repeat R3 MYBs has been limited to an analysis of only a subset of these six genes, and furthermore, they have limited their attention to epidermal development in only one or two of the organs. In addition, the transcriptional regulation of these single-repeat R3 MYB genes remains largely unknown. Results By analyzing multiple mutant lines, we report here that TCL1 functions redundantly with other single-repeat R3 MYB transcription factors to control both leaf trichome and root hair formation. On the other hand, ETC1 and ETC3 participate in controlling trichome formation on inflorescence stems and pedicles. Further, we discovered that single-repeat R3 MYBs suppress trichome formation on cotyledons and siliques, organs that normally do not bear any trichomes. By using Arabidopsis protoplast transfection assays, we found that all single-repeat R3 MYBs examined interact with GL3, and that GL1 or WER and GL3 or EGL3 are required and sufficient to activate the transcription of TRY, CPC, ETC1 and ETC3, but not TCL1 and ETC2. Furthermore, only ETC1's transcription was greatly reduced in the gl3 egl3 double mutants. Conclusion Our comprehensive analysis enables us to draw broader conclusions about the role of single-repeat R3 MYB gene family than were possible in the earlier

  17. Interaction with diurnal and circadian regulation results in dynamic metabolic and transcriptional changes during cold acclimation in Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Carmen Espinoza

    Full Text Available In plants, there is a large overlap between cold and circadian regulated genes and in Arabidopsis, we have shown that cold (4°C affects the expression of clock oscillator genes. However, a broader insight into the significance of diurnal and/or circadian regulation of cold responses, particularly for metabolic pathways, and their physiological relevance is lacking. Here, we performed an integrated analysis of transcripts and primary metabolites using microarrays and gas chromatography-mass spectrometry. As expected, expression of diurnally regulated genes was massively affected during cold acclimation. Our data indicate that disruption of clock function at the transcriptional level extends to metabolic regulation. About 80% of metabolites that showed diurnal cycles maintained these during cold treatment. In particular, maltose content showed a massive night-specific increase in the cold. However, under free-running conditions, maltose was the only metabolite that maintained any oscillations in the cold. Furthermore, although starch accumulates during cold acclimation we show it is still degraded at night, indicating significance beyond the previously demonstrated role of maltose and starch breakdown in the initial phase of cold acclimation. Levels of some conventional cold induced metabolites, such as γ-aminobutyric acid, galactinol, raffinose and putrescine, exhibited diurnal and circadian oscillations and transcripts encoding their biosynthetic enzymes often also cycled and preceded their cold-induction, in agreement with transcriptional regulation. However, the accumulation of other cold-responsive metabolites, for instance homoserine, methionine and maltose, did not have consistent transcriptional regulation, implying that metabolic reconfiguration involves complex transcriptional and post-transcriptional mechanisms. These data demonstrate the importance of understanding cold acclimation in the correct day-night context, and are further

  18. Transcriptional Consequence and Impaired Gametogenesis with High-Grade Aneuploidy in Arabidopsis thaliana

    OpenAIRE

    Kuan-Lin Lo; Long-Chi Wang; I-Ju Chen; Yu-Chen Liu; Mei-Chu Chung; Wan-Sheng Lo

    2014-01-01

    Aneuploidy features a numerical chromosome variant that the number of chromosomes in the nucleus of a cell is not an exact multiple of the haploid number, which may have an impact on morphology and gene expression. Here we report a tertiary trisomy uncovered by characterizing a T-DNA insertion mutant (aur2-1/+) in the Arabidopsis (Arabidopsis thaliana) AURORA2 locus. Whole-genome analysis with DNA tiling arrays revealed a chromosomal translocation linked to the aur2-1 allele, which collective...

  19. 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...

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

    NARCIS (Netherlands)

    Armengaud, Patrick; Breitling, Rainer; Amtmann, Anna

    2010-01-01

    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

  1. Tracking transcription factor mobility and interaction in arabidopsis roots with fluorescence correlation spectroscopy

    NARCIS (Netherlands)

    Clark, Natalie M.; Hinde, Elizabeth; Hinde, Elizabeth; Fisher, Adam P.; Crosti, Giuseppe; Blilou, Ikram; Gratton, Enrico; Benfey, Philip N.; Sozzani, Rosangela

    2016-01-01

    To understand complex regulatory processes in multicellular organisms, it is critical to be able to quantitatively analyze protein movement and protein-protein interactions in time and space. During Arabidopsis development, the intercellular movement of SHORTROOT (SHR) and subsequent interaction

  2. Arabidopsis TRANSPARENT TESTA GLABRA2 is directly regulated by R2R3 MYB transcription factors and is involved in regulation of GLABRA2 transcription in epidermal differentiation.

    Science.gov (United States)

    Ishida, Tetsuya; Hattori, Sayoko; Sano, Ryosuke; Inoue, Kayoko; Shirano, Yumiko; Hayashi, Hiroaki; Shibata, Daisuke; Sato, Shusei; Kato, Tomohiko; Tabata, Satoshi; Okada, Kiyotaka; Wada, Takuji

    2007-08-01

    Arabidopsis thaliana TRANSPARENT TESTA GLABRA2 (TTG2) encodes a WRKY transcription factor and is expressed in young leaves, trichomes, seed coats, and root hairless cells. An examination of several trichome and root hair mutants indicates that MYB and bHLH genes regulate TTG2 expression. Two MYB binding sites in the TTG2 5' regulatory region act as cis regulatory elements and as direct targets of R2R3 MYB transcription factors such as WEREWOLF, GLABRA1, and TRANSPARENT TESTA2. Mutations in TTG2 cause phenotypic defects in trichome development and seed color pigmentation. Transgenic plants expressing a chimeric repressor version of the TTG2 protein (TTG2:SRDX) showed defects in trichome formation, anthocyanin accumulation, seed color pigmentation, and differentiation of root hairless cells. GLABRA2 (GL2) expression was markedly reduced in roots of ProTTG2:TTG2:SRDX transgenic plants, suggesting that TTG2 is involved in the regulation of GL2 expression, although GL2 expression in the ttg2 mutant was similar to that in the wild type. Our analysis suggests a new step in a regulatory cascade of epidermal differentiation, in which complexes containing R2R3 MYB and bHLH transcription factors regulate the expression of TTG2, which then regulates GL2 expression with complexes containing R2R3 MYB and bHLH in the differentiation of trichomes and root hairless cells.

  3. Ectopic expression of R3 MYB transcription factor gene OsTCL1 in Arabidopsis, but not rice, affects trichome and root hair formation

    Science.gov (United States)

    Zheng, Kaijie; Tian, Hainan; Hu, Qingnan; Guo, Hongyan; Yang, Li; Cai, Ling; Wang, Xutong; Liu, Bao; Wang, Shucai

    2016-01-01

    In Arabidopsis, a MYB-bHLH-WD40 (MBW) transcriptional activator complex activates the homeodomain protein gene GLABRA2 (GL2), leading to the promotion of trichome formation and inhibition of root hair formation. The same MBW complex also activates single-repeat R3 MYB genes. R3 MYBs in turn, play a negative feedback role by competing with R2R3 MYB proteins for binding bHLH proteins, thus blocking the formation of the MBW complex. By BLASTing the rice (Oryza sativa) protein database using the entire amino acid sequence of Arabidopsis R3 MYB transcription factor TRICHOMELESS1 (TCL1), we found that there are two genes in rice genome encoding R3 MYB transcription factors, namely Oryza sativa TRICHOMELESS1 (OsTCL1) and OsTCL2. Expressing OsTCL1 in Arabidopsis inhibited trichome formation and promoted root hair formation, and OsTCL1 interacted with GL3 when tested in Arabidopsis protoplasts. Consistent with these observations, expression levels of GL2, R2R3 MYB transcription factor gene GLABRA1 (GL1) and several R3 MYB genes were greatly reduced, indicating that OsTCL1 is functional R3 MYB. However, trichome and root hair formation in transgenic rice plants overexpressing OsTCL1 remained largely unchanged, and elevated expression of OsGL2 was observed in the transgenic rice plants, indicating that rice may use different mechanisms to regulate trichome formation. PMID:26758286

  4. A wheat salinity-induced WRKY transcription factor TaWRKY93 confers multiple abiotic stress tolerance in Arabidopsis thaliana.

    Science.gov (United States)

    Qin, Yuxiang; Tian, Yanchen; Liu, Xiuzhi

    2015-08-21

    Wheat is an important crop in the world. But most of the cultivars are salt sensitive, and often adversely affected by salt stress. WRKY transcription factors play a major role in plant responses to salt stress, but the effective salinity regulatory WRKYs identified in bread wheat are limited and the mechanism of salt stress tolerance is also not well explored. Here, we identified a salt (NaCl) induced class II WRKY transcription factor TaWRKY93. Its transcript level was strongly induced by salt (NaCl) and exogenous abscisic acid (ABA). Over-expression of TaWRKY93 in Arabidopsis thaliana enhanced salt (NaCl), drought, low temperature and osmotic (mannitol) stress tolerance, mainly demonstrated by transgenic plants forming longer primary roots or more lateral roots on MS plates supplemented with NaCl and mannitol individually, higher survival rate under drought and low temperature stress. Further, transgenic plants maintained a more proline content, higher relative water content and less electrolyte leakage than the wild type plants. The transcript abundance of a series of abiotic stress-related genes was up-regulated in the TaWRKY93 transgenic plants. In summary, TaWRKY93 is a new positive regulator of abiotic stress, it may increase salinity, drought and low temperature stress tolerance through enhancing osmotic adjustment, maintaining membrane stability and increasing transcription of stress related genes, and contribute to the superior agricultural traits of SR3 through promoting root development. It can be used as a candidate gene for wheat transgenic engineering breeding against abiotic stress.

  5. Melatonin induces the transcripts of CBF/DREB1s and their involvement in both abiotic and biotic stresses in Arabidopsis.

    Science.gov (United States)

    Shi, Haitao; Qian, Yongqiang; Tan, Dun-Xian; Reiter, Russel J; He, Chaozu

    2015-10-01

    Melatonin (N-acetyl-5-methoxytryptamine) is a naturally occurring small molecule that acts as an important secondary messenger in plant stress responses. However, the mechanism underlying the melatonin-mediated signaling pathway in plant stress responses has not been established. C-repeat-binding factors (CBFs)/Drought response element Binding 1 factors (DREB1s) encode transcription factors that play important roles in plant stress responses. This study has determined that endogenous melatonin and transcripts level of CBFs (AtCBF1, AtCBF2, and AtCBF3) in Arabidopsis leaves were significantly induced by salt, drought, and cold stresses and by pathogen Pseudomonas syringe pv. tomato (Pst) DC3000 infection. Moreover, both exogenous melatonin treatment and overexpression of CBFs conferred enhanced resistance to both abiotic and biotic stresses in Arabidopsis. Notably, AtCBFs and exogenous melatonin treatment positively regulated the mRNA expression of several stress-responsive genes (COR15A, RD22, and KIN1) and accumulation of soluble sugars content such as sucrose in Arabidopsis under control and stress conditions. Additionally, exogenous sucrose also conferred improved resistance to both abiotic and biotic stresses in Arabidopsis. Taken together, this study indicates that AtCBFs confer enhanced resistance to both abiotic and biotic stresses, and AtCBF-mediated signaling pathway and sugar accumulation may be involved in melatonin-mediated stress response in Arabidopsis, at least partially.

  6. Melatonin induces the transcripts of CBF/DREB1s and their involvement in both abiotic and biotic stresses in Arabidopsis.

    Science.gov (United States)

    Shi, Haitao; Qian, Yongqiang; Tan, Dun-Xian; Reiter, Russel J; He, Chaozu

    2015-10-01

    Melatonin (N-acetyl-5-methoxytryptamine) is a naturally occurring small molecule that acts as an important secondary messenger in plant stress responses. However, the mechanism underlying the melatonin-mediated signaling pathway in plant stress responses has not been established. C-repeat-binding factors (CBFs)/Drought response element Binding 1 factors (DREB1s) encode transcription factors that play important roles in plant stress responses. This study has determined that endogenous melatonin and transcripts level of CBFs (AtCBF1, AtCBF2, and AtCBF3) in Arabidopsis leaves were significantly induced by salt, drought, and cold stresses and by pathogen Pseudomonas syringe pv. tomato (Pst) DC3000 infection. Moreover, both exogenous melatonin treatment and overexpression of CBFs conferred enhanced resistance to both abiotic and biotic stresses in Arabidopsis. Notably, AtCBFs and exogenous melatonin treatment positively regulated the mRNA expression of several stress-responsive genes (COR15A, RD22, and KIN1) and accumulation of soluble sugars content such as sucrose in Arabidopsis under control and stress conditions. Additionally, exogenous sucrose also conferred improved resistance to both abiotic and biotic stresses in Arabidopsis. Taken together, this study indicates that AtCBFs confer enhanced resistance to both abiotic and biotic stresses, and AtCBF-mediated signaling pathway and sugar accumulation may be involved in melatonin-mediated stress response in Arabidopsis, at least partially. PMID:26182834

  7. The Arabidopsis transcriptional regulator DPB3-1 enhances heat stress tolerance without growth retardation in rice.

    Science.gov (United States)

    Sato, Hikaru; Todaka, Daisuke; Kudo, Madoka; Mizoi, Junya; Kidokoro, Satoshi; Zhao, Yu; Shinozaki, Kazuo; Yamaguchi-Shinozaki, Kazuko

    2016-08-01

    The enhancement of heat stress tolerance in crops is an important challenge for food security to facilitate adaptation to global warming. In Arabidopsis thaliana, the transcriptional regulator DNA polymerase II subunit B3-1 (DPB3-1)/nuclear factor Y subunit C10 (NF-YC10) has been reported as a positive regulator of Dehydration-responsive element binding protein 2A (DREB2A), and the overexpression of DPB3-1 enhances heat stress tolerance without growth retardation. Here, we show that DPB3-1 interacts with DREB2A homologues in rice and soya bean. Transactivation analyses with Arabidopsis and rice mesophyll protoplasts indicate that DPB3-1 and its rice homologue OsDPB3-2 function as positive regulators of DREB2A homologues. Overexpression of DPB3-1 did not affect plant growth or yield in rice under nonstress conditions. Moreover, DPB3-1-overexpressing rice showed enhanced heat stress tolerance. Microarray analysis revealed that many heat stress-inducible genes were up-regulated in DPB3-1-overexpressing rice under heat stress conditions. However, the overexpression of DPB3-1 using a constitutive promoter had almost no effect on the expression of these genes under nonstress conditions. This may be because DPB3-1 is a coactivator and thus lacks inherent transcriptional activity. We conclude that DPB3-1, a coactivator that functions specifically under abiotic stress conditions, could be utilized to increase heat stress tolerance in crops without negative effects on vegetative and reproductive growth. PMID:26841113

  8. Heat stress enhances the accumulation of polyadenylated mitochondrial transcripts in Arabidopsis thaliana.

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    Alessio Adamo

    Full Text Available BACKGROUND: Polyadenylation of RNA has a decisive influence on RNA stability. Depending on the organisms or subcellular compartment, it either enhances transcript stability or targets RNAs for degradation. In plant mitochondria, polyadenylation promotes RNA degradation, and polyadenylated mitochondrial transcripts are therefore widely considered to be rare and unstable. We followed up a surprising observation that a large number of mitochondrial transcripts are detectable in microarray experiments that used poly(A-specific RNA probes, and that these transcript levels are significantly enhanced after heat treatment. METHODOLOGY/PRINCIPAL FINDINGS: As the Columbia genome contains a complete set of mitochondrial genes, we had to identify polymorphisms to differentiate between nuclear and mitochondrial copies of a mitochondrial transcript. We found that the affected transcripts were uncapped transcripts of mitochondrial origin, which were polyadenylated at multiple sites within their 3'region. Heat-induced enhancement of these transcripts was quickly restored during a short recovery period. CONCLUSIONS/SIGNIFICANCE: Our results show that polyadenylated transcripts of mitochondrial origin are more stable than previously suggested, and that their steady-state levels can even be significantly enhanced under certain conditions. As many microarrays contain mitochondrial probes, due to the frequent transfer of mitochondrial genes into the genome, these effects need to be considered when interpreting microarray data.

  9. Arabidopsis Ovate Family Proteins, a Novel Transcriptional Repressor Family, Control Multiple Aspects of Plant Growth and Development

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Shucai [University of British Columbia, Vancouver; Chang, Ying [Northeast Agricultural University; Guo, Jianjun [Harvard University; Zeng, Qingning [University of British Columbia, Vancouver; Ellis, Brian [University of British Columbia, Vancouver; Chen, Jay [ORNL

    2011-01-01

    BACKGROUND: The Arabidopsis genome contains 18 genes that are predicted to encode Ovate Family Proteins (AtOFPs), a protein family characterized by a conserved OVATE domain, an approximately 70-amino acid domain that was originally found in tomato OVATE protein. Among AtOFP family members, AtOFP1 has been shown to suppress cell elongation, in part, by suppressing the expression of AtGA20ox1, AtOFP4 has been shown to regulate secondary cell wall formation by interact with KNOTTED1-LIKE HOMEODOMAIN PROTEIN 7 (KNAT7), and AtOFP5 has been shown to regulate the activity of a BEL1-LIKEHOMEODOMAIN 1(BLH1)-KNAT3 complex during early embryo sac development, but little is known about the function of other AtOFPs. METHODOLOGY/PRINCIPAL FINDINGS: We demonstrated here that AtOFP proteins could function as effective transcriptional repressors in the Arabidopsis protoplast transient expression system. The analysis of loss-of-function alleles of AtOFPs suggested AtOFP genes may have overlapping function in regulating plant growth and development, because none of the single mutants identified, including T-DNA insertion mutants in AtOFP1, AtOFP4, AtOFP8, AtOFP10, AtOFP15 and AtOFP16, displayed any apparent morphological defects. Further, Atofp1 Atofp4 and Atofp15 Atofp16 double mutants still did not differ significantly from wild-type. On the other hand, plants overexpressing AtOFP genes displayed a number of abnormal phenotypes, which could be categorized into three distinct classes, suggesting that AtOFP genes may also have diverse functions in regulating plant growth and development. Further analysis suggested that AtOFP1 regulates cotyledon development in a postembryonic manner, and global transcript profiling revealed that it suppress the expression of many other genes. CONCLUSIONS/SIGNIFICANCE: Our results showed that AtOFPs function as transcriptional repressors and they regulate multiple aspects of plant growth and development. These results provided the first overview of a

  10. Arabidopsis ovate family proteins, a novel transcriptional repressor family, control multiple aspects of plant growth and development.

    Directory of Open Access Journals (Sweden)

    Shucai Wang

    Full Text Available BACKGROUND: The Arabidopsis genome contains 18 genes that are predicted to encode Ovate Family Proteins (AtOFPs, a protein family characterized by a conserved OVATE domain, an approximately 70-amino acid domain that was originally found in tomato OVATE protein. Among AtOFP family members, AtOFP1 has been shown to suppress cell elongation, in part, by suppressing the expression of AtGA20ox1, AtOFP4 has been shown to regulate secondary cell wall formation by interact with KNOTTED1-LIKE HOMEODOMAIN PROTEIN 7 (KNAT7, and AtOFP5 has been shown to regulate the activity of a BEL1-LIKEHOMEODOMAIN 1(BLH1-KNAT3 complex during early embryo sac development, but little is known about the function of other AtOFPs. METHODOLOGY/PRINCIPAL FINDINGS: We demonstrated here that AtOFP proteins could function as effective transcriptional repressors in the Arabidopsis protoplast transient expression system. The analysis of loss-of-function alleles of AtOFPs suggested AtOFP genes may have overlapping function in regulating plant growth and development, because none of the single mutants identified, including T-DNA insertion mutants in AtOFP1, AtOFP4, AtOFP8, AtOFP10, AtOFP15 and AtOFP16, displayed any apparent morphological defects. Further, Atofp1 Atofp4 and Atofp15 Atofp16 double mutants still did not differ significantly from wild-type. On the other hand, plants overexpressing AtOFP genes displayed a number of abnormal phenotypes, which could be categorized into three distinct classes, suggesting that AtOFP genes may also have diverse functions in regulating plant growth and development. Further analysis suggested that AtOFP1 regulates cotyledon development in a postembryonic manner, and global transcript profiling revealed that it suppress the expression of many other genes. CONCLUSIONS/SIGNIFICANCE: Our results showed that AtOFPs function as transcriptional repressors and they regulate multiple aspects of plant growth and development. These results provided the

  11. Transcriptional and metabolomic analysis of Ascophyllum nodosum mediated freezing tolerance in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Nair Prasanth

    2012-11-01

    Full Text Available Abstract Background We have previously shown that lipophilic components (LPC of the brown seaweed Ascophyllum nodosum (ANE improved freezing tolerance in Arabidopsis thaliana. However, the mechanism(s of this induced freezing stress tolerance is largely unknown. Here, we investigated LPC induced changes in the transcriptome and metabolome of A. thaliana undergoing freezing stress. Results Gene expression studies revealed that the accumulation of proline was mediated by an increase in the expression of the proline synthesis genes P5CS1 and P5CS2 and a marginal reduction in the expression of the proline dehydrogenase (ProDH gene. Moreover, LPC application significantly increased the concentration of total soluble sugars in the cytosol in response to freezing stress. Arabidopsis sfr4 mutant plants, defective in the accumulation of free sugars, treated with LPC, exhibited freezing sensitivity similar to that of untreated controls. The 1H NMR metabolite profile of LPC-treated Arabidopsis plants exposed to freezing stress revealed a spectrum dominated by chemical shifts (δ representing soluble sugars, sugar alcohols, organic acids and lipophilic components like fatty acids, as compared to control plants. Additionally, 2D NMR spectra suggested an increase in the degree of unsaturation of fatty acids in LPC treated plants under freezing stress. These results were supported by global transcriptome analysis. Transcriptome analysis revealed that LPC treatment altered the expression of 1113 genes (5% in comparison with untreated plants. A total of 463 genes (2% were up regulated while 650 genes (3% were down regulated. Conclusion Taken together, the results of the experiments presented in this paper provide evidence to support LPC mediated freezing tolerance enhancement through a combination of the priming of plants for the increased accumulation of osmoprotectants and alteration of cellular fatty acid composition.

  12. Transcriptional consequence and impaired gametogenesis with high-grade aneuploidy in Arabidopsis thaliana.

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    Kuan-Lin Lo

    Full Text Available Aneuploidy features a numerical chromosome variant that the number of chromosomes in the nucleus of a cell is not an exact multiple of the haploid number, which may have an impact on morphology and gene expression. Here we report a tertiary trisomy uncovered by characterizing a T-DNA insertion mutant (aur2-1/+ in the Arabidopsis (Arabidopsis thaliana AURORA2 locus. Whole-genome analysis with DNA tiling arrays revealed a chromosomal translocation linked to the aur2-1 allele, which collectively accounted for a tertiary trisomy 2. Morphologic, cytogenetic and genetic analyses of aur2-1 progeny showed impaired male and female gametogenesis to various degrees and a tight association of the aur2-1 allele with the tertiary trisomy that was preferentially inherited. Transcriptome analysis showed overlapping and distinct gene expression profiles between primary and tertiary trisomy 2 plants, particularly genes involved in response to stress and various types of external and internal stimuli. Additionally, transcriptome and gene ontology analyses revealed an overrepresentation of nuclear-encoded organelle-related genes functionally involved in plastids, mitochondria and peroxisomes that were differentially expressed in at least three if not all Arabidopsis trisomics. These observations support a previous hypothesis that aneuploid cells have higher energy requirement to overcome the detrimental effects of an unbalanced genome. Moreover, our findings extend the knowledge of the complex nature of the T-DNA insertion event influencing plant genomic integrity by creating high-grade trisomy. Finally, gene expression profiling results provide useful information for future research to compare primary and tertiary trisomics for the effects of aneuploidy on plant cell physiology.

  13. Dormant and after-Ripened Arabidopsis thaliana Seeds are Distinguished by Early Transcriptional Differences in the Imbibed State

    Science.gov (United States)

    Dekkers, Bas J. W.; Pearce, Simon P.; van Bolderen-Veldkamp, R. P. M.; Holdsworth, Michael J.; Bentsink, Leónie

    2016-01-01

    Seed dormancy is a genetically controlled block preventing the germination of imbibed seeds in favorable conditions. It requires a period of dry storage (after-ripening) or certain environmental conditions to be overcome. Dormancy is an important seed trait, which is under selective pressure, to control the seasonal timing of seed germination. Dormant and non-dormant (after-ripened) seeds are characterized by large sets of differentially expressed genes. However, little information is available concerning the temporal and spatial transcriptional changes during early stages of rehydration in dormant and non-dormant seeds. We employed genome-wide transcriptome analysis on seeds of the model plant Arabidopsis thaliana to investigate transcriptional changes in dry seeds upon rehydration. We analyzed gene expression of dormant and after-ripened seeds of the Cvi accession over four time points and two seed compartments (the embryo and surrounding single cell layer endosperm), during the first 24 h after sowing. This work provides a global view of gene expression changes in dormant and non-dormant seeds with temporal and spatial detail, and these may be visualized via a web accessible tool (http://www.wageningenseedlab.nl/resources). A large proportion of transcripts change similarly in both dormant and non-dormant seeds upon rehydration, however, the first differences in transcript abundances become visible shortly after the initiation of imbibition, indicating that changes induced by after-ripening are detected and responded to rapidly upon rehydration. We identified several gene expression profiles which contribute to differential gene expression between dormant and non-dormant samples. Genes with enhanced expression in the endosperm of dormant seeds were overrepresented for stress-related Gene Ontology categories, suggesting a protective role for the endosperm against biotic and abiotic stress to support persistence of the dormant seed in its environment. PMID

  14. Dormant and after-Ripened Arabidopsis thaliana Seeds are Distinguished by Early Transcriptional Differences in the Imbibed State.

    Science.gov (United States)

    Dekkers, Bas J W; Pearce, Simon P; van Bolderen-Veldkamp, R P M; Holdsworth, Michael J; Bentsink, Leónie

    2016-01-01

    Seed dormancy is a genetically controlled block preventing the germination of imbibed seeds in favorable conditions. It requires a period of dry storage (after-ripening) or certain environmental conditions to be overcome. Dormancy is an important seed trait, which is under selective pressure, to control the seasonal timing of seed germination. Dormant and non-dormant (after-ripened) seeds are characterized by large sets of differentially expressed genes. However, little information is available concerning the temporal and spatial transcriptional changes during early stages of rehydration in dormant and non-dormant seeds. We employed genome-wide transcriptome analysis on seeds of the model plant Arabidopsis thaliana to investigate transcriptional changes in dry seeds upon rehydration. We analyzed gene expression of dormant and after-ripened seeds of the Cvi accession over four time points and two seed compartments (the embryo and surrounding single cell layer endosperm), during the first 24 h after sowing. This work provides a global view of gene expression changes in dormant and non-dormant seeds with temporal and spatial detail, and these may be visualized via a web accessible tool (http://www.wageningenseedlab.nl/resources). A large proportion of transcripts change similarly in both dormant and non-dormant seeds upon rehydration, however, the first differences in transcript abundances become visible shortly after the initiation of imbibition, indicating that changes induced by after-ripening are detected and responded to rapidly upon rehydration. We identified several gene expression profiles which contribute to differential gene expression between dormant and non-dormant samples. Genes with enhanced expression in the endosperm of dormant seeds were overrepresented for stress-related Gene Ontology categories, suggesting a protective role for the endosperm against biotic and abiotic stress to support persistence of the dormant seed in its environment. PMID

  15. Post-transcriptional regulation of ethylene perception and signaling in Arabidopsis

    Energy Technology Data Exchange (ETDEWEB)

    Schaller, George Eric

    2014-03-19

    The simple gas ethylene functions as an endogenous regulator of plant growth and development, and modulates such energy relevant processes as photosynthesis and biomass accumulation. Ethylene is perceived in the plant Arabidopsis by a five-member family of receptors related to bacterial histidine kinases. Our data support a general model in which the receptors exist as parts of larger protein complexes. Our goals have been to (1) characterize physical interactions among members of the signaling complex; (2) the role of histidine-kinase transphosphorylation in signaling by the complex; and (3) the role of a novel family of proteins that regulate signal output by the receptors.

  16. The DOF transcription factor Dof5.1 influences leaf axial patterning by promoting Revoluta transcription in Arabidopsis

    KAUST Repository

    Kim, Hyungsae

    2010-10-05

    Dof proteins are transcription factors that have a conserved single zinc finger DNA-binding domain. In this study, we isolated an activation tagging mutant Dof5.1-D exhibiting an upward-curling leaf phenotype due to enhanced expression of the REV gene that is required for establishing adaxialabaxial polarity. Dof5.1-D plants also had reduced transcript levels for IAA6 and IAA19 genes, indicating an altered auxin biosynthesis in Dof5.1-D. An electrophoretic mobility shift assay using the Dof5.1 DNA-binding motif and the REV promoter region indicated that the DNA-binding domain of Dof5.1 binds to a TAAAGT motif located in the 5′-distal promoter region of the REV promoter. Further, transient and chromatin immunoprecipitation assays verified binding activity of the Dof5.1 DNA-binding motif with the REV promoter. Consistent with binding assays, constitutive over-expression of the Dof5.1 DNA-binding domain in wild-type plants caused a downward-curling phenotype, whereas crossing Dof5.1-D to a rev mutant reverted the upward-curling phenotype of the Dof5.1-D mutant leaf to the wild-type. These results suggest that the Dof5.1 protein directly binds to the REV promoter and thereby regulates adaxialabaxial polarity. © 2010 Blackwell Publishing Ltd.

  17. The Hv NAC6 transcription factor: a positive regulator of penetration resistance in barley and Arabidopsis

    DEFF Research Database (Denmark)

    Jensen, Michael Krogh; Rung, Jesper Henrik; Gregersen, Per Langkjaer;

    2007-01-01

    Pathogens induce the expression of many genes encoding plant transcription factors, though specific knowledge of the biological function of individual transcription factors remains scarce. NAC transcription factors are encoded in plants by a gene family with proposed functions in both abiotic...... powdery mildew fungus, Blumeria graminis f.sp. hordei (Bgh). The full-length cDNA clone was obtained using 5'-RACE and termed HvNAC6, due to its high similarity to the rice homologue, OsNAC6. Gene silencing of HvNAC6 during Bgh inoculation compromises penetration resistance in barley epidermal cells...

  18. ZmNAC55, a maize stress-responsive NAC transcription factor, confers drought resistance in transgenic Arabidopsis.

    Science.gov (United States)

    Mao, Hude; Yu, Lijuan; Han, Ran; Li, Zhanjie; Liu, Hui

    2016-08-01

    Abiotic stress has been shown to significantly limit the growth and productivity of crops. NAC transcription factors play essential roles in response to various abiotic stresses. However, only little information regarding stress-related NAC genes is available in maize. Here, we cloned a maize NAC transcription factor ZmNAC55 and identified its function in drought stress. Transient expression and transactivation assay demonstrated that ZmNAC55 was localized in the nucleus and had transactivation activity. Expression analysis of ZmNAC55 in maize showed that this gene was induced by drought, high salinity and cold stresses and by abscisic acid (ABA). Promoter analysis demonstrated that multiple stress-related cis-acting elements exist in promoter region of ZmNAC55. Overexpression of ZmNAC55 in Arabidopsis led to hypersensitivity to ABA at the germination stage, but enhanced drought resistence compared to wild-type seedlings. Transcriptome analysis identified a number of differentially expressed genes between 35S::ZmNAC55 transgenic and wild-type plants, and many of which are involved in stress response, including twelve qRT-PCR confirmed well-known drought-responsive genes. These results highlight the important role of ZmNAC55 in positive regulates of drought resistence, and may have potential applications in transgenic breeding of drought-tolerant crops. PMID:27085597

  19. The Arabidopsis AP2/ERF Transcription Factor RAP2.11 Modulates Plant Response to Low-Potassium Conditions

    Institute of Scientific and Technical Information of China (English)

    Min Jung Kim; Daniel Ruzicka; Ryoung Shin; Daniel P.Schachtman

    2012-01-01

    Plants respond to low-nutrient conditions through metabolic and morphology changes that increase their ability to survive and grow.The transcription factor RAP2.11 was identified as a component in the response to low potassium through regulation of the high-affinity K+ uptake transporter AtHAK5 and other components of the lowpotassium signal transduction pathway.RAP2.11 was identified through the activation tagging of Arabidopsis lines that contained a luciferase marker driven by the AtHAK5 promoter that is normally only induced by low potassium.This factor bound to a GCC-box of the AtHAK5 promoter in vitro and in vivo.Transcript profiling revealed that a large number of genes were up-regulated in roots by RAP2.11 overexpression.Many regulated genes were identified to be in functional categories that are important in low-K+ signaling.These categories included ethylene signaling,reactive oxygen species production,and calcium signaling.Promoter regions of the up-regulated genes were enriched in the GCCGGC motif also contained in the AtHAK5 promoter.These results suggest that RAP2.11 regulates AtHAK5 expression under low-K+ conditions and also contributes to a coordinated response to low-potassium conditions through the regulation of other genes in the low-K+ signaling cascade.

  20. Novel NAC transcription factor TaNAC67 confers enhanced multi-abiotic stress tolerances in Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Xinguo Mao

    Full Text Available Abiotic stresses are major environmental factors that affect agricultural productivity worldwide. NAC transcription factors play pivotal roles in abiotic stress signaling in plants. As a staple crop, wheat production is severely constrained by abiotic stresses whereas only a few NAC transcription factors have been characterized functionally. To promote the application of NAC genes in wheat improvement by biotechnology, a novel NAC gene designated TaNAC67 was characterized in common wheat. To determine its role, transgenic Arabidopsis overexpressing TaNAC67-GFP controlled by the CaMV-35S promoter was generated and subjected to various abiotic stresses for morphological and physiological assays. Gene expression showed that TaNAC67 was involved in response to drought, salt, cold and ABA treatments. Localization assays revealed that TaNAC67 localized in the nucleus. Morphological analysis indicated the transgenics had enhanced tolerances to drought, salt and freezing stresses, simultaneously supported by enhanced expression of multiple abiotic stress responsive genes and improved physiological traits, including strengthened cell membrane stability, retention of higher chlorophyll contents and Na(+ efflux rates, improved photosynthetic potential, and enhanced water retention capability. Overexpression of TaNAC67 resulted in pronounced enhanced tolerances to drought, salt and freezing stresses, therefore it has potential for utilization in transgenic breeding to improve abiotic stress tolerance in crops.

  1. A transcriptional analysis of carotenoid, chlorophyll and plastidial isoprenoid biosynthesis genes during development and osmotic stress responses in Arabidopsis thaliana

    KAUST Repository

    Meier, Stuart

    2011-05-19

    Background: The carotenoids are pure isoprenoids that are essential components of the photosynthetic apparatus and are coordinately synthesized with chlorophylls in chloroplasts. However, little is known about the mechanisms that regulate carotenoid biosynthesis or the mechanisms that coordinate this synthesis with that of chlorophylls and other plastidial synthesized isoprenoid-derived compounds, including quinones, gibberellic acid and abscisic acid. Here, a comprehensive transcriptional analysis of individual carotenoid and isoprenoid-related biosynthesis pathway genes was performed in order to elucidate the role of transcriptional regulation in the coordinated synthesis of these compounds and to identify regulatory components that may mediate this process in Arabidopsis thaliana.Results: A global microarray expression correlation analysis revealed that the phytoene synthase gene, which encodes the first dedicated and rate-limiting enzyme of carotenogenesis, is highly co-expressed with many photosynthesis-related genes including many isoprenoid-related biosynthesis pathway genes. Chemical and mutant analysis revealed that induction of the co-expressed genes following germination was dependent on gibberellic acid and brassinosteroids (BR) but was inhibited by abscisic acid (ABA). Mutant analyses further revealed that expression of many of the genes is suppressed in dark grown plants by Phytochrome Interacting transcription Factors (PIFs) and activated by photoactivated phytochromes, which in turn degrade PIFs and mediate a coordinated induction of the genes. The promoters of PSY and the co-expressed genes were found to contain an enrichment in putative BR-auxin response elements and G-boxes, which bind PIFs, further supporting a role for BRs and PIFs in regulating expression of the genes. In osmotically stressed root tissue, transcription of Calvin cycle, methylerythritol 4-phosphate pathway and carotenoid biosynthesis genes is induced and uncoupled from that of

  2. A membrane-tethered transcription factor ANAC089 negatively regulates floral initiation in Arabidopsis thaliana

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The plant-specific NAC (NAM, ATAF1/2,and CUC2) transcription factors have a regulatory function in developmental processes and stress responses. Notably a group of NAC members named NTLs (NTM1-Like) are membrane-tethered, ensuring plants rapidly respond to developmental changes and environmental stimuli. Our results indicated that ANAC089 was a membrane-tethered transcription factor and its truncated form was responsible for the physiological function in flowering time control.

  3. An ABA down-regulated bHLH transcription repressor gene, bHLH129 regulates root elongation and ABA response when overexpressed in Arabidopsis

    Science.gov (United States)

    Tian, Hainan; Guo, Hongyan; Dai, Xuemei; Cheng, Yuxin; Zheng, Kaijie; Wang, Xiaoping; Wang, Shucai

    2015-01-01

    Plant hormone abscisic acid (ABA) plays a crucial role in modulating plant responses to environmental stresses. Basic helix-loop-helix (bHLH) transcription factors are one of the largest transcription factor families that regulate multiple aspects of plant growth and development, as well as of plant metabolism in Arabidopsis. Several bHLH transcription factors have been shown to be involved in the regulation of ABA signaling. We report here the characterization of bHLH129, a bHLH transcription factor in Arabidopsis. We found that the expression level of bHLH129 was reduced in response to exogenously applied ABA, and elevated in the ABA biosynthesis mutant aba1-5. Florescence observation of transgenic plants expressing bHLH129-GFP showed that bHLH129 was localized in the nucleus, and transient expression of bHLH129 in protoplasts inhibited reporter gene expression. When expressed in Arabidopsis under the control of the 35S promoter, bHLH129 promoted root elongation, and the transgenic plants were less sensitivity to ABA in root elongation assays. Quantitative RT-PCR results showed that ABA response of several genes involved in ABA signaling, including ABI1, SnRK2.2, SnRK2.3 and SnRK2.6 were altered in the transgenic plants overexpressing bHLH129. Taken together, our study suggests that bHLH129 is a transcription repressor that negatively regulates ABA response in Arabidopsis. PMID:26625868

  4. Diverse Transcriptional Programs Associated with Environmental Stress and Hormones in the Arabidopsis Receptor-Like Kinase Gene Family

    Institute of Scientific and Technical Information of China (English)

    Lee Chae; Sylvia Sudat; Sandrine Dudoit; Tong Zhu; Sheng Luan

    2009-01-01

    The genome of Arabidopsis thaliana encodes more than 600 receptor-like kinase (RLK) genes, by far the dominant class of receptors found in land plants. Although similar to the mammalian receptor tyrosine kinases, plant RLKs are serine/threonine kinases that represent a novel signaling innovation unique to plants and, consequently, an excellent opportunity to understand how extracellular signaling evolved and functions in plants as opposed to animals. RLKs are predicted to be major components of the signaling pathways that allow plants to respond to environmental and developmental conditions. However, breakthroughs in identifying these processes have been limited to only a handful of individual RLKs. Here, we used a Syngenta custom Arabidopsis GeneChip array to compile a detailed profile of the transcriptional activity of 604 receptor-like kinase genes after exposure to a cross-section of known signaling factors in plants,including abiotic stresses, biotic stresses, and hormones. In the 68 experiments comprising the study, we found that 582 of the 604 RLK genes displayed a two-fold or greater change in expression to at least one of 12 types of treatments, thereby providing a large body of experimental evidence for targeted functional screens of individual RLK genes. We investigated whether particular subfamilies of RLK genes are responsive to specific types of signals and found that each subfamily displayed broad ranges of expression, as opposed to being targeted towards particular signal classes. Finally, by analyzing the divergence of sequence and gene expression among the RLK subfamilies, we present evidence as to the functional basis for the expansion of the RLKs and how this expansion may have affected conservation and divergences in their function. Taken as a whole, our study represents a preliminary, working model of processes and interactions in which the members of the RLK gene family may be involved, where such information has remained elusive for so many

  5. Within and between whorls: comparative transcriptional profiling of Aquilegia and Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Claudia Voelckel

    Full Text Available BACKGROUND: The genus Aquilegia is an emerging model system in plant evolutionary biology predominantly because of its wide variation in floral traits and associated floral ecology. The anatomy of the Aquilegia flower is also very distinct. There are two whorls of petaloid organs, the outer whorl of sepals and the second whorl of petals that form nectar spurs, as well as a recently evolved fifth whorl of staminodia inserted between stamens and carpels. METHODOLOGY/PRINCIPAL FINDINGS: We designed an oligonucleotide microarray based on EST sequences from a mixed tissue, normalized cDNA library of an A. formosa x A. pubescens F2 population representing 17,246 unigenes. We then used this array to analyze floral gene expression in late pre-anthesis stage floral organs from a natural A. formosa population. In particular, we tested for gene expression patterns specific to each floral whorl and to combinations of whorls that correspond to traditional and modified ABC model groupings. Similar analyses were performed on gene expression data of Arabidopsis thaliana whorls previously obtained using the Ath1 gene chips (data available through The Arabidopsis Information Resource. CONCLUSIONS/SIGNIFICANCE: Our comparative gene expression analyses suggest that 1 petaloid sepals and petals of A. formosa share gene expression patterns more than either have organ-specific patterns, 2 petals of A. formosa and A. thaliana may be independently derived, 3 staminodia express B and C genes similar to stamens but the staminodium genetic program has also converged on aspects of the carpel program and 4 staminodia have unique up-regulation of regulatory genes and genes that have been implicated with defense against microbial infection and herbivory. Our study also highlights the value of comparative gene expression profiling and the Aquilegia microarray in particular for the study of floral evolution and ecology.

  6. Transcriptional profiling of the Arabidopsis abscission mutant hae hsl2 by RNA-Seq

    Directory of Open Access Journals (Sweden)

    Niederhuth Chad E

    2013-01-01

    Full Text Available Abstract Background Abscission is a mechanism by which plants shed entire organs in response to both developmental and environmental signals. Arabidopsis thaliana, in which only the floral organs abscise, has been used extensively to study the genetic, molecular and cellular processes controlling abscission. Abscission in Arabidopsis requires two genes that encode functionally redundant receptor-like protein kinases, HAESA (HAE and HAESA-LIKE 2 (HSL2. Double hae hsl2 mutant plants fail to abscise their floral organs at any stage of floral development and maturation. Results Using RNA-Seq, we compare the transcriptomes of wild-type and hae hsl2 stage 15 flowers, using the floral receptacle which is enriched for abscission zone cells. 2034 genes were differentially expressed with a False Discovery Rate adjusted p INFLORESCENCE DEFICIENT IN ABSCISSION (ida mutants shows that many of the same genes are co-regulated by IDA and HAE HSL2 and support the role of IDA in the HAE and HSL2 signaling pathway. Comparison to microarray data from stamen abscission zones show distinct patterns of expression of genes that are dependent on HAE HSL2 and reveal HAE HSL2- independent pathways. Conclusion HAE HSL2-dependent and HAE HSL2-independent changes in genes expression are required for abscission. HAE and HSL2 affect the expression of cell wall modifying and defense related genes necessary for abscission. The HAE HSL2-independent genes also appear to have roles in abscission and additionally are involved in processes such as hormonal signaling, senescence and callose deposition.

  7. A non canonical subtilase attenuates the transcriptional activation of defence responses in Arabidopsis thaliana

    Science.gov (United States)

    Serrano, Irene; Buscaill, Pierre; Audran, Corinne; Pouzet, Cécile; Jauneau, Alain; Rivas, Susana

    2016-01-01

    Proteases play crucial physiological functions in all organisms by controlling the lifetime of proteins. Here, we identified an atypical protease of the subtilase family [SBT5.2(b)] that attenuates the transcriptional activation of plant defence independently of its protease activity. The SBT5.2 gene produces two distinct transcripts encoding a canonical secreted subtilase [SBT5.2(a)] and an intracellular protein [SBT5.2(b)]. Concomitant to SBT5.2(a) downregulation, SBT5.2(b) expression is induced after bacterial inoculation. SBT5.2(b) localizes to endosomes where it interacts with and retains the defence-related transcription factor MYB30. Nuclear exclusion of MYB30 results in its reduced transcriptional activation and, thus, suppressed resistance. sbt5.2 mutants, with abolished SBT5.2(a) and SBT5.2(b) expression, display enhanced defence that is suppressed in a myb30 mutant background. Moreover, overexpression of SBT5.2(b), but not SBT5.2(a), in sbt5.2 plants reverts the phenotypes displayed by sbt5.2 mutants. Overall, we uncover a regulatory mode of the transcriptional activation of defence responses previously undescribed in eukaryotes. DOI: http://dx.doi.org/10.7554/eLife.19755.001 PMID:27685353

  8. AtRTD2: A Reference Transcript Dataset for accurate quantification of alternative splicing and expression changes in Arabidopsis thaliana RNA-seq data

    KAUST Repository

    Zhang, Runxuan

    2016-05-06

    Background Alternative splicing is the major post-transcriptional mechanism by which gene expression is regulated and affects a wide range of processes and responses in most eukaryotic organisms. RNA-sequencing (RNA-seq) can generate genome-wide quantification of individual transcript isoforms to identify changes in expression and alternative splicing. RNA-seq is an essential modern tool but its ability to accurately quantify transcript isoforms depends on the diversity, completeness and quality of the transcript information. Results We have developed a new Reference Transcript Dataset for Arabidopsis (AtRTD2) for RNA-seq analysis containing over 82k non-redundant transcripts, whereby 74,194 transcripts originate from 27,667 protein-coding genes. A total of 13,524 protein-coding genes have at least one alternatively spliced transcript in AtRTD2 such that about 60% of the 22,453 protein-coding, intron-containing genes in Arabidopsis undergo alternative splicing. More than 600 putative U12 introns were identified in more than 2,000 transcripts. AtRTD2 was generated from transcript assemblies of ca. 8.5 billion pairs of reads from 285 RNA-seq data sets obtained from 129 RNA-seq libraries and merged along with the previous version, AtRTD, and Araport11 transcript assemblies. AtRTD2 increases the diversity of transcripts and through application of stringent filters represents the most extensive and accurate transcript collection for Arabidopsis to date. We have demonstrated a generally good correlation of alternative splicing ratios from RNA-seq data analysed by Salmon and experimental data from high resolution RT-PCR. However, we have observed inaccurate quantification of transcript isoforms for genes with multiple transcripts which have variation in the lengths of their UTRs. This variation is not effectively corrected in RNA-seq analysis programmes and will therefore impact RNA-seq analyses generally. To address this, we have tested different genome

  9. Thirty-seven transcription factor genes differentially respond to a harpin protein and affect resistance to the green peach aphid in Arabidopsis

    Indian Academy of Sciences (India)

    Ruoxue Liu; Beibei Lü; Xiaomeng Wang; Chunling Zhang; Shuping Zhang; Jun Qian; Lei Chen; Haojie Shi; Hansong Dong

    2010-09-01

    The harpin protein HrpNEa induces Arabidopsis resistance to the green peach aphid by activating the ethylene signalling pathway and by recruiting EIN2, an essential regulator of ethylene signalling, for a defence response in the plant. We investigated 37 ethylene-inducible Arabidopsis transcription factor genes for their effects on the activation of ethylene signalling and insect defence. Twenty-eight of the 37 genes responded to both ethylene and HrpNEa, and showed either increased or inhibited transcription, while 18 genes showed increased transcription not only by ethylene but also by HrpNEa. In response to HrpNEa, transcription levels of 22 genes increased, with AtMYB44 being the most inducible, six genes had decreased transcript levels, and nine remained unchanged. When Arabidopsis mutants previously generated by mutagenicity at the 37 genes were surveyed, 24 mutants were similar to the wild type plant while four mutants were more resistant and nine mutants were more susceptible than wild type to aphid infestation. Aphid-susceptible mutants showed a greater susceptibility for atmyb15, atmyb38 and atmyb44, which were generated previously by T-DNA insertion into the exon region of AtMYB15 and the promoter regions of AtMYB38 and AtMYB44. The atmyb44 mutant was the most susceptible to aphid infestation and most compromised in induced resistance. Resistance accompanied the expression of PDF1.2, an ethylene signalling marker gene that requires EIN2 for transcription in wild type but not in atmyb15, atmyb38, and atmyb44, suggesting a disruption of ethylene signalling in the mutants. However, only atmyb44 incurred an abrogation in induced EIN2 expression, suggesting a close relationship between AtMYB44 and EIN2.

  10. Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy.

    Science.gov (United States)

    Clark, Natalie M; Hinde, Elizabeth; Winter, Cara M; Fisher, Adam P; Crosti, Giuseppe; Blilou, Ikram; Gratton, Enrico; Benfey, Philip N; Sozzani, Rosangela

    2016-06-11

    To understand complex regulatory processes in multicellular organisms, it is critical to be able to quantitatively analyze protein movement and protein-protein interactions in time and space. During Arabidopsis development, the intercellular movement of SHORTROOT (SHR) and subsequent interaction with its downstream target SCARECROW (SCR) control root patterning and cell fate specification. However, quantitative information about the spatio-temporal dynamics of SHR movement and SHR-SCR interaction is currently unavailable. Here, we quantify parameters including SHR mobility, oligomeric state, and association with SCR using a combination of Fluorescent Correlation Spectroscopy (FCS) techniques. We then incorporate these parameters into a mathematical model of SHR and SCR, which shows that SHR reaches a steady state in minutes, while SCR and the SHR-SCR complex reach a steady-state between 18 and 24 hr. Our model reveals the timing of SHR and SCR dynamics and allows us to understand how protein movement and protein-protein stoichiometry contribute to development.

  11. Microarray Analysis of Transcriptional Responses to Abscisic Acid and Salt Stress in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Yucheng Wang

    2013-05-01

    Full Text Available Abscisic acid (ABA plays a crucial role in plant responses to abiotic stress. To investigate differences in plant responses to salt and ABA stimulus, differences in gene expression in Arabidopsis in response to salt and ABA were compared using an Agilent oligo microarray. A total of 144 and 139 genes were significantly up- and downregulated, respectively, under NaCl stress, while 406 and 381 genes were significantly up- and downregulated, respectively, under ABA stress conditions. In addition, 31 genes were upregulated by both NaCl and ABA stresses, and 23 genes were downregulated by these stressors, suggesting that these genes may play similar roles in plant responses to salt and ABA stress. Gene ontology (GO analysis revealed four subgroups of genes, including genes in the GO categories “Molecular transducer activity”, “Growth”, “Biological adhesion” and “Pigmentation”, which were expressed in response to ABA stress but not NaCl stress. In addition, genes that play specific roles during salt or ABA stress were identified. Our results may help elucidate differences in the response of plants to salt and ABA stress.

  12. Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy.

    Science.gov (United States)

    Clark, Natalie M; Hinde, Elizabeth; Winter, Cara M; Fisher, Adam P; Crosti, Giuseppe; Blilou, Ikram; Gratton, Enrico; Benfey, Philip N; Sozzani, Rosangela

    2016-01-01

    To understand complex regulatory processes in multicellular organisms, it is critical to be able to quantitatively analyze protein movement and protein-protein interactions in time and space. During Arabidopsis development, the intercellular movement of SHORTROOT (SHR) and subsequent interaction with its downstream target SCARECROW (SCR) control root patterning and cell fate specification. However, quantitative information about the spatio-temporal dynamics of SHR movement and SHR-SCR interaction is currently unavailable. Here, we quantify parameters including SHR mobility, oligomeric state, and association with SCR using a combination of Fluorescent Correlation Spectroscopy (FCS) techniques. We then incorporate these parameters into a mathematical model of SHR and SCR, which shows that SHR reaches a steady state in minutes, while SCR and the SHR-SCR complex reach a steady-state between 18 and 24 hr. Our model reveals the timing of SHR and SCR dynamics and allows us to understand how protein movement and protein-protein stoichiometry contribute to development. PMID:27288545

  13. Identification of plant defence regulators through transcriptional profiling of Arabidopsis thaliana cdd1 mutant

    Indian Academy of Sciences (India)

    Swadhin Swain; Nidhi Singh; Ashis Kumar Nandi

    2015-03-01

    A sustainable balance between defence and growth is essential for optimal fitness under pathogen stress. Plants activate immune response at the cost of normal metabolic requirements. Thus, plants that constitutively activate defence are deprived of growth. Arabidopsis thaliana mutant constitutive defence without defect in growth and development1 (cdd1) is an exception. The cdd1 mutant is constitutive for salicylic acid accumulation, signalling, and defence against biotrophic and hemibiotrophic pathogens, without having much impact on growth. Thus, cdd1 offers an ideal genetic background to identify novel regulators of plant defence. Here we report the differential gene expression profile between cdd1 and wild-type plants as obtained by microarray hybridization. Expression of several defence-related genes also supports constitutive activation of defence in cdd1. We screened T-DNA insertion mutant lines of selected genes, for resistance against virulent bacterial pathogen Pseudomonas syringae pv. tomato DC3000 (Pst DC3000). Through bacterial resistance, callose deposition and pathogenesis-associated expression analyses, we identified four novel regulators of plant defence. Resistance levels in the mutants suggest that At2g19810 and [rom] At5g05790 are positive regulators, whereas At1g61370 and At3g42790 are negative regulators of plant defence against bacterial pathogens.

  14. Arabidopsis MAP Kinase 4 regulates gene expression via transcription factor release in the nucleus

    DEFF Research Database (Denmark)

    Qiu, Jin-Long; Fiil, Berthe Katrine; Petersen, Klaus;

    2008-01-01

    kinase 4 (MPK4) exists in nuclear complexes with the WRKY33 transcription factor. This complex depends on the MPK4 substrate MKS1. Challenge with Pseudomonas syringae or flagellin leads to the activation of MPK4 and phosphorylation of MKS1. Subsequently, complexes with MKS1 and WRKY33 are released from...... MPK4, and WRKY33 targets the promoter of PHYTOALEXIN DEFICIENT3 (PAD3) encoding an enzyme required for the synthesis of antimicrobial camalexin. Hence, wrky33 mutants are impaired in the accumulation of PAD3 mRNA and camalexin production upon infection. That WRKY33 is an effector of MPK4 is further...... supported by the suppression of PAD3 expression in mpk4-wrky33 double mutant backgrounds. Our data establish direct links between MPK4 and innate immunity and provide an example of how a plant MAP kinase can regulate gene expression by releasing transcription factors in the nucleus upon activation....

  15. Interaction of Arabidopsis Trihelix-Domain Transcription Factors VFP3 and VFP5 with Agrobacterium Virulence Protein VirF.

    Directory of Open Access Journals (Sweden)

    Elena García-Cano

    Full Text Available Agrobacterium is a natural genetic engineer of plants that exports several virulence proteins into host cells in order to take advantage of the cell machinery to facilitate transformation and support bacterial growth. One of these effectors is the F-box protein VirF, which presumably uses the host ubiquitin/proteasome system (UPS to uncoat the packaging proteins from the invading bacterial T-DNA. By analogy to several other bacterial effectors, VirF most likely has several functions in the host cell and, therefore, several interacting partners among host proteins. Here we identify one such interactor, an Arabidopsis trihelix-domain transcription factor VFP3, and further show that its very close homolog VFP5 also interacted with VirF. Interestingly, interactions of VirF with either VFP3 or VFP5 did not activate the host UPS, suggesting that VirF might play other UPS-independent roles in bacterial infection. To better understand the potential scope of VFP3 function, we used RNAi to reduce expression of the VFP3 gene. Transcriptome profiling of these VFP3-silenced plants using high-throughput cDNA sequencing (RNA-seq revealed that VFP3 substantially affected plant gene expression; specifically, 1,118 genes representing approximately 5% of all expressed genes were significantly either up- or down-regulated in the VFP3 RNAi line compared to wild-type Col-0 plants. Among the 507 up-regulated genes were genes implicated in the regulation of transcription, protein degradation, calcium signaling, and hormone metabolism, whereas the 611 down-regulated genes included those involved in redox regulation, light reactions of photosynthesis, and metabolism of lipids, amino acids, and cell wall. Overall, this pattern of changes in gene expression is characteristic of plants under stress. Thus, VFP3 likely plays an important role in controlling plant homeostasis.

  16. Arabidopsis transcriptional response to extracellular Ca2þ depletion involves a transient rise in cytosolic Ca2þ

    Institute of Scientific and Technical Information of China (English)

    Zhi Qi

    2015-01-01

    Ecological evidence indicates a worldwide trend of dramatical y decreased soil Ca2þ levels caused by increased acid deposition and massive timber harvesting. Little is known about the genetic and cel ular mechanism of plants’ responses to Ca2þ depletion. In this study, transcriptional profiling analysis helped identify multiple extracel ular Ca2þ ([Ca2þ]ext) depletion‐respon-sive genes in Arabidopsis thaliana L., many of which are involved in response to other environmental stresses. Interestingly, a group of genes encoding putative cytosolic Ca2þ ([Ca2þ]cyt) sensors were significantly upregulated, implying that [Ca2þ]cyt has a role in sensing [Ca2þ]ext depletion. Consistent with this observation, [Ca2þ]ext depletion stimulated a transient rise in [Ca2þ]cyt that was negatively influenced by [Kþ]ext, suggesting the involvement of a membrane potential‐sensitive component. The [Ca2þ]cyt response to [Ca2þ]ext depletion was significantly desensitized after the initial treatment, which is typical of a receptor‐mediated signaling event. The response was insensi-tive to an animal Ca2þ sensor antagonist, but was suppressed by neomycin, an inhibitor of phospholipase C. Gd3þ, an inhibitor of Ca2þ channels, suppressed the [Ca2þ]ext‐triggered rise in [Ca2þ]cyt and downstream changes in gene expression. Taken together, this study demonstrates that [Ca2þ]cyt plays an important role in the putative receptor‐mediated cel ular and transcriptional response to [Ca2þ]ext depletion of plant cel s.

  17. Improvement of enzymatic saccharification yield in Arabidopsis thaliana by ectopic expression of the rice SUB1A-1 transcription factor

    Directory of Open Access Journals (Sweden)

    Lizeth Núñez-López

    2015-03-01

    Full Text Available Saccharification of polysaccharides releases monosaccharides that can be used by ethanol-producing microorganisms in biofuel production. To improve plant biomass as a raw material for saccharification, factors controlling the accumulation and structure of carbohydrates must be identified. Rice SUB1A-1 is a transcription factor that represses the turnover of starch and postpones energy-consuming growth processes under submergence stress. Arabidopsis was employed to test if heterologous expression of SUB1A-1 or SUB1C-1 (a related gene can be used to improve saccharification. Cellulolytic and amylolytic enzymatic treatments confirmed that SUB1A-1 transgenics had better saccharification yield than wild-type (Col-0, mainly from accumulated starch. This improved saccharification yield was developmentally controlled; when compared to Col-0, young transgenic vegetative plants yielded 200–300% more glucose, adult vegetative plants yielded 40–90% more glucose and plants in reproductive stage had no difference in yield. We measured photosynthetic parameters, starch granule microstructure, and transcript abundance of genes involved in starch degradation (SEX4, GWD1, juvenile transition (SPL3-5 and meristematic identity (FUL, SOC1 but found no differences to Col-0, indicating that starch accumulation may be controlled by down-regulation of CONSTANS and FLOWERING LOCUS T by SUB1A-1 as previously reported. SUB1A-1 transgenics also offered less resistance to deformation than wild-type concomitant to up-regulation of AtEXP2 expansin and BGL2 glucan-1,3,-beta-glucosidase. We conclude that heterologous SUB1A-1 expression can improve saccharification yield and softness, two traits needed in bioethanol production.

  18. The Arabidopsis transcription factor ABIG1 relays ABA signaled growth inhibition and drought induced senescence

    Science.gov (United States)

    Liu, Tie; Longhurst, Adam D; Talavera-Rauh, Franklin; Hokin, Samuel A; Barton, M Kathryn

    2016-01-01

    Drought inhibits plant growth and can also induce premature senescence. Here we identify a transcription factor, ABA INSENSITIVE GROWTH 1 (ABIG1) required for abscisic acid (ABA) mediated growth inhibition, but not for stomatal closure. ABIG1 mRNA levels are increased both in response to drought and in response to ABA treatment. When treated with ABA, abig1 mutants remain greener and produce more leaves than comparable wild-type plants. When challenged with drought, abig1 mutants have fewer yellow, senesced leaves than wild-type. Induction of ABIG1 transcription mimics ABA treatment and regulates a set of genes implicated in stress responses. We propose a model in which drought acts through ABA to increase ABIG1 transcription which in turn restricts new shoot growth and promotes leaf senescence. The results have implications for plant breeding: the existence of a mutant that is both ABA resistant and drought resistant points to new strategies for isolating drought resistant genetic varieties. DOI: http://dx.doi.org/10.7554/eLife.13768.001 PMID:27697148

  19. Negative Regulation of Anthocynanin Biosynthesis in Arabidopsis by a miR156-Targeted SPL Transcription Factor

    Energy Technology Data Exchange (ETDEWEB)

    Gou, J.Y.; Liu, C.; Felippes, F. F.; Weigel, D.; Wang, J.-W.

    2011-04-01

    Flavonoids are synthesized through an important metabolic pathway that leads to the production of diverse secondary metabolites, including anthocyanins, flavonols, flavones, and proanthocyanidins. Anthocyanins and flavonols are derived from Phe and share common precursors, dihydroflavonols, which are substrates for both flavonol synthase and dihydroflavonol 4-reductase. In the stems of Arabidopsis thaliana, anthocyanins accumulate in an acropetal manner, with the highest level at the junction between rosette and stem. We show here that this accumulation pattern is under the regulation of miR156-targeted SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes, which are deeply conserved and known to have important roles in regulating phase change and flowering. Increased miR156 activity promotes accumulation of anthocyanins, whereas reduced miR156 activity results in high levels of flavonols. We further provide evidence that at least one of the miR156 targets, SPL9, negatively regulates anthocyanin accumulation by directly preventing expression of anthocyanin biosynthetic genes through destabilization of a MYB-bHLH-WD40 transcriptional activation complex. Our results reveal a direct link between the transition to flowering and secondary metabolism and provide a potential target for manipulation of anthocyanin and flavonol content in plants.

  20. Arabidopsis IRE1 catalyses unconventional splicing of bZIP60 mRNA to produce the active transcription factor

    KAUST Repository

    Nagashima, Yukihiro

    2011-07-01

    IRE1 plays an essential role in the endoplasmic reticulum (ER) stress response in yeast and mammals. We found that a double mutant of Arabidopsis IRE1A and IRE1B (ire1a/ire1b) is more sensitive to the ER stress inducer tunicamycin than the wild-type. Transcriptome analysis revealed that genes whose induction was reduced in ire1a/ire1b largely overlapped those in the bzip60 mutant. We observed that the active form of bZIP60 protein detected in the wild-type was missing in ire1a/ire1b. We further demonstrated that bZIP60 mRNA is spliced by ER stress, removing 23 ribonucleotides and therefore causing a frameshift that replaces the C-terminal region of bZIP60 including the transmembrane domain (TMD) with a shorter region without a TMD. This splicing was detected in ire1a and ire1b single mutants, but not in the ire1a/ire1b double mutant. We conclude that IRE1A and IRE1B catalyse unconventional splicing of bZIP60 mRNA to produce the active transcription factor.

  1. An SGS3-like protein functions in RNA-directed DNA methylation and transcriptional gene silencing in Arabidopsis

    KAUST Repository

    Zheng, Zhimin

    2010-01-06

    RNA-directed DNA methylation (RdDM) is an important epigenetic mechanism for silencing transgenes and endogenous repetitive sequences such as transposons. The RD29A promoter-driven LUCIFERASE transgene and its corresponding endogenous RD29A gene are hypermethylated and silenced in the Arabidopsis DNA demethylase mutant ros1. By screening for second-site suppressors of ros1, we identified the RDM12 locus. The rdm12 mutation releases the silencing of the RD29A-LUC transgene and the endogenous RD29A gene by reducing the promoter DNA methylation. The rdm12 mutation also reduces DNA methylation at endogenous RdDM target loci, including transposons and other repetitive sequences. In addition, the rdm12 mutation affects the levels of small interfering RNAs (siRNAs) from some of the RdDM target loci. RDM12 encodes a protein with XS and coiled-coil domains, and is similar to SGS3, which is a partner protein of RDR6 and can bind to double-stranded RNAs with a 5′ overhang, and is required for several post-transcriptional gene silencing pathways. Our results show that RDM12 is a component of the RdDM pathway, and suggest that RdDM may involve double-stranded RNAs with a 5′ overhang and the partnering between RDM12 and RDR2. © 2010 Blackwell Publishing Ltd.

  2. Functional analysis of water stress-responsive soybean GmNAC003 and GmNAC004 transcription factors in lateral root development in arabidopsis.

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    Truyen N Quach

    Full Text Available In Arabidopsis, NAC (NAM, ATAF and CUC transcription factors have been found to promote lateral root number through the auxin signaling pathway. In the present study, the role of water stress-inducible soybean GmNAC003 and GmNAC004 genes in the enhancement of lateral root development under water deficit conditions was investigated. Both genes were highly expressed in roots, leaves and flowers of soybean and were strongly induced by water stress and moderately induced by a treatment with abscisic acid (ABA. They showed a slight response to treatment with 2,4-dichlorophenoxyacetic acid (2,4-D. The transgenic Arabidopsis plants overexpressing GmNAC004 showed an increase in lateral root number and length under non-stress conditions and maintained higher lateral root number and length under mild water stress conditions compared to the wild-type (WT, while the transgenic plants overexpressing GmNAC003 did not show any response. However, LR development of GmNAC004 transgenic Arabidopsis plants was not enhanced in the water-stressed compared to the well-watered treatment. In the treatment with ABA, LR density of the GmNAC004 transgenic Arabidopsis was less suppressed than that of the WT, suggesting that GmNAC004 counteracts ABA-induced inhibition of lateral root development. In the treatment with 2,4-D, lateral root density was enhanced in both GmNAC004 transgenic Arabidopsis and WT plants but the promotion was higher in the transgenic plants. Conversely, in the treatment with naphthylphthalamic acid (NPA, lateral root density was inhibited and there was no difference in the phenotype of the GmNAC004 transgenic Arabidopsis and WT plants, indicating that auxin is required for the action of GmNAC004. Transcript analysis for a number of known auxin and ABA related genes showed that GmNAC004's role may suppress ABA signaling but promote auxin signaling to increase lateral root development in the Arabidopsis heterologous system.

  3. Characterization of MADS-domain transcription factor complexes in Arabidopsis flower development

    Science.gov (United States)

    Smaczniak, Cezary; Immink, Richard G. H.; Muiño, Jose M.; Blanvillain, Robert; Busscher, Marco; Busscher-Lange, Jacqueline; Dinh, Q. D. (Peter); Liu, Shujing; Westphal, Adrie H.; Boeren, Sjef; Parcy, François; Xu, Lin; Carles, Cristel C.; Angenent, Gerco C.; Kaufmann, Kerstin

    2012-01-01

    Floral organs are specified by the combinatorial action of MADS-domain transcription factors, yet the mechanisms by which MADS-domain proteins activate or repress the expression of their target genes and the nature of their cofactors are still largely unknown. Here, we show using affinity purification and mass spectrometry that five major floral homeotic MADS-domain proteins (AP1, AP3, PI, AG, and SEP3) interact in floral tissues as proposed in the “floral quartet” model. In vitro studies confirmed a flexible composition of MADS-domain protein complexes depending on relative protein concentrations and DNA sequence. In situ bimolecular fluorescent complementation assays demonstrate that MADS-domain proteins interact during meristematic stages of flower development. By applying a targeted proteomics approach we were able to establish a MADS-domain protein interactome that strongly supports a mechanistic link between MADS-domain proteins and chromatin remodeling factors. Furthermore, members of other transcription factor families were identified as interaction partners of floral MADS-domain proteins suggesting various specific combinatorial modes of action. PMID:22238427

  4. PPP1, a plant-specific regulator of transcription controls Arabidopsis development and PIN expression.

    Science.gov (United States)

    Benjamins, René; Barbez, Elke; Ortbauer, Martina; Terpstra, Inez; Lucyshyn, Doris; Moulinier-Anzola, Jeanette; Khan, Muhammad Asaf; Leitner, Johannes; Malenica, Nenad; Butt, Haroon; Korbei, Barbara; Scheres, Ben; Kleine-Vehn, Jürgen; Luschnig, Christian

    2016-01-01

    Directional transport of auxin is essential for plant development, with PIN auxin transport proteins representing an integral part of the machinery that controls hormone distribution. However, unlike the rapidly emerging framework of molecular determinants regulating PIN protein abundance and subcellular localization, insights into mechanisms controlling PIN transcription are still limited. Here we describe PIN2 PROMOTER BINDING PROTEIN 1 (PPP1), an evolutionary conserved plant-specific DNA binding protein that acts on transcription of PIN genes. Consistent with PPP1 DNA-binding activity, PPP1 reporter proteins are nuclear localized and analysis of PPP1 null alleles and knockdown lines indicated a function as a positive regulator of PIN expression. Furthermore, we show that ppp1 pleiotropic mutant phenotypes are partially reverted by PIN overexpression, and results are presented that underline a role of PPP1-PIN promoter interaction in PIN expression control. Collectively, our findings identify an elementary, thus far unknown, plant-specific DNA-binding protein required for post-embryonic plant development, in general, and correct expression of PIN genes, in particular. PMID:27553690

  5. Transcriptional and metabolic insights into the differential physiological responses of arabidopsis to optimal and supraoptimal atmospheric CO2.

    Directory of Open Access Journals (Sweden)

    Fatma Kaplan

    Full Text Available BACKGROUND: In tightly closed human habitats such as space stations, locations near volcano vents and closed culture vessels, atmospheric CO(2 concentration may be 10 to 20 times greater than Earth's current ambient levels. It is known that super-elevated (SE CO(2 (>1,200 µmol mol(-1 induces physiological responses different from that of moderately elevated CO(2 (up to 1,200 µmol mol(-1, but little is known about the molecular responses of plants to supra-optimal [CO(2]. METHODOLOGY/PRINCIPAL FINDINGS: To understand the underlying molecular causes for differential physiological responses, metabolite and transcript profiles were analyzed in aerial tissue of Arabidopsis plants, which were grown under ambient atmospheric CO(2 (400 µmol mol(-1, elevated CO(2 (1,200 µmol mol(-1 and SE CO(2 (4,000 µmol mol(-1, at two developmental stages early and late vegetative stage. Transcript and metabolite profiling revealed very different responses to elevated versus SE [CO(2]. The transcript profiles of SE CO(2 treated plants were closer to that of the control. Development stage had a clear effect on plant molecular response to elevated and SE [CO(2]. Photosynthetic acclimation in terms of down-regulation of photosynthetic gene expression was observed in response to elevated [CO(2], but not that of SE [CO(2] providing the first molecular evidence that there appears to be a fundamental disparity in the way plants respond to elevated and SE [CO(2]. Although starch accumulation was induced by both elevated and SE [CO(2], the increase was less at the late vegetative stage and accompanied by higher soluble sugar content suggesting an increased starch breakdown to meet sink strength resulting from the rapid growth demand. Furthermore, many of the elevated and SE CO(2-responsive genes found in the present study are also regulated by plant hormone and stress. CONCLUSIONS/SIGNIFICANCE: This study provides new insights into plant acclimation to elevated and SE [CO

  6. Regulation of Arabidopsis thaliana plasma membrane glucose-responsive regulator (AtPGR) expression by A. thaliana storekeeper-like transcription factor, AtSTKL, modulates glucose response in Arabidopsis.

    Science.gov (United States)

    Chung, Moon-Soo; Lee, Sungbeom; Min, Ji-Hee; Huang, Ping; Ju, Hyun-Woo; Kim, Cheol Soo

    2016-07-01

    Biochemical, genetic, physiological, and molecular research in plants has demonstrated a central role of glucose (Glc) in the control of plant growth, metabolism, and development, and has revealed networks that integrate light, stresses, nutrients, and hormone signaling. Previous studies have reported that AtPGR protein as potential candidates for Glc signaling protein. In the present study, we characterized transcription factors that bind to the upstream region of the AtPGR gene isolated using the yeast one-hybrid screening with an Arabidopsis cDNA library. One of the selected genes (AtSTKL) appeared to confer elevated sensitivity to Glc response. Overexpression of AtSTKLs (AtSTKL1 and AtSTKL2) increased the sensitivity to Glc during the post-germination stages. In contrast, atstkl1 and atstkl2 antisense lines displayed reduced sensitivity to high Glc concentration during the early seedling stage. Furthermore, we showed that the two AtSTKLs bind to the 5'-GCCT-3' element of the upstream promoter region of the AtPGR gene in vitro and repress the beta-glucuronidase (GUS) activity in AtPGR promoter-GUS (P999-GUS) transgenic plants. Green fluorescent protein (GFP)-tagged AtSTKLs were localized in the nuclei of transgenic Arabidopsis cells. Collectively, these results suggest that AtSTKL1 and AtSTKL2 function both as repressors of AtPGR transcription and as novel transcription factors in the Glc signaling pathway. PMID:27031427

  7. Regulation of secondary cell wall biosynthesis by poplar R2R3 MYB transcription factor PtrMYB152 in Arabidopsis

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Shucai [Northeast Normal Univ., Changchun (China); Univ. of British Columbia, Vancouver, BC (Canada); Li, Eryang [Univ. of British Columbia, Vancouver, BC (Canada); Porth, Ilga [Univ. of British Columbia, Vancouver, BC (Canada); Chen, Jin-Gui [Univ. of British Columbia, Vancouver, BC (Canada); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Mansfield, Shawn D. [Univ. of British Columbia, Vancouver, BC (Canada); Douglas, Carl [Univ. of British Columbia, Vancouver, BC (Canada)

    2014-05-23

    Poplar has 192 annotated R2R3 MYB genes, of which only three have been shown to play a role in the regulation of secondary cell wall formation. Here we report the characterization of PtrMYB152, a poplar homolog of the Arabidopsis R2R3 MYB transcription factor AtMYB43, in the regulation of secondary cell wall biosynthesis. The expression of PtrMYB152 in secondary xylem is about 18 times of that in phloem. When expressed in Arabidopsis under the control of either 35S or PtrCesA8 promoters, PtrMYB152 increased secondary cell wall thickness, which is likely caused by increased lignification. Accordingly, elevated expression of genes encoding sets of enzymes in secondary wall biosynthesis were observed in transgenic plants expressing PtrMYB152. Arabidopsis protoplast transfection assays suggested that PtrMYB152 functions as a transcriptional activator. Taken together, our results suggest that PtrMYB152 may be part of a regulatory network activating expression of discrete sets of secondary cell wall biosynthesis genes.

  8. SEUSS Integrates Gibberellin Signaling with Transcriptional Inputs from the SHR-SCR-SCL3 Module to Regulate Middle Cortex Formation in the Arabidopsis Root.

    Science.gov (United States)

    Gong, Xue; Flores-Vergara, Miguel A; Hong, Jing Han; Chu, Huangwei; Lim, Jun; Franks, Robert G; Liu, Zhongchi; Xu, Jian

    2016-03-01

    A decade of studies on middle cortex (MC) formation in the root endodermis of Arabidopsis (Arabidopsis thaliana) have revealed a complex regulatory network that is orchestrated by several GRAS family transcription factors, including SHORT-ROOT (SHR), SCARECROW (SCR), and SCARECROW-LIKE3 (SCL3). However, how their functions are regulated remains obscure. Here we show that mutations in the SEUSS (SEU) gene led to a higher frequency of MC formation. seu mutants had strongly reduced expression of SHR, SCR, and SCL3, suggesting that SEU positively regulates these genes. Our results further indicate that SEU physically associates with upstream regulatory sequences of SHR, SCR, and SCL3; and that SEU has distinct genetic interactions with these genes in the control of MC formation, with SCL3 being epistatic to SEU. Similar to SCL3, SEU was repressed by the phytohormone GA and induced by the GA biosynthesis inhibitor paclobutrazol, suggesting that SEU acts downstream of GA signaling to regulate MC formation. Consistently, we found that SEU mediates the regulation of SCL3 by GA signaling. Together, our study identifies SEU as a new critical player that integrates GA signaling with transcriptional inputs from the SHR-SCR-SCL3 module to regulate MC formation in the Arabidopsis root.

  9. ORS1,an H2O2-Responsive NAC Transcription Factor,Controls Senescence in Arabidopsis thaliana

    Institute of Scientific and Technical Information of China (English)

    Salma Balazadeh; Miroslaw Kwasniewski; Camila Caldana; Mohammad Mehrnia; María Inés Zanor; Gang-Ping Xue; Bernd Mueller-Roeber

    2011-01-01

    We report here that ORS1,a previously uncharacterized member of the NAC transcription factor family,controls leaf senescence in Arabidopsis thaliana. Overexpression of ORS1 accelerates senescence in transgenic plants,whereas its inhibition delays it. Genes acting downstream of ORS1 were identified by global expression analysis using transgenic plants producing dexamethasone-inducible ORS1-GR fusion protein. Of the 42 up-regulated genes,30 (~70%) were previously shown to be up-regulated during age-dependent senescence. We also observed that 32 (~76%) of the ORS1-de-pendent genes were induced by long-term (4 d),but not short-term (6 h) salinity stress (150 mM NaCI). Furthermore,expression of 16 and 24 genes,respectively,was induced after 1 and 5 h of treatment with hydrogen peroxide (H2O2),a reactive oxygen species known to accumulate during salinity stress. ORS1 itself was found to be rapidly and strongly induced by H2O2 treatment in both leaves and roots. Using in vitro binding site selection,we determined the preferred binding motif of ORS1 and found it to be present in half of the ORS1 -dependent genes. ORS1 is a paralog of ORE1/ ANAC092/AtNAC2,a previously reported regulator of leaf senescence. Phylogenetic footprinting revealed evolutionary conservation of the ORS1 and ORE1 promoter sequences in different Brassicaceae species,indicating strong positive selection acting on both genes. We conclude that ORS1,similarly to ORE1,triggers expression of senescence-associated genes through a regulatory network that may involve cross-talk with salt- and H2O2-dependent signaling pathways.

  10. High REDOX RESPONSIVE TRANSCRIPTION FACTOR1 Levels Result in Accumulation of Reactive Oxygen Species in Arabidopsis thaliana Shoots and Roots.

    Science.gov (United States)

    Matsuo, Mitsuhiro; Johnson, Joy Michal; Hieno, Ayaka; Tokizawa, Mutsutomo; Nomoto, Mika; Tada, Yasuomi; Godfrey, Rinesh; Obokata, Junichi; Sherameti, Irena; Yamamoto, Yoshiharu Y; Böhmer, Frank-D; Oelmüller, Ralf

    2015-08-01

    Redox Responsive Transcription Factor1 (RRTF1) in Arabidopsis is rapidly and transiently upregulated by H2O2, as well as biotic- and abiotic-induced redox signals. RRTF1 is highly conserved in angiosperms, but its physiological role remains elusive. Here we show that inactivation of RRTF1 restricts and overexpression promotes reactive oxygen species (ROS) accumulation in response to stress. Transgenic lines overexpressing RRTF1 are impaired in root and shoot development, light sensitive, and susceptible to Alternaria brassicae infection. These symptoms are diminished by the beneficial root endophyte Piriformospora indica, which reduces ROS accumulation locally in roots and systemically in shoots, and by antioxidants and ROS inhibitors that scavenge ROS. More than 800 genes were detected in mature leaves and seedlings of transgenic lines overexpressing RRTF1; ∼ 40% of them have stress-, redox-, ROS-regulated-, ROS-scavenging-, defense-, cell death- and senescence-related functions. Bioinformatic analyses and in vitro DNA binding assays demonstrate that RRTF1 binds to GCC-box-like sequences in the promoter of RRTF1-responsive genes. Upregulation of RRTF1 by stress stimuli and H2O2 requires WRKY18/40/60. RRTF1 is co-regulated with the phylogenetically related RAP2.6, which contains a GCC-box-like sequence in its promoter, but transgenic lines overexpressing RAP2.6 do not accumulate higher ROS levels. RRTF1 also stimulates systemic ROS accumulation in distal non-stressed leaves. We conclude that the elevated levels of the highly conserved RRTF1 induce ROS accumulation in response to ROS and ROS-producing abiotic and biotic stress signals.

  11. Arabidopsis resistance protein SNC1 activates immune responses through association with a transcriptional corepressor

    Science.gov (United States)

    Zhu, Zhaohai; Xu, Fang; Zhang, Yaxi; Cheng, Yu Ti; Wiermer, Marcel; Li, Xin; Zhang, Yuelin

    2010-01-01

    In both plants and animals, nucleotide-binding (NB) domain and leucine-rich repeat (LRR)-containing proteins (NLR) function as sensors of pathogen-derived molecules and trigger immune responses. Although NLR resistance (R) proteins were first reported as plant immune receptors more than 15 years ago, how these proteins activate downstream defense responses is still unclear. Here we report that the Toll-like/interleukin-1 receptor (TIR)-NB-LRR R protein, suppressor of npr1-1, constitutive 1 (SNC1) functions through its associated protein, Topless-related 1 (TPR1). Knocking out TPR1 and its close homologs compromises immunity mediated by SNC1 and several other TIR-NB-LRR–type R proteins, whereas overexpression of TPR1 constitutively activates SNC1-mediated immune responses. TPR1 functions as a transcriptional corepressor and associates with histone deacetylase 19 in vivo. Among the target genes of TPR1 are Defense no Death 1 (DND1) and Defense no Death 2 (DND2), two known negative regulators of immunity that are repressed during pathogen infection, suggesting that TPR1 activates R protein-mediated immune responses through repression of negative regulators. PMID:20647385

  12. Arabidopsis sigma factor binding proteins are activators of the WRKY33 transcription factor in plant defense.

    Science.gov (United States)

    Lai, Zhibing; Li, Ying; Wang, Fei; Cheng, Yuan; Fan, Baofang; Yu, Jing-Quan; Chen, Zhixiang

    2011-10-01

    Necrotrophic pathogens are important plant pathogens that cause many devastating plant diseases. Despite their impact, our understanding of the plant defense response to necrotrophic pathogens is limited. The WRKY33 transcription factor is important for plant resistance to necrotrophic pathogens; therefore, elucidation of its functions will enhance our understanding of plant immunity to necrotrophic pathogens. Here, we report the identification of two WRKY33-interacting proteins, nuclear-encoded SIGMA FACTOR BINDING PROTEIN1 (SIB1) and SIB2, which also interact with plastid-encoded plastid RNA polymerase SIGMA FACTOR1. Both SIB1 and SIB2 contain an N-terminal chloroplast targeting signal and a putative nuclear localization signal, suggesting that they are dual targeted. Bimolecular fluorescence complementation indicates that WRKY33 interacts with SIBs in the nucleus of plant cells. Both SIB1 and SIB2 contain a short VQ motif that is important for interaction with WRKY33. The two VQ motif-containing proteins recognize the C-terminal WRKY domain and stimulate the DNA binding activity of WRKY33. Like WRKY33, both SIB1 and SIB2 are rapidly and strongly induced by the necrotrophic pathogen Botrytis cinerea. Resistance to B. cinerea is compromised in the sib1 and sib2 mutants but enhanced in SIB1-overexpressing transgenic plants. These results suggest that dual-targeted SIB1 and SIB2 function as activators of WRKY33 in plant defense against necrotrophic pathogens.

  13. HYPER RECOMBINATION1 of the THO/TREX complex plays a role in controlling transcription of the REVERSION-TO-ETHYLENE SENSITIVITY1 gene in Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Congyao Xu

    2015-02-01

    Full Text Available Arabidopsis REVERSION-TO-ETHYLENE SENSITIVITY1 (RTE1 represses ethylene hormone responses by promoting ethylene receptor ETHYLENE RESPONSE1 (ETR1 signaling, which negatively regulates ethylene responses. To investigate the regulation of RTE1, we performed a genetic screening for mutations that suppress ethylene insensitivity conferred by RTE1 overexpression in Arabidopsis. We isolated HYPER RECOMBINATION1 (HPR1, which is required for RTE1 overexpressor (RTE1ox ethylene insensitivity at the seedling but not adult stage. HPR1 is a component of the THO complex, which, with other proteins, forms the TRanscription EXport (TREX complex. In yeast, Drosophila, and humans, the THO/TREX complex is involved in transcription elongation and nucleocytoplasmic RNA export, but its role in plants is to be fully determined. We investigated how HPR1 is involved in RTE1ox ethylene insensitivity in Arabidopsis. The hpr1-5 mutation may affect nucleocytoplasmic mRNA export, as revealed by in vivo hybridization of fluorescein-labeled oligo(dT45 with unidentified mRNA in the nucleus. The hpr1-5 mutation reduced the total and nuclear RTE1 transcript levels to a similar extent, and RTE1 transcript reduction rate was not affected by hpr1-5 with cordycepin treatment, which prematurely terminates transcription. The defect in the THO-interacting TEX1 protein of TREX but not the mRNA export factor SAC3B also reduced the total and nuclear RTE1 levels. SERINE-ARGININE-RICH (SR proteins are involved mRNA splicing, and we found that SR protein SR33 co-localized with HPR1 in nuclear speckles, which agreed with the association of human TREX with the splicing machinery. We reveal a role for HPR1 in RTE1 expression during transcription elongation and less likely during export. Gene expression involved in ethylene signaling suppression was not reduced by the hpr1-5 mutation, which indicates selectivity of HPR1 for RTE1 expression affecting the consequent ethylene response. Thus

  14. Iron and FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR-dependent regulation of proteins and genes in Arabidopsis thaliana roots.

    Science.gov (United States)

    Mai, Hans-Jörg; Lindermayr, Christian; von Toerne, Christine; Fink-Straube, Claudia; Durner, Jörg; Bauer, Petra

    2015-09-01

    Iron is an essential micronutrient for plants, and iron deficiency requires a variety of physiological adaptations. FIT (FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR) is essential for the regulation of iron uptake in Arabidopsis thaliana roots. FIT is transcriptionally as well as posttranscriptionally regulated in response to iron supply. To investigate to which extent posttranscriptional regulation upon iron deficiency applies to proteins and to determine the dependency on FIT, we performed a parallel proteomic and transcriptomic study with wild-type, a fit knock-out mutant, and a FIT overexpressing Arabidopsis line. Among 92 proteins differentially regulated by iron and/or FIT, we identified 30 proteins, which displayed differential regulation at the transcriptional level. Eleven protein spots were regulated in at least one of the data points even contrary to the respective genes dependent on FIT. We found ten proteins in at least two forms. The analysis of functional classification showed enriched GO terms among the posttranscriptionally regulated genes and of proteins, that were downregulated or absent in the fit knock-out mutant. Taken together, we provide evidence for iron and FIT-dependent posttranscriptional regulation in iron homeostasis in A. thaliana.

  15. Arabidopsis WRKY6 Transcription Factor Acts as a Positive Regulator of Abscisic Acid Signaling during Seed Germination and Early Seedling Development.

    Science.gov (United States)

    Huang, Yun; Feng, Cui-Zhu; Ye, Qing; Wu, Wei-Hua; Chen, Yi-Fang

    2016-02-01

    The phytohormone abscisic acid (ABA) plays important roles during seed germination and early seedling development. Here, we characterized the function of the Arabidopsis WRKY6 transcription factor in ABA signaling. The transcript of WRKY6 was repressed during seed germination and early seedling development, and induced by exogenous ABA. The wrky6-1 and wrky6-2 mutants were ABA insensitive, whereas WRKY6-overexpressing lines showed ABA-hypersensitive phenotypes during seed germination and early seedling development. The expression of RAV1 was suppressed in the WRKY6-overexpressing lines and elevated in the wrky6 mutants, and the expression of ABI3, ABI4, and ABI5, which was directly down-regulated by RAV1, was enhanced in the WRKY6-overexpressing lines and repressed in the wrky6 mutants. Electrophoretic mobility shift and chromatin immunoprecipitation assays showed that WRKY6 could bind to the RAV1 promoter in vitro and in vivo. Overexpression of RAV1 in WRKY6-overexpressing lines abolished their ABA-hypersensitive phenotypes, and the rav1 wrky6-2 double mutant showed an ABA-hypersensitive phenotype, similar to rav1 mutant. Together, the results demonstrated that the Arabidopsis WRKY6 transcription factor played important roles in ABA signaling by directly down-regulating RAV1 expression.

  16. ZINC FINGER OF ARABIDOPSIS THALIANA12 (ZAT12) Interacts with FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT) Linking Iron Deficiency and Oxidative Stress Responses.

    Science.gov (United States)

    Le, Cham Thi Tuyet; Brumbarova, Tzvetina; Ivanov, Rumen; Stoof, Claudia; Weber, Eva; Mohrbacher, Julia; Fink-Straube, Claudia; Bauer, Petra

    2016-01-01

    Plants grown under iron (Fe)-deficient conditions induce a set of genes that enhance the efficiency of Fe uptake by the roots. In Arabidopsis (Arabidopsis thaliana), the central regulator of this response is the basic helix-loop-helix transcription factor FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT). FIT activity is regulated by protein-protein interactions, which also serve to integrate external signals that stimulate and possibly inhibit Fe uptake. In the search of signaling components regulating FIT function, we identified ZINC FINGER OF ARABIDOPSIS THALIANA12 (ZAT12), an abiotic stress-induced transcription factor. ZAT12 interacted with FIT, dependent on the presence of the ethylene-responsive element-binding factor-associated amphiphilic repression motif. ZAT12 protein was found expressed in the root early differentiation zone, where its abundance was modulated in a root layer-specific manner. In the absence of ZAT12, FIT expression was upregulated, suggesting a negative effect of ZAT12 on Fe uptake. Consistently, zat12 loss-of-function mutants had higher Fe content than the wild type at sufficient Fe. We found that under Fe deficiency, hydrogen peroxide (H2O2) levels were enhanced in a FIT-dependent manner. FIT protein, in turn, was stabilized by H2O2 but only in the presence of ZAT12, showing that H2O2 serves as a signal for Fe deficiency responses. We propose that oxidative stress-induced ZAT12 functions as a negative regulator of Fe acquisition. A model where H2O2 mediates the negative regulation of plant responses to prolonged stress might be applicable to a variety of stress conditions.

  17. ZINC FINGER OF ARABIDOPSIS THALIANA12 (ZAT12) Interacts with FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT) Linking Iron Deficiency and Oxidative Stress Responses.

    Science.gov (United States)

    Le, Cham Thi Tuyet; Brumbarova, Tzvetina; Ivanov, Rumen; Stoof, Claudia; Weber, Eva; Mohrbacher, Julia; Fink-Straube, Claudia; Bauer, Petra

    2016-01-01

    Plants grown under iron (Fe)-deficient conditions induce a set of genes that enhance the efficiency of Fe uptake by the roots. In Arabidopsis (Arabidopsis thaliana), the central regulator of this response is the basic helix-loop-helix transcription factor FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT). FIT activity is regulated by protein-protein interactions, which also serve to integrate external signals that stimulate and possibly inhibit Fe uptake. In the search of signaling components regulating FIT function, we identified ZINC FINGER OF ARABIDOPSIS THALIANA12 (ZAT12), an abiotic stress-induced transcription factor. ZAT12 interacted with FIT, dependent on the presence of the ethylene-responsive element-binding factor-associated amphiphilic repression motif. ZAT12 protein was found expressed in the root early differentiation zone, where its abundance was modulated in a root layer-specific manner. In the absence of ZAT12, FIT expression was upregulated, suggesting a negative effect of ZAT12 on Fe uptake. Consistently, zat12 loss-of-function mutants had higher Fe content than the wild type at sufficient Fe. We found that under Fe deficiency, hydrogen peroxide (H2O2) levels were enhanced in a FIT-dependent manner. FIT protein, in turn, was stabilized by H2O2 but only in the presence of ZAT12, showing that H2O2 serves as a signal for Fe deficiency responses. We propose that oxidative stress-induced ZAT12 functions as a negative regulator of Fe acquisition. A model where H2O2 mediates the negative regulation of plant responses to prolonged stress might be applicable to a variety of stress conditions. PMID:26556796

  18. Zinc-Finger Transcription Factor ZAT6 Positively Regulates Cadmium Tolerance through the Glutathione-Dependent Pathway in Arabidopsis1[OPEN

    Science.gov (United States)

    Chen, Jian; Yan, Xingxing; Liu, Yunlei; Wang, Ren; Fan, Tingting; Ren, Yongbing; Tang, Xiaofeng; Xiao, Fangming

    2016-01-01

    Cadmium (Cd) is an environmental pollutant with high toxicity to animals and plants. It has been established that the glutathione (GSH)-dependent phytochelatin (PC) synthesis pathway is one of the most important mechanisms contributing to Cd accumulation and tolerance in plants. However, the transcription factors involved in regulating GSH-dependent PC synthesis pathway remain largely unknown. Here, we identified an Arabidopsis (Arabidopsis thaliana) Cd-resistant mutant xcd2-D (XVE system-induced cadmium-tolerance2) using a forward genetics approach. The mutant gene underlying xcd2-D mutation was revealed to encode a known zinc-finger transcription factor, ZAT6. Transgenic plants overexpressing ZAT6 showed significant increase of Cd tolerance, whereas loss of function of ZAT6 led to decreased Cd tolerance. Increased Cd accumulation and tolerance in ZAT6-overexpressing lines was GSH dependent and associated with Cd-activated synthesis of PC, which was correlated with coordinated activation of PC-synthesis related gene expression. By contrast, loss of function of ZAT6 reduced Cd accumulation and tolerance, which was accompanied by abolished PC synthesis and gene expression. Further analysis revealed that ZAT6 positively regulates the transcription of GSH1, GSH2, PCS1, and PCS2, but ZAT6 is capable of specifically binding to GSH1 promoter in vivo. Consistently, overexpression of GSH1 has been shown to restore Cd sensitivity in the zat6-1 mutant, suggesting that GSH1 is a key target of ZAT6. Taken together, our data provide evidence that ZAT6 coordinately activates PC synthesis-related gene expression and directly targets GSH1 to positively regulate Cd accumulation and tolerance in Arabidopsis. PMID:26983992

  19. Studies on Differential Nuclear Translocation Mechanism and Assembly of the Three Subunits of the Arabidopsis thaliana Transcription Factor NF-Y

    Institute of Scientific and Technical Information of China (English)

    Dieter Hackenberg; Yanfang Wu; Andrea Voigt; Robert Adams; Peter Schramm; Bernhard Grimm

    2012-01-01

    The eukaryotic transcription factor NF-Y consists of three subunits(A,B,and C),which are encoded in Arabidopsis thaliana in multigene families consisting of 10,13,and 13 genes,respectively.In principle,all potential combinations of the subunits are possible for the assembly of the heterotrimeric complex.We aimed at assessing the probability of each subunit to participate in the assembly of NF-Y.The evaluation of physical interactions among all members of the NF-Y subunit families indicate a strong requirement for NF-YB/NF-YC heterodimerization before the entire complex can be accomplished.By means of a modified yeast two-hybrid system assembly of all three subunits to a heterotrimeric complex was demonstrated.Using GFP fusion constructs,NF-YA and NF-YC localization in the nucleus was demonstrated,while NFYB is solely imported into the nucleus as a NF-YC-associated heterodimer NF-YC.This piggyback transport of the two Arabidopsis subunits differs from the import of the NF-Y heterotrimer of heterotrophic organisms.Based on a peptide structure model of the histone-fold-motifs,disulfide bonding among intramolecular conserved cysteine residues of NF-YB,which is responsible for the redox-regulated assembly of NF-YB and NF-YC in human and Aspergillus nidulans,can be excluded for Arabidopsis NF-YB.

  20. The bHLH Transcription Factor MYC3 Interacts with the Jasmonate ZIM-Domain Proteins to Mediate Jasmonate Response in Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    Zhiwei Cheng; Li Sun; Tiancong Qi; Bosen Zhang; Wen Peng; Yule Liu; Daoxin Xie

    2011-01-01

    The Arabidopsis Jasmonate ZIM-domain proteins (JAZs) act as substrates of SCFCOI1 complex to repress their downstream targets,which are essential for JA-regulated plant development and defense. The bHLH transcription factor MYC2 was found to interact with JAZs and mediate JA responses including JA-inhibitory root growth. Here,we identified another bHLH transcription factor MYC3 which directly interacted with JAZs by virtue of its N-terminal region to regulate JA responses. The transgenic plants with overexpression of MYC3 exhibited hypersensitivity in JA-inhibitory root elongation and seedling development. The JAZ-interacting pattern and the JA-induced expression pattern of MYC3 were distinguishable from those of MYC2. We speculate that MYC3 and MYC2 may have redundant but also distinguishable functions in regulation of JA responses.

  1. Transcriptional regulation of heat shock proteins and ascorbate peroxidase by CtHsfA2b from African bermudagrass conferring heat tolerance in Arabidopsis

    Science.gov (United States)

    Wang, Xiuyun; Huang, Wanlu; Yang, Zhimin; Liu, Jun; Huang, Bingru

    2016-01-01

    Heat stress transcription factor A2s (HsfA2s) are key regulators in plant response to high temperature. Our objectives were to isolate an HsfA2 gene (CtHsfA2b) from a warm-season grass species, African bermudagrass (Cynodon transvaalensis Burtt-Davy), and to determine the physiological functions and transcriptional regulation of HsfA2 for improving heat tolerance. Gene expression analysis revealed that CtHsfA2b was heat-inducible and exhibited rapid response to increasing temperature. Ectopic expression of CtHsfA2b improved heat tolerance in Arabidopsis and restored heat-sensitive defects of Arabidopsis hsfa2 mutant, which was demonstrated by higher survival rate and photosynthetic parameters, and lower electrolyte leakage in transgenic plants compared to the WT or hsfa2 mutant. CtHsfA2b transgenic plants showed elevated transcriptional regulation of several downstream genes, including those encoding ascorbate peroxidase (AtApx2) and heat shock proteins [AtHsp18.1-CI, AtHsp22.0-ER, AtHsp25.3-P and AtHsp26.5-P(r), AtHsp70b and AtHsp101-3]. CtHsfA2b was found to bind to the heat shock element (HSE) on the promoter of AtApx2 and enhanced transcriptional activity of AtApx2. These results suggested that CtHsfA2b could play positive roles in heat protection by up-regulating antioxidant defense and chaperoning mechanisms. CtHsfA2b has the potential to be used as a candidate gene to genetically modify cool-season species for improving heat tolerance. PMID:27320381

  2. Transcriptional responses to polycyclic aromatic hydrocarbon-induced stress in Arabidopsis thaliana reveal the involvement of hormone and defense signaling pathways

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    Colón-Carmona Adán

    2010-04-01

    Full Text Available Abstract Background Polycyclic aromatic hydrocarbons (PAHs are toxic, widely-distributed, environmentally persistent, and carcinogenic byproducts of carbon-based fuel combustion. Previously, plant studies have shown that PAHs induce oxidative stress, reduce growth, and cause leaf deformation as well as tissue necrosis. To understand the transcriptional changes that occur during these processes, we performed microarray experiments on Arabidopsis thaliana L. under phenanthrene treatment, and compared the results to published Arabidopsis microarray data representing a variety of stress and hormone treatments. In addition, to probe hormonal aspects of PAH stress, we assayed transgenic ethylene-inducible reporter plants as well as ethylene pathway mutants under phenanthrene treatment. Results Microarray results revealed numerous perturbations in signaling and metabolic pathways that regulate reactive oxygen species (ROS and responses related to pathogen defense. A number of glutathione S-transferases that may tag xenobiotics for transport to the vacuole were upregulated. Comparative microarray analyses indicated that the phenanthrene response was closely related to other ROS conditions, including pathogen defense conditions. The ethylene-inducible transgenic reporters were activated by phenanthrene. Mutant experiments showed that PAH inhibits growth through an ethylene-independent pathway, as PAH-treated ethylene-insensitive etr1-4 mutants exhibited a greater growth reduction than WT. Further, phenanthrene-treated, constitutive ethylene signaling mutants had longer roots than the untreated control plants, indicating that the PAH inhibits parts of the ethylene signaling pathway. Conclusions This study identified major physiological systems that participate in the PAH-induced stress response in Arabidopsis. At the transcriptional level, the results identify specific gene targets that will be valuable in finding lead compounds and engineering increased

  3. The Transcription Factor AtDOF4.7 Is Involved in Ethylene- and IDA-Mediated Organ Abscission in Arabidopsis

    Science.gov (United States)

    Wang, Gao-Qi; Wei, Peng-Cheng; Tan, Feng; Yu, Man; Zhang, Xiao-Yan; Chen, Qi-Jun; Wang, Xue-Chen

    2016-01-01

    Organ abscission is an important plant developmental process that occurs in response to environmental stress or pathogens. In Arabidopsis, ligand signals, such as ethylene or INFLORESCENCE DEFICIENT IN ABSCISSION (IDA), can regulate organ abscission. Previously, we reported that overexpression of AtDOF4.7, a transcription factor gene, directly suppresses the expression of the abscission-related gene ARABIDOPSIS DEHISCENCE ZONE POLYGALACTURONASE 2 (ADPG2), resulting in a deficiency of floral organ abscission. However, the relationship between AtDOF4.7 and abscission pathways still needs to be investigated. In this study, we showed that ethylene regulates the expression of AtDOF4.7, and the peptide ligand, IDA negatively regulates AtDOF4.7 at the transcriptional level. Genetic evidence indicates that AtDOF4.7 and IDA are involved in a common pathway, and a MAPK cascade can phosphorylate AtDOF4.7 in vitro. Further in vivo data suggest that AtDOF4.7 protein levels may be regulated by this phosphorylation. Collectively, our results indicate that ethylene regulates AtDOF4.7 that is involved in the IDA-mediated floral organ abscission pathway. PMID:27379143

  4. 拟南芥B3转录因子基因超家族%Research progress of Arabidopsis B3 transcription factor gene superfamily

    Institute of Scientific and Technical Information of China (English)

    罗光宇; 叶玲飞; 陈信波

    2013-01-01

    B3类转录因子基因组成了植物所特有的B3基因超家族,按照其结构和功能的特征可将其进一步分为LAV(LEAFY COTYLEDON2 [LEC2]-ABSCISIC ACID INSENSITIVE3 [ABI3]-VAL)、RF(AUXINRESPONSE FACTOR)、RAV(RELATED TO ABI3 and VPl)和REM(REPRODUCTIVE MERISTEM)等4个家族.B3基因超家族主要存在于裸子植物、苔藓和绿藻类植物中,并在植物逆境胁迫响应和生长发育过程中起着极其重要的作用.目前已在拟南芥中发现了118个B3类转录因子,本文综述了拟南芥中B3转录因子基因超家族的系统发育和功能鉴定方面的研究进展.%The B3 transcription factor genes form a plant-specific B3 gene superfamily and can be further classified into four families:LAV (LEAFY COTYLEDON2 [LEC2]-ABSCISIC ACID INSENSITIVE3 [ABI3]-VAL),ARF (AUXIN RESPONSE FACTOR),RAV (RELATED TO ABI3 and VP1) and REM (REPRODUCTIVE MERISTEM) family.The B3 transcription factor genes exist mainly in gymnosperms,mosses and green algae and play extremely important roles in plant stress responses and plant growth and development.In Arabidopsis,118 B3 superfamily transcription factor genes have been identified.This review aims to overview the research progress of the phylogenetical and functional characterization of the B3 gene superfamily in Arabidopsis.

  5. The Clock Protein CCA1 and the bZIP Transcription Factor HY5 Physically Interact to Regulate Gene Expression in Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    Christos Andronis; Simon Barak; Stephen M.Knowles; Shoji Sugano; Elaine M.Tobin

    2008-01-01

    The circadian clock regulates the expression of an array of Arabidopsis genes such as those encoding the LIGHT-HARVESTING CHLOROPHYLL A/B (Lhcb) proteins. We have previously studied the promoters of two of these Arabidopsis genes-Lhcb1*1 and Lhcb1*3-and identified a sequence that binds the clock protein CIRCADIAN CLOCK ASSOCIATED 1 (CCA1). This sequence, designated CCAl-binding site (CBS), is necessary for phytochrome and circadian responsiveness of these genes. In close proximity to this sequence, there exists a G-box core element that has been shown to bind the bZIP transcription factor HY5 in other light-regulated plant promoters. In the present study, we examined the importance of the interaction of transcription factors binding the CBS and the G-box core element in the control of normal circadian rhythmic expression of Lhcb genes. Our results show that HY5 is able to specifically bind the G-box element in the Lhcb promoters and that CCA1 can alter the binding activity of HY5. We further show that CCA1 and HY5 can physically interact and that they can act synergistically on transcription in a yeast reporter gene assay. An absence of HY5 leads to a shorter period of Lhcb1*1 circadian expression but does not affect the circadian expression of CATALASE3 (CAT3), whose promoter lacks a G-box element. Our results suggest that interaction of the HY5 and CCA1 proteins on Lhcb promoters is necessary for normal circadian expression of the Lhcb genes.

  6. Transcriptional and metabolic signatures of Arabidopsis responses to chewing damage by an insect herbivore and bacterial infection and the consequences of their interaction

    Directory of Open Access Journals (Sweden)

    Heidi M Appel

    2014-09-01

    Full Text Available Plants use multiple interacting signaling systems to identify and respond to biotic stresses. Although it is often assumed that there is specificity in signaling responses to specific pests, this is rarely examined outside of the gene-for-gene relationships of plant-pathogen interactions. In this study, we first compared early events in gene expression and later events in metabolite profiles of Arabidopsis thaliana following attack by either the caterpillar Spodoptera exigua or avirulent (DC3000 avrRpm1 Pseudomonas syringae pv. tomato at three time points. Transcriptional responses of the plant to caterpillar feeding were rapid, occurring within 1 h of feeding, and then decreased at 6 h and 24 h. In contrast, plant response to the pathogen was undetectable at 1 h but grew larger and more significant at 6 h and 24 h. There was a surprisingly large amount of overlap in jasmonate and salicylate signaling in responses to the insect and pathogen, including levels of gene expression and individual hormones. The caterpillar and pathogen treatments induced different patterns of expression of glucosinolate biosynthesis genes and levels of glucosinolates. This suggests that when specific responses develop, their regulation is complex and best understood by characterizing expression of many genes and metabolites. We then examined the effect of feeding by the caterpillar Spodoptera exigua on Arabidopsis susceptibility to virulent (DC3000 and avirulent (DC3000 avrRpm1 P. syringae pv. tomato, and found that caterpillar feeding enhanced Arabidopsis resistance to the avirulent pathogen and lowered resistance to the virulent strain. We conclude that efforts to improve plant resistance to bacterial pathogens are likely to influence resistance to insects and vice versa. Studies explicitly comparing plant responses to multiple stresses, including the role of elicitors at early time points, are critical to understanding how plants organize responses in natural

  7. The Development of Protein Microarrays and Their Applications in DNA-Protein and Protein-Protein Interaction Analyses of Arabidopsis Transcription Factors

    Institute of Scientific and Technical Information of China (English)

    Wei Gong; Kun He; Mike Covington; S.R Dinesh-Kumar; Michael Snyder; Stacey L.Harmer; Yu-Xian Zhu; Xing Wang Deng

    2008-01-01

    We used our collection of Arabidopsis transcription factor (TF) ORFeome clones to constructprotein microarrays containing as many as 802 TF proteins. These protein microarrays were used for both protein-DNA and proteinprotein interaction analyses. For protein-DNA interaction studies, we examined AP2/ERF family TFs and their cognate cis-elements. By careful comparison of the DNA-binding specificity of 13 TFs on the protein microarray with previous non-microarray data, we showed that protein microarrays provide an efficient and high throughput tool for genome-wide analysis of TF-DNA interactions. This microarray protein-DNA interaction analysis allowed us to derive a comprehensive view of DNA-binding profiles of AP2/ERF family proteins in Arabidopsis. It also revealed four TFs that bound the EE (evening element) and had the expected phased gene expression under clock-regulation, thus providing a basis for further functional analysis of their roles in clock regulation of gene expression. We also developed procedures for detecting protein interactions using this TF protein microarray and discovered four novel partners that interact with HY5, which can be validated by yeast two-hybrid assays. Thus, plant TF protein microarrays offer an attractive high-throughput alternative to traditional techniques for TF functional characterization on a global scale.

  8. A R2R3-MYB transcription factor from Lablab purpureus induced by drought increases tolerance to abiotic stress in Arabidopsis.

    Science.gov (United States)

    Yao, Luming; Jiang, Yina; Lu, Xinxin; Wang, Biao; Zhou, Pei; Wu, Tianlong

    2016-10-01

    Few regulators for drought tolerance have been identified in Lablab purpureus which is a multipurpose leguminous crop. The transcription factor MYB is involved in regulatory networks in response to abiotic and biotic stresses in plants. A novel R2R3-MYB factor in L. purpureus has been identified. An suppression subtraction hybridization (SSH) library was constructed using root tissues of L. purpureus MEIDOU 2012 from well-watered and water-stress treatments that were subjected to drought stress for 10 days. In addition, the cDNA of LpMYB1 was identified based on the SSH library. The cDNA of LpMYB1 is 858 bp and encodes a 285-amino acid protein with a calculated mass of 33.4 kDa. The LpMYB1 protein localizes to the nucleus and has transactivation activity with the activation domain in the C terminal region of the protein. In LpMYB1 overexpressed Arabidopsis, the tolerance of transgenic seedlings to drought and salt was improved, and the germination potential of transgenic seeds increase in the presence of NaCl or ABA. LpMYB1 is a drought-responsive R2R3-MYB factor that can increase the drought and salt tolerance of LpMYB1-overexpressed Arabidopsis. PMID:27565983

  9. The beet cyst nematode Heterodera schachtii modulates the expression of WRKY transcription factors in syncytia to favour its development in Arabidopsis roots.

    Science.gov (United States)

    Ali, Muhammad Amjad; Wieczorek, Krzysztof; Kreil, David P; Bohlmann, Holger

    2014-01-01

    Cyst nematodes invade the roots of their host plants as second stage juveniles and induce a syncytium which is the only source of nutrients throughout their life. A recent transcriptome analysis of syncytia induced by the beet cyst nematode Heterodera schachtii in Arabidopsis roots has shown that thousands of genes are up-regulated or down-regulated in syncytia as compared to root segments from uninfected plants. Among the down-regulated genes are many which code for WRKY transcription factors. Arabidopsis contains 66 WRKY genes with 59 represented by the ATH1 GeneChip. Of these, 28 were significantly down-regulated and 6 up-regulated in syncytia as compared to control root segments. We have studied here the down-regulated genes WRKY6, WRKY11, WRKY17 and WRKY33 in detail. We confirmed the down-regulation in syncytia with promoter::GUS lines. Using various overexpression lines and mutants it was shown that the down-regulation of these WRKY genes is important for nematode development, probably through interfering with plant defense reactions. In case of WRKY33, this might involve the production of the phytoalexin camalexin.

  10. The beet cyst nematode Heterodera schachtii modulates the expression of WRKY transcription factors in syncytia to favour its development in Arabidopsis roots.

    Directory of Open Access Journals (Sweden)

    Muhammad Amjad Ali

    Full Text Available Cyst nematodes invade the roots of their host plants as second stage juveniles and induce a syncytium which is the only source of nutrients throughout their life. A recent transcriptome analysis of syncytia induced by the beet cyst nematode Heterodera schachtii in Arabidopsis roots has shown that thousands of genes are up-regulated or down-regulated in syncytia as compared to root segments from uninfected plants. Among the down-regulated genes are many which code for WRKY transcription factors. Arabidopsis contains 66 WRKY genes with 59 represented by the ATH1 GeneChip. Of these, 28 were significantly down-regulated and 6 up-regulated in syncytia as compared to control root segments. We have studied here the down-regulated genes WRKY6, WRKY11, WRKY17 and WRKY33 in detail. We confirmed the down-regulation in syncytia with promoter::GUS lines. Using various overexpression lines and mutants it was shown that the down-regulation of these WRKY genes is important for nematode development, probably through interfering with plant defense reactions. In case of WRKY33, this might involve the production of the phytoalexin camalexin.

  11. A seed preferential heat shock transcription factor from wheat provides abiotic stress tolerance and yield enhancement in transgenic Arabidopsis under heat stress environment.

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    Harsh Chauhan

    Full Text Available Reduction in crop yield and quality due to various abiotic stresses is a worldwide phenomenon. In the present investigation, a heat shock factor (HSF gene expressing preferentially in developing seed tissues of wheat grown under high temperatures was cloned. This newly identified heat shock factor possesses the characteristic domains of class A type plant HSFs and shows high similarity to rice OsHsfA2d, hence named as TaHsfA2d. The transcription factor activity of TaHsfA2d was confirmed through transactivation assay in yeast. Transgenic Arabidopsis plants overexpressing TaHsfA2d not only possess higher tolerance towards high temperature but also showed considerable tolerance to salinity and drought stresses, they also showed higher yield and biomass accumulation under constant heat stress conditions. Analysis of putative target genes of AtHSFA2 through quantitative RT-PCR showed higher and constitutive expression of several abiotic stress responsive genes in transgenic Arabidopsis plants over-expressing TaHsfA2d. Under stress conditions, TaHsfA2d can also functionally complement the T-DNA insertion mutants of AtHsfA2, although partially. These observations suggest that TaHsfA2d may be useful in molecular breeding of crop plants, especially wheat, to improve yield under abiotic stress conditions.

  12. The Arabidopsis MYB96 Transcription Factor Is a Positive Regulator of ABSCISIC ACID-INSENSITIVE4 in the Control of Seed Germination.

    Science.gov (United States)

    Lee, Kyounghee; Lee, Hong Gil; Yoon, Seongmun; Kim, Hyun Uk; Seo, Pil Joon

    2015-06-01

    Seed germination is a key developmental transition that initiates the plant life cycle. The timing of germination is determined by the coordinated action of two phytohormones, gibberellin and abscisic acid (ABA). In particular, ABA plays a key role in integrating environmental information and inhibiting the germination process. The utilization of embryonic lipid reserves contributes to seed germination by acting as an energy source, and ABA suppresses lipid degradation to modulate the germination process. Here, we report that the ABA-responsive R2R3-type MYB transcription factor MYB96, which is highly expressed in embryo, regulates seed germination by controlling the expression of abscisic acid-insensitive4 (ABI4) in Arabidopsis (Arabidopsis thaliana). In the presence of ABA, germination was accelerated in MYB96-deficient myb96-1 seeds, whereas the process was significantly delayed in MYB96-overexpressing activation-tagging myb96-ox seeds. Consistently, myb96-1 seeds degraded a larger extent of lipid reserves even in the presence of ABA, while reduced lipid mobilization was observed in myb96-ox seeds. MYB96 directly regulates ABI4, which acts as a repressor of lipid breakdown, to define its spatial and temporal expression. Genetic analysis further demonstrated that ABI4 is epistatic to MYB96 in the control of seed germination. Taken together, the MYB96-ABI4 module regulates lipid mobilization specifically in the embryo to ensure proper seed germination under suboptimal conditions.

  13. CFLAP1 and CFLAP2 Are Two bHLH Transcription Factors Participating in Synergistic Regulation of AtCFL1-Mediated Cuticle Development in Arabidopsis.

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    Shibai Li

    2016-01-01

    Full Text Available The cuticle is a hydrophobic lipid layer covering the epidermal cells of terrestrial plants. Although many genes involved in Arabidopsis cuticle development have been identified, the transcriptional regulation of these genes is largely unknown. Previously, we demonstrated that AtCFL1 negatively regulates cuticle development by interacting with the HD-ZIP IV transcription factor HDG1. Here, we report that two bHLH transcription factors, AtCFL1 associated protein 1 (CFLAP1 and CFLAP2, are also involved in AtCFL1-mediated regulation of cuticle development. CFLAP1 and CFLAP2 interact with AtCFL1 both in vitro and in vivo. Overexpression of either CFLAP1 or CFLAP2 led to expressional changes of genes involved in fatty acids, cutin and wax biosynthesis pathways and caused multiple cuticle defective phenotypes such as organ fusion, breakage of the cuticle layer and decreased epicuticular wax crystal loading. Functional inactivation of CFLAP1 and CFLAP2 by chimeric repression technology caused opposite phenotypes to the CFLAP1 overexpressor plants. Interestingly, we find that, similar to the transcription factor HDG1, the function of CFLAP1 in cuticle development is dependent on the presence of AtCFL1. Furthermore, both HDG1 and CFLAP1/2 interact with the same C-terminal C4 zinc finger domain of AtCFL1, a domain that is essential for AtCFL1 function. These results suggest that AtCFL1 may serve as a master regulator in the transcriptional regulation of cuticle development, and that CFLAP1 and CFLAP2 are involved in the AtCFL1-mediated regulation pathway, probably through competing with HDG1 to bind to AtCFL1.

  14. A Dual-Function Transcription Factor, AtYY1, Is a Novel Negative Regulator of the Arabidopsis ABA Response Network.

    Science.gov (United States)

    Li, Tian; Wu, Xiu-Yun; Li, Hui; Song, Jian-Hui; Liu, Jin-Yuan

    2016-05-01

    Abscisic acid (ABA) plays crucial roles in plant growth and development, as well as in response to various environmental stresses. To date, many regulatory genes involved in the ABA response network have been identified; however, their roles have remained to be fully elucidated. In this study, we identified AtYY1, an Arabidopsis homolog of the mammalian C2H2 zinc-finger transcription factor Yin Yang 1 (YY1), as a novel negative regulator of the ABA response. AtYY1 is a dual-function transcription factor with both repression and activation domains. The expression of AtYY1 was induced by ABA and stress conditions including high salt and dehydration. The yy1 mutant was more sensitive to ABA and NaCl than the wild-type, while overexpressing AtYY1 plants were less sensitive. AtYY1 loss also enhanced ABA-induced stomatal closing and drought resistance. Moreover, AtYY1 can bind the ABA REPRESSOR1 (ABR1) promoter and directly upregulate ABR1 expression, as well as negatively regulate ABA- and salt-responsive gene expression. Additional analysis indicated that ABA INSENSITIVE4 (ABI4) might positively regulate AtYY1 expression and that ABR1 can antagonize this regulation. Our findings provide direct evidence that AtYY1 is a novel negative regulator of the ABA response network and that the ABI4-AtYY1-ABR1 regulatory pathway may fine-tune ABA-responsive gene expression in Arabidopsis. PMID:26961720

  15. STOP2 Activates Transcription of Several Genesfor AI- and Low pH-Tolerance that Are Regulatedby STOP1 in Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    2014-01-01

    The zinc-finger protein STOP1 (sensitive to proton rhizotoxicity 1) regulates transcription of multiple genescritical for tolerance to aluminum (AI) and low pH in Arabidopsis. We evaluated the contributions of genes that are sup-pressed in the stop1 mutant to AI- and low pH-tolerance using T-DNA-inserted disruptants, and transgenic stop1 mutantsexpressing each of the suppressed genes. STOP2, a STOP1 homolog, partially recovered AI- and low pH-tolerance byrecovering the expression of genes regulated by STOP1. Growth and root tip viability under proton stress were partiallyrescued in the STOP2-complemented line. STOP2 localized in the nucleus and regulated transcription of two genes (PGIP1and PGIP2) associated with cell wall stabilization at low pH. GUS assays revealed that STOP1 and STOP2 showed similarcellular expression in the root. However, the expression level of STOP2 was much lower than that of STOP1. In a STOP1promoter::STOP2-complemented line, AI tolerance was slightly recovered, concomitant with the recovery of expressionof ALS3 (aluminum sensitive 3) and AtMATE (Arabidopsis thaliana multidrug and toxic compound extrusion), while theexpression of AtALMT1 (aluminum-activated malate transporter 1) was not recovered. These analyses indicated thatSTOP2 is a physiologically minor isoform of STOP1, but it can activate expression of some genes regulated by STOP1.

  16. Positive- and negative-acting regulatory elements contribute to the tissue-specific expression of INNER NO OUTER, a YABBY-type transcription factor gene in Arabidopsis

    Directory of Open Access Journals (Sweden)

    Simon Marissa K

    2012-11-01

    Full Text Available Abstract Background The INNER NO OUTER (INO gene, which encodes a YABBY-type transcription factor, specifies and promotes the growth of the outer integument of the ovule in Arabidopsis. INO expression is limited to the abaxial cell layer of the developing outer integument of the ovule and is regulated by multiple regions of the INO promoter, including POS9, a positive element that when present in quadruplicate can produce low-level expression in the normal INO pattern. Results Significant redundancy in activity between different regions of the INO promoter is demonstrated. For specific regulatory elements, multimerization or the addition of the cauliflower mosaic virus 35S general enhancer was able to activate expression of reporter gene constructs that were otherwise incapable of expression on their own. A new promoter element, POS6, is defined and is shown to include sufficient positive regulatory information to reproduce the endogenous pattern of expression in ovules, but other promoter regions are necessary to fully suppress expression outside of ovules. The full-length INO promoter, but not any of the INO promoter deletions tested, is able to act as an enhancer-blocking insulator to prevent the ectopic activation of expression by the 35S enhancer. Sequence conservation between the promoter regions of Arabidopsis thaliana, Brassica oleracea and Brassica rapa aligns closely with the functional definition of the POS6 and POS9 regions, and with a defined INO minimal promoter. The B. oleracea INO promoter is sufficient to promote a similar pattern and level of reporter gene expression in Arabidopsis to that observed for the Arabidopsis promoter. Conclusions At least two independent regions of the INO promoter contain sufficient regulatory information to direct the specific pattern but not the level of INO gene expression. These regulatory regions act in a partially redundant manner to promote the expression in a specific pattern in the ovule and

  17. Antagonistic regulation of growth and immunity by the Arabidopsis basic helix-loop-helix transcription factor homolog of brassinosteroid enhanced expression2 interacting with increased leaf inclination1 binding bHLH1

    DEFF Research Database (Denmark)

    Malinovsky, Frederikke Gro; Batoux, Martine; Schwessinger, Benjamin;

    2014-01-01

    mechanisms is needed. Here, we identify the basic helix-loop-helix (bHLH) transcription factor homolog of brassinosteroid enhanced expression2 interacting with IBH1 (HBI1) as a negative regulator of PTI signaling in Arabidopsis (Arabidopsis thaliana). HBI1 expression is down-regulated in response...... to different PAMPs. HBI1 overexpression leads to reduced PAMP-triggered responses. This inhibition correlates with reduced steady-state expression of immune marker genes, leading to increased susceptibility to the bacterium Pseudomonas syringae. Overexpression of the HBI1-related bHLHs brassinosteroid enhanced...

  18. A DNA-binding-site landscape and regulatory network analysis for NAC transcription factors in Arabidopsis thaliana

    DEFF Research Database (Denmark)

    Lindemose, Søren; Jensen, Michael Krogh; de Velde, Jan Van;

    2014-01-01

    Target gene identification for transcription factors is a prerequisite for the systems wide understanding of organismal behaviour. NAM-ATAF1/2-CUC2 (NAC) transcription factors are amongst the largest transcription factor families in plants, yet limited data exist from unbiased approaches to resolve...... regulatory networks of 12 NAC transcription factors. Our data offer specific single-base resolution fingerprints for most TFs studied and indicate that NAC DNA-binding specificities might be predicted from their DNA-binding domain's sequence. The developed methodology, including the application...... with the workflow associated with functional modules offer a strong resource to unravel the regulatory potential of NAC genes and that this workflow could be used to study other families of transcription factors....

  19. The WRKY6 transcription factor modulates PHOSPHATE1 expression in response to low Pi stress in Arabidopsis.

    Science.gov (United States)

    Chen, Yi-Fang; Li, Li-Qin; Xu, Qian; Kong, You-Han; Wang, Hui; Wu, Wei-Hua

    2009-11-01

    Arabidopsis thaliana WRKY family comprises 74 members and some of them are involved in plant responses to biotic and abiotic stresses. This study demonstrated that WRKY6 is involved in Arabidopsis responses to low-Pi stress through regulating PHOSPHATE1 (PHO1) expression. WRKY6 overexpression lines, similar to the pho1 mutant, were more sensitive to low Pi stress and had lower Pi contents in shoots compared with wild-type seedlings and the wrky6-1 mutant. Immunoprecipitation assays demonstrated that WRKY6 can bind to two W-boxes of the PHO1 promoter. RNA gel blot and beta-glucuronidase activity assays showed that PHO1 expression was repressed in WRKY6-overexpressing lines and enhanced in the wrky6-1 mutant. Low Pi treatment reduced WRKY6 binding to the PHO1 promoter, which indicates that PHO1 regulation by WRKY6 is Pi dependent and that low Pi treatment may release inhibition of PHO1 expression. Protein gel blot analysis showed that the decrease in WRKY6 protein induced by low Pi treatment was inhibited by a 26S proteosome inhibitor, MG132, suggesting that low Pi-induced release of PHO1 repression may result from 26S proteosome-mediated proteolysis. In addition, WRKY42 also showed binding to W-boxes of the PHO1 promoter and repressed PHO1 expression. Our results demonstrate that WRKY6 and WRKY42 are involved in Arabidopsis responses to low Pi stress by regulation of PHO1 expression.

  20. Arabidopsis Type II Phosphatidylinositol 4-Kinase PI4Kγ5 Regulates Auxin Biosynthesis and Leaf Margin Development through Interacting with Membrane-Bound Transcription Factor ANAC078.

    Science.gov (United States)

    Tang, Yong; Zhao, Chun-Yan; Tan, Shu-Tang; Xue, Hong-Wei

    2016-08-01

    Normal leaf margin development is important for leaf morphogenesis and contributes to diverse leaf shapes in higher plants. We here show the crucial roles of an atypical type II phosphatidylinositol 4-kinase, PI4Kγ5, in Arabidopsis leaf margin development. PI4Kγ5 presents a dynamics expression pattern along with leaf development and a T-DNA mutant lacking PI4Kγ5, pi4kγ5-1, presents serrated leaves, which is resulted from the accelerated cell division and increased auxin concentration at serration tips. Studies revealed that PI4Kγ5 interacts with and phosphorylates a membrane-bound NAC transcription factor, ANAC078. Previous studies demonstrated that membrane-bound transcription factors regulate gene transcription by undergoing proteolytic process to translocate into nucleus, and ANAC078 undergoes proteolysis by cleaving off the transmembrane region and carboxyl terminal. Western blot analysis indeed showed that ANAC078 deleting of carboxyl terminal is significantly reduced in pi4kγ5-1, indicating that PI4Kγ5 is important for the cleavage of ANAC078. This is consistent with the subcellular localization observation showing that fluorescence by GFP-ANAC078 is detected at plasma membrane but not nucleus in pi4kγ5-1 mutant and that expression of ANAC078 deleting of carboxyl terminal, driven by PI4Kγ5 promoter, could rescue the leaf serration defects of pi4kγ5-1. Further analysis showed that ANAC078 suppresses the auxin synthesis by directly binding and regulating the expression of auxin synthesis-related genes. These results indicate that PI4Kγ5 interacts with ANAC078 to negatively regulate auxin synthesis and hence influences cell proliferation and leaf development, providing informative clues for the regulation of in situ auxin synthesis and cell division, as well as the cleavage and functional mechanism of membrane-bound transcription factors. PMID:27529511

  1. Redundant ERF-VII Transcription Factors Bind to an Evolutionarily Conserved cis-Motif to Regulate Hypoxia-Responsive Gene Expression in Arabidopsis.

    Science.gov (United States)

    Gasch, Philipp; Fundinger, Moritz; Müller, Jana T; Lee, Travis; Bailey-Serres, Julia; Mustroph, Angelika

    2016-01-01

    The response of Arabidopsis thaliana to low-oxygen stress (hypoxia), such as during shoot submergence or root waterlogging, includes increasing the levels of ∼50 hypoxia-responsive gene transcripts, many of which encode enzymes associated with anaerobic metabolism. Upregulation of over half of these mRNAs involves stabilization of five group VII ethylene response factor (ERF-VII) transcription factors, which are routinely degraded via the N-end rule pathway of proteolysis in an oxygen- and nitric oxide-dependent manner. Despite their importance, neither the quantitative contribution of individual ERF-VIIs nor the cis-regulatory elements they govern are well understood. Here, using single- and double-null mutants, the constitutively synthesized ERF-VIIs RELATED TO APETALA2.2 (RAP2.2) and RAP2.12 are shown to act redundantly as principle activators of hypoxia-responsive genes; constitutively expressed RAP2.3 contributes to this redundancy, whereas the hypoxia-induced HYPOXIA RESPONSIVE ERF1 (HRE1) and HRE2 play minor roles. An evolutionarily conserved 12-bp cis-regulatory motif that binds to and is sufficient for activation by RAP2.2 and RAP2.12 is identified through a comparative phylogenetic motif search, promoter dissection, yeast one-hybrid assays, and chromatin immunopurification. This motif, designated the hypoxia-responsive promoter element, is enriched in promoters of hypoxia-responsive genes in multiple species. PMID:26668304

  2. Effects of molybdenum deficiency and defects in molybdate transporter MOT1 on transcript accumulation and nitrogen/sulphur metabolism in Arabidopsis thaliana.

    Science.gov (United States)

    Ide, Yoko; Kusano, Miyako; Oikawa, Akira; Fukushima, Atsushi; Tomatsu, Hajime; Saito, Kazuki; Hirai, Masami Yokota; Fujiwara, Toru

    2011-02-01

    Molybdenum (Mo) is a micronutrient essential for plant growth, as several key enzymes of plant metabolic pathways contain Mo cofactor in their catalytic centres. Mo-containing oxidoreductases include nitrate reductase, sulphite oxidase, xanthine dehydrogenase, and aldehyde oxidase. These are involved in nitrate assimilation, sulphite detoxification, purine metabolism or the synthesis of abscisic acid, auxin and glucosinolates in plants. To understand the effects of Mo deficiency and a mutation in a molybdate transporter, MOT1, on nitrogen and sulphur metabolism in Arabidopsis thaliana, transcript and metabolite profiling of the mutant lacking MOT1 was conducted in the presence or absence of Mo. Transcriptome analysis revealed that Mo deficiency had impacts on genes involved in metabolisms, transport, stress responses, and signal transductions. The transcript level of a nitrate reductase NR1 was highly induced under Mo deficiency in mot1-1. The metabolite profiles were analysed further by using gas chromatography time-of-flight mass spectrometry, capillary electrophoresis time-of-flight mass spectrometry, and ultra high performance liquid chromatography. The levels of amino acids, sugars, organic acids, and purine metabolites were altered significantly in the Mo-deficient plants. These results are the first investigation of the global effect of Mo nutrition and MOT1 on plant gene expressions and metabolism. PMID:21131548

  3. The BEACH Domain Protein SPIRRIG Is Essential for Arabidopsis Salt Stress Tolerance and Functions as a Regulator of Transcript Stabilization and Localization.

    Directory of Open Access Journals (Sweden)

    Alexandra Steffens

    2015-07-01

    Full Text Available Members of the highly conserved class of BEACH domain containing proteins (BDCPs have been established as broad facilitators of protein-protein interactions and membrane dynamics in the context of human diseases like albinism, bleeding diathesis, impaired cellular immunity, cancer predisposition, and neurological dysfunctions. Also, the Arabidopsis thaliana BDCP SPIRRIG (SPI is important for membrane integrity, as spi mutants exhibit split vacuoles. In this work, we report a novel molecular function of the BDCP SPI in ribonucleoprotein particle formation. We show that SPI interacts with the P-body core component DECAPPING PROTEIN 1 (DCP1, associates to mRNA processing bodies (P-bodies, and regulates their assembly upon salt stress. The finding that spi mutants exhibit salt hypersensitivity suggests that the local function of SPI at P-bodies is of biological relevance. Transcriptome-wide analysis revealed qualitative differences in the salt stress-regulated transcriptional response of Col-0 and spi. We show that SPI regulates the salt stress-dependent post-transcriptional stabilization, cytoplasmic agglomeration, and localization to P-bodies of a subset of salt stress-regulated mRNAs. Finally, we show that the PH-BEACH domains of SPI and its human homolog FAN (Factor Associated with Neutral sphingomyelinase activation interact with DCP1 isoforms from plants, mammals, and yeast, suggesting the evolutionary conservation of an association of BDCPs and P-bodies.

  4. Dual-level regulation of ACC synthase activity by MPK3/MPK6 cascade and its downstream WRKY transcription factor during ethylene induction in Arabidopsis.

    Science.gov (United States)

    Li, Guojing; Meng, Xiangzong; Wang, Ruigang; Mao, Guohong; Han, Ling; Liu, Yidong; Zhang, Shuqun

    2012-06-01

    Plants under pathogen attack produce high levels of ethylene, which plays important roles in plant immunity. Previously, we reported the involvement of ACS2 and ACS6, two Type I ACS isoforms, in Botrytis cinerea-induced ethylene biosynthesis and their regulation at the protein stability level by MPK3 and MPK6, two Arabidopsis pathogen-responsive mitogen-activated protein kinases (MAPKs). The residual ethylene induction in the acs2/acs6 double mutant suggests the involvement of additional ACS isoforms. It is also known that a subset of ACS genes, including ACS6, is transcriptionally induced in plants under stress or pathogen attack. However, the importance of ACS gene activation and the regulatory mechanism(s) are not clear. In this report, we demonstrate using genetic analysis that ACS7 and ACS11, two Type III ACS isoforms, and ACS8, a Type II ACS isoform, also contribute to the B. cinerea-induced ethylene production. In addition to post-translational regulation, transcriptional activation of the ACS genes also plays a critical role in sustaining high levels of ethylene induction. Interestingly, MPK3 and MPK6 not only control the stability of ACS2 and ACS6 proteins via direct protein phosphorylation but also regulate the expression of ACS2 and ACS6 genes. WRKY33, another MPK3/MPK6 substrate, is involved in the MPK3/MPK6-induced ACS2/ACS6 gene expression based on genetic analyses. Furthermore, chromatin-immunoprecipitation assay reveals the direct binding of WRKY33 to the W-boxes in the promoters of ACS2 and ACS6 genes in vivo, suggesting that WRKY33 is directly involved in the activation of ACS2 and ACS6 expression downstream of MPK3/MPK6 cascade in response to pathogen invasion. Regulation of ACS activity by MPK3/MPK6 at both transcriptional and protein stability levels plays a key role in determining the kinetics and magnitude of ethylene induction.

  5. Transcription of DWARF4 plays a crucial role in auxin-regulated root elongation in addition to brassinosteroid homeostasis in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Yuya Yoshimitsu

    Full Text Available The expression of DWARF4 (DWF4, which encodes a C-22 hydroxylase, is crucial for brassinosteroid (BR biosynthesis and for the feedback control of endogenous BR levels. To advance our knowledge of BRs, we examined the effects of different plant hormones on DWF4 transcription in Arabidopsis thaliana. Semi-quantitative reverse-transcriptase PCR showed that the amount of the DWF4 mRNA precursor either decreased or increased, similarly with its mature form, in response to an exogenously applied bioactive BR, brassinolide (BL, and a BR biosynthesis inhibitor, brassinazole (Brz, respectively. The response to these chemicals in the levels of β-glucuronidase (GUS mRNA and its enzymatic activity is similar to the response of native DWF4 mRNA in DWF4::GUS plants. Contrary to the effects of BL, exogenous auxin induced GUS activity, but this enhancement was suppressed by anti-auxins, such as α-(phenylethyl-2-one-IAA and α-tert-butoxycarbonylaminohexyl-IAA, suggesting the involvement of SCF(TIR1-mediated auxin signaling in auxin-induced DWF4 transcription. Auxin-enhanced GUS activity was observed exclusively in roots; it was the most prominent in the elongation zones of both primary and lateral roots. Furthermore, auxin-induced lateral root elongation was suppressed by both Brz application and the dwf4 mutation, and this suppression was rescued by BL, suggesting that BRs act positively on root elongation under the control of auxin. Altogether, our results indicate that DWF4 transcription plays a novel role in the BR-auxin crosstalk associated with root elongation, in addition to its role in BR homeostasis.

  6. The bacterial effector HopX1 targets JAZ transcriptional repressors to activate jasmonate signaling and promote infection in Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Selena Gimenez-Ibanez

    2014-02-01

    Full Text Available Pathogenicity of Pseudomonas syringae is dependent on a type III secretion system, which secretes a suite of virulence effector proteins into the host cytoplasm, and the production of a number of toxins such as coronatine (COR, which is a mimic of the plant hormone jasmonate-isoleuce (JA-Ile. Inside the plant cell, effectors target host molecules to subvert the host cell physiology and disrupt defenses. However, despite the fact that elucidating effector action is essential to understanding bacterial pathogenesis, the molecular function and host targets of the vast majority of effectors remain largely unknown. Here, we found that effector HopX1 from Pseudomonas syringae pv. tabaci (Pta 11528, a strain that does not produce COR, interacts with and promotes the degradation of JAZ proteins, a key family of JA-repressors. We show that hopX1 encodes a cysteine protease, activity that is required for degradation of JAZs by HopX1. HopX1 associates with JAZ proteins through its central ZIM domain and degradation occurs in a COI1-independent manner. Moreover, ectopic expression of HopX1 in Arabidopsis induces the expression of JA-dependent genes, represses salicylic acid (SA-induced markers, and complements the growth of a COR-deficient P. syringae pv. tomato (Pto DC3000 strain during natural bacterial infections. Furthermore, HopX1 promoted susceptibility when delivered by the natural type III secretion system, to a similar extent as the addition of COR, and this effect was dependent on its catalytic activity. Altogether, our results indicate that JAZ proteins are direct targets of bacterial effectors to promote activation of JA-induced defenses and susceptibility in Arabidopsis. HopX1 illustrates a paradigm of an alternative evolutionary solution to COR with similar physiological outcome.

  7. AthaMap web tools for the analysis of transcriptional and posttranscriptional regulation of gene expression in Arabidopsis thaliana.

    Science.gov (United States)

    Hehl, Reinhard; Bülow, Lorenz

    2014-01-01

    The AthaMap database provides a map of verified and predicted transcription factor (TF) and small RNA-binding sites for the A. thaliana genome. The database can be used for bioinformatic predictions of putative regulatory sites. Several online web tools are available that address specific questions. Starting with the identification of transcription factor-binding sites (TFBS) in any gene of interest, colocalizing TFBS can be identified as well as common TFBS in a set of user-provided genes. Furthermore, genes can be identified that are potentially targeted by specific transcription factors or small inhibitory RNAs. This chapter provides detailed information on how each AthaMap web tool can be used online. Examples on how this database is used to address questions in circadian and diurnal regulation are given. Furthermore, complementary databases and databases that go beyond questions addressed with AthaMap are discussed. PMID:24792049

  8. The Arabidopsis thaliana NAC transcription factor family: structure-function relationships and determinants of ANAC019 stress signalling

    DEFF Research Database (Denmark)

    Jensen, Michael K; Kjaersgaard, Trine; Nielsen, Michael M.;

    2010-01-01

    TFs (transcription factors) are modular proteins minimally containing a DBD (DNA-binding domain) and a TRD (transcription regulatory domain). NAC [for NAM (no apical meristem), ATAF, CUC (cup-shaped cotyledon)] proteins comprise one of the largest plant TF families. They are key regulators......-termini. Nine of the ten NAC domains analysed bind a previously identified conserved DNA target sequence with a CGT[GA] core, although with different affinities. Likewise, all but one of the NAC proteins analysed is dependent on the C-terminal region for transactivational activity. In silico analyses show...

  9. Di- and Tri- but Not Monomethylation on Histone H3 Lysine 36 Marks Active Transcription of Genes Involved in Flowering Time Regulation and Other Processes in Arabidopsis thaliana▿ †

    OpenAIRE

    Xu, Lin; Zhao, Zhong; Dong, Aiwu; Soubigou-Taconnat, Ludivine; Renou, Jean-Pierre; Steinmetz, Andre; Shen, Wen-Hui

    2007-01-01

    Histone lysines can be mono-, di-, or trimethylated, providing an ample magnitude of epigenetic information for transcription regulation. In fungi, SET2 is the sole methyltransferase responsible for mono-, di-, and trimethylation of H3K36. Here we show that in Arabidopsis thaliana, the degree of H3K36 methylation is regulated by distinct methyltransferases. The SET2 homologs SDG8 and SDG26 each can methylate oligonucleosomes in vitro, and both proteins are localized in the nucleus. While the ...

  10. Integration of genome-scale modeling and transcript profiling reveals metabolic pathways underlying light and temperature acclimation in Arabidopsis.

    Science.gov (United States)

    Töpfer, Nadine; Caldana, Camila; Grimbs, Sergio; Willmitzer, Lothar; Fernie, Alisdair R; Nikoloski, Zoran

    2013-04-01

    Understanding metabolic acclimation of plants to challenging environmental conditions is essential for dissecting the role of metabolic pathways in growth and survival. As stresses involve simultaneous physiological alterations across all levels of cellular organization, a comprehensive characterization of the role of metabolic pathways in acclimation necessitates integration of genome-scale models with high-throughput data. Here, we present an integrative optimization-based approach, which, by coupling a plant metabolic network model and transcriptomics data, can predict the metabolic pathways affected in a single, carefully controlled experiment. Moreover, we propose three optimization-based indices that characterize different aspects of metabolic pathway behavior in the context of the entire metabolic network. We demonstrate that the proposed approach and indices facilitate quantitative comparisons and characterization of the plant metabolic response under eight different light and/or temperature conditions. The predictions of the metabolic functions involved in metabolic acclimation of Arabidopsis thaliana to the changing conditions are in line with experimental evidence and result in a hypothesis about the role of homocysteine-to-Cys interconversion and Asn biosynthesis. The approach can also be used to reveal the role of particular metabolic pathways in other scenarios, while taking into consideration the entirety of characterized plant metabolism.

  11. Identification of Synchronized Role of Transcription Factors, Genes, and Enzymes in Arabidopsis thaliana under Four Abiotic Stress Responsive Pathways

    Directory of Open Access Journals (Sweden)

    Samsad Razzaque

    2014-01-01

    Full Text Available Microarray datasets are widely used resources to predict and characterize functional entities of the whole genomics. The study initiated here aims to identify overexpressed stress responsive genes using microarray datasets applying in silico approaches. The target also extended to build a protein-protein interaction model of regulatory genes with their upstream and downstream connection in Arabidopsis thaliana. Four microarray datasets generated treating abiotic stresses like salinity, cold, drought, and abscisic acid (ABA were chosen. Retrieved datasets were firstly filtered based on their expression comparing to control. Filtered datasets were then used to create an expression hub. Extensive literature mining helped to identify the regulatory molecules from the expression hub. The study brought out 42 genes/TF/enzymes as the role player during abiotic stress response. Further bioinformatics study and also literature mining revealed that thirty genes from those forty-two were highly correlated in all four datasets and only eight from those thirty genes were determined as highly responsive to the above abiotic stresses. Later their protein-protein interaction (PPI, conserved sequences, protein domains, and GO biasness were studied. Some web based tools and software like String database, Gene Ontology, InterProScan, NCBI BLASTn suite, etc. helped to extend the study arena.

  12. Global transcriptional analysis reveals unique and shared responses in Arabidopsis thaliana exposed to combined drought and pathogen stress

    Directory of Open Access Journals (Sweden)

    Aarti eGupta

    2016-05-01

    Full Text Available With frequent fluctuations in global climate, plants are exposed to co-occurring drought and pathogen infection and this combination adversely affects plant survival. In the past, some studies indicated that morpho-physiological responses of plants to the combined stress are different from the individual stressed plants. However, interaction of drought stressed plants with pathogen has not been widely studied at molecular level. Such studies are important to understand the defense pathways that operate as part of combined stress tolerance mechanism. In this study, Arabidopsis thaliana was exposed to individual drought stress, Pseudomonas syringae pv tomato DC3000 (Pst DC3000 infection and their combination. Using Affymetrix WT gene 1.0 ST array, global transcriptome profiling of leaves under individual drought stress and pathogen infection was compared with their combination. The results obtained from pathway mapping (KAAS and MAPMAN demonstrated the modulation in defense pathways in A. thaliana under drought and host pathogen Pst DC3000 infection. Further, our study revealed ‘tailored’ responses under combined stress and the time of occurrence of each stress during their concurrence has showed differences in transcriptome profile. Our results from microarray and RT-qPCR revealed unique regulation of 20 novel genes exclusively during the stress interaction. This study indicates that plants exposed to concurrent drought and pathogen stress experience a new state of stress. Thus, under frequently changing climatic conditions each combination of stressor and their timing defines the plant responses and should thus be studied explicitly.

  13. Knockout analysis of Arabidopsis transcription factors TGA2, TGA5, and TGA6 reveals their redundant and essential roles in systemic acquired resistance.

    Science.gov (United States)

    Zhang, Yuelin; Tessaro, Mark J; Lassner, Michael; Li, Xin

    2003-11-01

    Arabidopsis nonexpresser of pathogenesis-related (PR) genes (NPR1) is the sole positive regulator that has been shown to be essential for the induction of systemic acquired resistance. In npr1 mutant plants, salicylic acid (SA)-mediated PR gene expression and pathogen resistance are abolished completely. NPR1 has been shown to interact with three closely related TGA transcription factors-TGA2, TGA5, and TGA6-in yeast two-hybrid assays. To elucidate the biological functions of these three TGA transcription factors, we analyzed single and combined deletion knockout mutants of TGA2, TGA5, and TGA6 for SA-induced PR gene expression and pathogen resistance. Induction of PR gene expression and pathogen resistance by the SA analog 2,6-dichloroisonicotinic acid (INA) was blocked in tga6-1 tga2-1 tga5-1 but not in tga6-1 or tga2-1 tga5-1 plants. Loss of INA-induced resistance to Peronospora parasitica Noco2 cosegregated with the tga6-1 mutation in progeny of multiple lines that were heterozygous for tga6-1 and homozygous for tga2-1 tga5-1 and could be complemented by genomic clones of wild-type TGA2 or TGA5, indicating that TGA2, TGA5, and TGA6 encode redundant and essential functions in the positive regulation of systemic acquired resistance. In addition, tga6-1 tga2-1 tga5-1 plants had reduced tolerance to high levels of SA and accumulated higher basal levels of PR-1 under noninducing conditions, suggesting that these TGA factors also are important for SA tolerance and the negative regulation of the basal expression of PR-1. PMID:14576289

  14. Arabidopsis Transcription Factor Genes NF-YA1,5, 6, and 9 Play Redundant Roles in Male Gametogenesis, Embryogenesis, and Seed Development

    Institute of Scientific and Technical Information of China (English)

    Jinye Mu; Helin Tan; Sulei Hong; Yan Liang; Jianru Zuo

    2013-01-01

    Nuclear factor Y (NF-Y) is a highly conserved transcription factor presented in all eukaryotic organisms,and is a heterotrimer consisting of three subunits:NF-YA,NF-YB,and NF-YC.In Arabidopsis,these three subunits are encoded by multigene families.The best-studied member of the NF-Y transcription factors is LEAFY COTYLEDON1 (LEC1),a NF-YB family member,which plays a critical role in embryogenesis and seed maturation.However,the function of most NF-Y genes remains elusive.Here,we report the characterization of four genes in the NF-YA family.We found that a gainof-function mutant of NF-YA1 showed defects in male gametogenesis and embryogenesis.Consistently,overexpression of NF-YA1,5,6,and 9 affects male gametogenesis,embryogenesis,seed morphology,and seed germination,with a stronger phenotype when overexpressing NF-YA1 and NF-YA9.Moreover,overexpression of these NF-YA genes also causes hypersensitivity to abscisic acid (ABA) during seed germination,retarded seedling growth,and late flowering at different degrees.Intriguingly,overexpmssion of NF-YA1,5,6,and 9 is sufficient to induce the formation of somatic embryos from the vegetative tissues.However,single or double mutants of these NF-YA genes do not have detectable phenotype.Collectively,these results provide evidence that NF-YA1,5,6,and 9 play redundant roles in male gametophyte development,embryogenesis,seed development,and post-germinative growth.

  15. Transcriptional Activation and Production of Tryptophan-Derived Secondary Metabolites in Arabidopsis Roots Contributes to the Defense against the Fungal Vascular Pathogen Verticillium Iongisporum

    Institute of Scientific and Technical Information of China (English)

    Tim Iven; Wolfgang Dr(o)ge-Laser; Stefanie K(o)nig; Seema Singh; Susanna A.Braus-Stromeyer; Matthias Bischoff; Lutz F.Tietze; Gerhard H.Braus; Volker Lipka; Ivo Feussner

    2012-01-01

    The soil-borne fungal pathogen Verticillium Iongisporum causes vascular disease on Brassicaceae host plants such as oilseed rape.The fungus colonizes the root xylem and moves upwards to the foliage where disease symptoms become visible.Using Arabidopsis as a model for early gene induction,we performed root transcriptome analyses in response to hyphal growth immediately after spore germination and during penetration of the root cortex,respectively.Infected roots showed a rapid reprogramming of gene expression such as activation of transcription factors,stress-,and defense-related genes.Here,we focused on the highly coordinated gene induction resulting in the production of tryptophan-derived secondary metabolites.Previous studies in leaves showed that enzymes encoded by CYP81F2 and PEN2 (PENETRATION2) execute the formation of antifungal indole glucosinolate (IGS) metabolites.In Verticillium-infected roots.we found transcriptional activation of CYP81F2 and the PEN2 homolog PEL1 (PEN2-LIKE1),but no increase in antifungal IGS breakdown products.In contrast,indole-3-carboxylic acid (I3CA) and the phytoalexin camalexin accumulated in infected roots but only camalexin inhibited Verticillium growth in vitro.Whereas genetic disruption of the individual metabolic pathways leading to either camalexin or CYP81F2-dependent IGS metabolites did not alter Verticillium-induced disease symptoms,a cyp79b2 cyp79b3 mutant impaired in both branches resulted in significantly enhanced susceptibility.Hence,our data provide an insight into root-specific early defenses and suggest tryptophan-derived metabolites as active antifungal compounds against a vascular pathogen.

  16. Arabidopsis ABA Receptor RCAR1/PYL9 Interacts with an R2R3-Type MYB Transcription Factor, AtMYB44

    Directory of Open Access Journals (Sweden)

    Dekuan Li

    2014-05-01

    Full Text Available Abscisic acid (ABA signaling plays important roles in plant growth, development and adaptation to various stresses. RCAR1/PYL9 has been known as a cytoplasm and nuclear ABA receptor in Arabidopsis. To obtain further insight into the regulatory mechanism of RCAR1/PYL9, a yeast two-hybrid approach was performed to screen for RCAR1/PYL9-interacting proteins and an R2R3-type MYB transcription factor, AtMYB44, was identified. The interaction between RCAR1/PYL9 and AtMYB44 was further confirmed by glutathione S-transferase (GST pull-down and bimolecular fluorescence complementation (BiFC assays. Gene expression analysis showed that AtMYB44 negatively regulated the expression of ABA-responsive gene RAB18, in contrast to the opposite role reported for RCAR1/PYL9. Competitive GST pull-down assay and analysis of phosphatase activity demonstrated that AtMYB44 and ABI1 competed for binding to RCAR1/PYL9 and thereby reduced the inhibitory effect of RCAR1/PYL9 on ABI1 phosphatase activity in the presence of ABA in vitro. Furthermore, transient activation assay in protoplasts revealed AtMYB44 probably also decreased RCAR1/PYL9-mediated inhibition of ABI1 activity in vivo. Taken together, our work provides a reasonable molecular mechanism of AtMYB44 in ABA signaling.

  17. The overexpression of the pine transcription factor PpDof5 in Arabidopsis leads to increased lignin content and affects carbon and nitrogen metabolism.

    Science.gov (United States)

    Rueda-López, Marina; Cañas, Rafael A; Canales, Javier; Cánovas, Francisco M; Ávila, Concepción

    2015-12-01

    PpDof 5 is a regulator of the expression of glutamine synthetase (GS; EC 6.3.1.2) genes in photosynthetic and non-photosynthetic tissues of maritime pine. We have used Arabidopsis thaliana as a model system to study PpDof 5 function in planta, generating transgenic lines overexpressing the pine transcription factor. The overexpression of PpDof 5 resulted in a substantial increase of lignin content with a simultaneous regulation of carbon and nitrogen key genes. In addition, partitioning in carbon and nitrogen compounds was spread via various secondary metabolic pathways. These results suggest pleiotropic effects of PpDof 5 expression on various metabolic pathways of carbon and nitrogen metabolism. Plants overexpressing PpDof 5 exhibited upregulation of genes encoding enzymes for sucrose and starch biosynthesis, with a parallel increase in the content of soluble sugars. When the plants were grown under nitrate as the sole nitrogen source, they exhibited a significant regulation of the expression of genes involved mainly in signaling, but similar growth rates to wild-type plants. However, plants grown under ammonium exhibited major induction of the expression of photosynthetic genes and differential expression of ammonium and nitrate transporters. All these data suggest that in addition to controlling ammonium assimilation, PpDof 5 could be also involved in the regulation of other pathways in carbon and nitrogen metabolism in pine trees. PMID:26333592

  18. DNA Damage-Induced Transcription of Transposable Elements and Long Non-coding RNAs in Arabidopsis Is Rare and ATM-Dependent.

    Science.gov (United States)

    Wang, Zhenxing; Schwacke, Rainer; Kunze, Reinhard

    2016-08-01

    Induction and mobilization of transposable elements (TEs) following DNA damage or other stresses has been reported in prokaryotes and eukaryotes. Recently it was discovered that eukaryotic TEs are frequently associated with long non-coding RNAs (lncRNAs), many of which are also upregulated by stress. Yet, it is unknown whether DNA damage-induced transcriptional activation of TEs and lncRNAs occurs sporadically or is a synchronized, genome-wide response. Here we investigated the transcriptome of Arabidopsis wild-type (WT) and ataxia telangiectasia mutated (atm) mutant plants 3 h after induction of DNA damage. In WT, expression of 5.2% of the protein-coding genes is ≥2-fold changed, whereas in atm plants, only 2.6% of these genes are regulated, and the response of genes associated with DNA repair, replication, and cell cycle is largely lost. In contrast, only less than 0.6% of TEs and lncRNAs respond to DNA damage in WT plants, and the regulation of ≥95% of them is ATM-dependent. The ATM-downstream factors BRCA1, DRM1, JMJ30, AGO2, and the ATM-independent AGO4 participate in the regulation of individual TEs and lncRNAs. Remarkably, protein-coding genes located adjacent to DNA damage-responsive TEs and lncRNAs are frequently coexpressed, which is consistent with the hypothesis that TEs and lncRNAs located close to genes commonly function as controlling elements. PMID:27150037

  19. Role of the Arabidopsis thaliana NAC transcription factors ANAC019 and ANAC055 in regulating jasmonic acid-signaled defense responses

    Institute of Scientific and Technical Information of China (English)

    Qingyun Bu; Hongling Jiang; Chang-Bao Li; Qingzhe Zhai; Jie Zhang; Xiaoyan Wu; Jiaqiang Sun; Qi Xie; Chuanyou Li

    2008-01-01

    Jasmonic acid (JA) is an important phytohormone that regulates plant defense responses against herbivore attack, pathogen infection and mechanical wounding. In this report, we provided biochemical and genetic evidence to show that the Arabidopsis thaliana NAC family proteins ANAC019 and ANAC055 might function as transcription activators to regulate JA-induced expression of defense genes. The role of the two NAC genes in JA signaling was examined with the anac019 anac055 double mutant and with transgenic plants overexpressing ANAC019 or ANAC055. The anac019 anac055 double mutant plants showed attenuated JA-induced VEGETATIVE STORAGE PROTEIN1 (VSP1) and LIPOXYGENASE2 (LOX2) expression, whereas transgenic plants overexpressing the two NAC genes showed enhanced JA-induced VSP1 and LOX2 expression. That the JA-induced expression of the two NAC genes depends on the function of COI1 and AtMYC2, together with the finding that overexpression of ANAC019 partially rescued the JA-related phenotype of the atmyc2-2 mutant, has led us to a hypothesis that the two NAC proteins act downstream of AtMYC2 to regulate JA-signaled defense responses. Further evidence to substantiate this idea comes from the observation that the response of the anac019 anac055 double mutant to a necrotrophic fungus showed high similarity to that of the atmyc2-2 mutant.

  20. Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3.

    Science.gov (United States)

    Porco, Silvana; Larrieu, Antoine; Du, Yujuan; Gaudinier, Allison; Goh, Tatsuaki; Swarup, Kamal; Swarup, Ranjan; Kuempers, Britta; Bishopp, Anthony; Lavenus, Julien; Casimiro, Ilda; Hill, Kristine; Benkova, Eva; Fukaki, Hidehiro; Brady, Siobhan M; Scheres, Ben; Péret, Benjamin; Bennett, Malcolm J

    2016-09-15

    Lateral root primordia (LRP) originate from pericycle stem cells located deep within parental root tissues. LRP emerge through overlying root tissues by inducing auxin-dependent cell separation and hydraulic changes in adjacent cells. The auxin-inducible auxin influx carrier LAX3 plays a key role concentrating this signal in cells overlying LRP. Delimiting LAX3 expression to two adjacent cell files overlying new LRP is crucial to ensure that auxin-regulated cell separation occurs solely along their shared walls. Multiscale modeling has predicted that this highly focused pattern of expression requires auxin to sequentially induce auxin efflux and influx carriers PIN3 and LAX3, respectively. Consistent with model predictions, we report that auxin-inducible LAX3 expression is regulated indirectly by AUXIN RESPONSE FACTOR 7 (ARF7). Yeast one-hybrid screens revealed that the LAX3 promoter is bound by the transcription factor LBD29, which is a direct target for regulation by ARF7. Disrupting auxin-inducible LBD29 expression or expressing an LBD29-SRDX transcriptional repressor phenocopied the lax3 mutant, resulting in delayed lateral root emergence. We conclude that sequential LBD29 and LAX3 induction by auxin is required to coordinate cell separation and organ emergence. PMID:27578783

  1. Dual-level regulation of ACC synthase activity by MPK3/MPK6 cascade and its downstream WRKY transcription factor during ethylene induction in Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Guojing Li

    2012-06-01

    Full Text Available Plants under pathogen attack produce high levels of ethylene, which plays important roles in plant immunity. Previously, we reported the involvement of ACS2 and ACS6, two Type I ACS isoforms, in Botrytis cinerea-induced ethylene biosynthesis and their regulation at the protein stability level by MPK3 and MPK6, two Arabidopsis pathogen-responsive mitogen-activated protein kinases (MAPKs. The residual ethylene induction in the acs2/acs6 double mutant suggests the involvement of additional ACS isoforms. It is also known that a subset of ACS genes, including ACS6, is transcriptionally induced in plants under stress or pathogen attack. However, the importance of ACS gene activation and the regulatory mechanism(s are not clear. In this report, we demonstrate using genetic analysis that ACS7 and ACS11, two Type III ACS isoforms, and ACS8, a Type II ACS isoform, also contribute to the B. cinerea-induced ethylene production. In addition to post-translational regulation, transcriptional activation of the ACS genes also plays a critical role in sustaining high levels of ethylene induction. Interestingly, MPK3 and MPK6 not only control the stability of ACS2 and ACS6 proteins via direct protein phosphorylation but also regulate the expression of ACS2 and ACS6 genes. WRKY33, another MPK3/MPK6 substrate, is involved in the MPK3/MPK6-induced ACS2/ACS6 gene expression based on genetic analyses. Furthermore, chromatin-immunoprecipitation assay reveals the direct binding of WRKY33 to the W-boxes in the promoters of ACS2 and ACS6 genes in vivo, suggesting that WRKY33 is directly involved in the activation of ACS2 and ACS6 expression downstream of MPK3/MPK6 cascade in response to pathogen invasion. Regulation of ACS activity by MPK3/MPK6 at both transcriptional and protein stability levels plays a key role in determining the kinetics and magnitude of ethylene induction.

  2. Phosphatidic Acid Interacts with a MYB Transcription Factor and Regulates Its Nuclear Localization and Function in Arabidopsis[C][W

    Science.gov (United States)

    Yao, Hongyan; Wang, Geliang; Guo, Liang; Wang, Xuemin

    2013-01-01

    Phosphatidic acid (PA) has emerged as a class of cellular mediators involved in various cellular and physiological processes, but little is known about its mechanism of action. Here we show that PA interacts with WEREWOLF (WER), a R2R3 MYB transcription factor involved in root hair formation. The PA-interacting region is confined to the end of the R2 subdomain. The ablation of the PA binding motif has no effect on WER binding to DNA, but abolishes its nuclear localization and its function in regulating epidermal cell fate. Inhibition of PA production by phospholipase Dζ also suppresses WER’s nuclear localization, root hair formation, and elongation. These results suggest a role for PA in promoting protein nuclear localization. PMID:24368785

  3. Phosphatidic acid interacts with a MYB transcription factor and regulates its nuclear localization and function in Arabidopsis.

    Science.gov (United States)

    Yao, Hongyan; Wang, Geliang; Guo, Liang; Wang, Xuemin

    2013-12-01

    Phosphatidic acid (PA) has emerged as a class of cellular mediators involved in various cellular and physiological processes, but little is known about its mechanism of action. Here we show that PA interacts with werewolf (WER), a R2R3 MYB transcription factor involved in root hair formation. The PA-interacting region is confined to the end of the R2 subdomain. The ablation of the PA binding motif has no effect on WER binding to DNA, but abolishes its nuclear localization and its function in regulating epidermal cell fate. Inhibition of PA production by phospholipase Dζ also suppresses WER's nuclear localization, root hair formation, and elongation. These results suggest a role for PA in promoting protein nuclear localization.

  4. Transcript profiling of cytokinin action in Arabidopsis roots and shoots discovers largely similar but also organ-specific responses

    Directory of Open Access Journals (Sweden)

    Brenner Wolfram G

    2012-07-01

    Full Text Available Abstract Background The plant hormone cytokinin regulates growth and development of roots and shoots in opposite ways. In shoots it is a positive growth regulator whereas it inhibits growth in roots. It may be assumed that organ-specific regulation of gene expression is involved in these differential activities, but little is known about it. To get more insight into the transcriptional events triggered by cytokinin in roots and shoots, we studied genome-wide gene expression in cytokinin-treated and cytokinin-deficient roots and shoots. Results It was found by principal component analysis of the transcriptomic data that the immediate-early response to a cytokinin stimulus differs from the later response, and that the transcriptome of cytokinin-deficient plants is different from both the early and the late cytokinin induction response. A higher cytokinin status in the roots activated the expression of numerous genes normally expressed predominantly in the shoot, while a lower cytokinin status in the shoot reduced the expression of genes normally more active in the shoot to a more root-like level. This shift predominantly affected nuclear genes encoding plastid proteins. An organ-specific regulation was assigned to a number of genes previously known to react to a cytokinin signal, including root-specificity for the cytokinin hydroxylase gene CYP735A2 and shoot specificity for the cell cycle regulator gene CDKA;1. Numerous cytokinin-regulated genes were newly discovered or confirmed, including the meristem regulator genes SHEPHERD and CLAVATA1, auxin-related genes (IAA7, IAA13, AXR1, PIN2, PID, several genes involved in brassinosteroid (CYP710A1, CYP710A2, DIM/DWF and flavonol (MYB12, CHS, FLS1 synthesis, various transporter genes (e.g. HKT1, numerous members of the AP2/ERF transcription factor gene family, genes involved in light signalling (PhyA, COP1, SPA1, and more than 80 ribosomal genes. However, contrasting with the fundamental difference of

  5. A novel bHLH transcription factor PebHLH35 from Populus euphratica confers drought tolerance through regulating stomatal development, photosynthesis and growth in Arabidopsis

    International Nuclear Information System (INIS)

    Highlights: • PebHLH35 is firstly cloned from Populus euphratica and characterized its functions. • PebHLH35 is important for earlier seedling establishment and vegetative growth. • PebHLH35 enhances tolerance to drought by regulating growth. • PebHLH35 enhances tolerance to drought by regulating stomatal development. • PebHLH35 enhances tolerance to drought by regulating photosynthesis and transpiration. - Abstract: Plant basic helix-loop-helix (bHLH) transcription factors (TFs) are involved in a variety of physiological processes including the regulation of plant responses to various abiotic stresses. However, few drought-responsive bHLH family members in Populus have been reported. In this study, a novel bHLH gene (PebHLH35) was cloned from Populus euphratica. Expression analysis in P. euphratica revealed that PebHLH35 was induced by drought and abscisic acid. Subcellular localization studies using a PebHLH35-GFP fusion showed that the protein was localized to the nucleus. Ectopic overexpression of PebHLH35 in Arabidopsis resulted in a longer primary root, more leaves, and a greater leaf area under well-watered conditions compared with vector control plants. Notably, PebHLH35 overexpression lines showed enhanced tolerance to water-deficit stress. This finding was supported by anatomical and physiological analyses, which revealed a reduced stomatal density, stomatal aperture, transpiration rate, and water loss, and a higher chlorophyll content and photosynthetic rate. Our results suggest that PebHLH35 functions as a positive regulator of drought stress responses by regulating stomatal density, stomatal aperture, photosynthesis and growth

  6. Ethylene antagonizes salt-induced growth retardation and cell death process via transcriptional controlling of ethylene-, BAG- and senescence-associated genes in Arabidopsis

    Directory of Open Access Journals (Sweden)

    YaJie ePan

    2016-05-01

    Full Text Available The existing question whether ethylene is involved in the modulation of salt-induced cell death to mediate plant salt tolerance is important for understanding the salt tolerance mechanisms. Here, we employed Arabidopsis plants to study the possible role of ethylene in salt-induced growth inhibition and programmed cell death (PCD profiles. The root length, DNA ladder and cell death indicated by Evan’s blue detection were measured by compared to the control or salt-stressed seedlings. Secondly, the protoplasts isolated from plant leaves and dyed with Annexin V-FITC were subjected to flow cytometric (FCM assay. Our results showed that ethylene works effectively in seedling protoplasts, antagonizing salt-included root retardation and restraining cell death both in seedlings or protoplasts. Due to salinity, the entire or partial insensitivity of ethylene signaling resulted in an elevated levels of cell death in ein2-5 and ein3-1 plants and the event were amended in ctr1-1 plants after salt treatment. The subsequent experiment with exogenous ACC further corroborated that ethylene could modulate salt-induced PCD process actively. Plant Bcl-2-associated athanogene (BAG family genes are recently identified to play an extensive role in plant PCD processes ranging from growth, development to stress responses and even cell death. Our result showed that salinity alone significantly suppressed the transcripts of BAG6, BAG7 and addition of ACC in the saline solution could obviously re-activate BAG6 and BAG7 expressions, which might play a key role to inhibit the salt-induced cell death. In summary, our research implies that ethylene and salinity antagonistically control BAG family-, ethylene-, and senescence-related genes to alleviate the salt-induced cell death.

  7. Ethylene Antagonizes Salt-Induced Growth Retardation and Cell Death Process via Transcriptional Controlling of Ethylene-, BAG- and Senescence-Associated Genes in Arabidopsis.

    Science.gov (United States)

    Pan, Ya-Jie; Liu, Ling; Lin, Ying-Chao; Zu, Yuan-Gang; Li, Lei-Peng; Tang, Zhong-Hua

    2016-01-01

    The existing question whether ethylene is involved in the modulation of salt-induced cell death to mediate plant salt tolerance is important for understanding the salt tolerance mechanisms. Here, we employed Arabidopsis plants to study the possible role of ethylene in salt-induced growth inhibition and programmed cell death (PCD) profiles. The root length, DNA ladder and cell death indicated by Evan's blue detection were measured by compared to the control or salt-stressed seedlings. Secondly, the protoplasts isolated from plant leaves and dyed with Annexin V-FITC were subjected to flow cytometric (FCM) assay. Our results showed that ethylene works effectively in seedling protoplasts, antagonizing salt-included root retardation and restraining cell death both in seedlings or protoplasts. Due to salinity, the entire or partial insensitivity of ethylene signaling resulted in an elevated levels of cell death in ein2-5 and ein3-1 plants and the event were amended in ctr1-1 plants after salt treatment. The subsequent experiment with exogenous ACC further corroborated that ethylene could modulate salt-induced PCD process actively. Plant Bcl-2-associated athanogene (BAG) family genes are recently identified to play an extensive role in plant PCD processes ranging from growth, development to stress responses and even cell death. Our result showed that salinity alone significantly suppressed the transcripts of BAG6, BAG7 and addition of ACC in the saline solution could obviously re-activate BAG6 and BAG7 expressions, which might play a key role to inhibit the salt-induced cell death. In summary, our research implies that ethylene and salinity antagonistically control BAG family-, ethylene-, and senescence-related genes to alleviate the salt-induced cell death. PMID:27242886

  8. A novel bHLH transcription factor PebHLH35 from Populus euphratica confers drought tolerance through regulating stomatal development, photosynthesis and growth in Arabidopsis

    Energy Technology Data Exchange (ETDEWEB)

    Dong, Yan [College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083 (China); Liaoning Forestry Vocational-Technical College, Shenyang 110101 (China); Wang, Congpeng; Han, Xiao; Tang, Sha; Liu, Sha [College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083 (China); Xia, Xinli, E-mail: xiaxl@bjfu.edu.cn [College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083 (China); Yin, Weilun, E-mail: yinwl@bjfu.edu.cn [College of Biological Sciences and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083 (China)

    2014-07-18

    Highlights: • PebHLH35 is firstly cloned from Populus euphratica and characterized its functions. • PebHLH35 is important for earlier seedling establishment and vegetative growth. • PebHLH35 enhances tolerance to drought by regulating growth. • PebHLH35 enhances tolerance to drought by regulating stomatal development. • PebHLH35 enhances tolerance to drought by regulating photosynthesis and transpiration. - Abstract: Plant basic helix-loop-helix (bHLH) transcription factors (TFs) are involved in a variety of physiological processes including the regulation of plant responses to various abiotic stresses. However, few drought-responsive bHLH family members in Populus have been reported. In this study, a novel bHLH gene (PebHLH35) was cloned from Populus euphratica. Expression analysis in P. euphratica revealed that PebHLH35 was induced by drought and abscisic acid. Subcellular localization studies using a PebHLH35-GFP fusion showed that the protein was localized to the nucleus. Ectopic overexpression of PebHLH35 in Arabidopsis resulted in a longer primary root, more leaves, and a greater leaf area under well-watered conditions compared with vector control plants. Notably, PebHLH35 overexpression lines showed enhanced tolerance to water-deficit stress. This finding was supported by anatomical and physiological analyses, which revealed a reduced stomatal density, stomatal aperture, transpiration rate, and water loss, and a higher chlorophyll content and photosynthetic rate. Our results suggest that PebHLH35 functions as a positive regulator of drought stress responses by regulating stomatal density, stomatal aperture, photosynthesis and growth.

  9. Overexpression of the Transcription Factors GmSHN1 and GmSHN9 Differentially Regulates Wax and Cutin Biosynthesis, Alters Cuticle Properties, and Changes Leaf Phenotypes in Arabidopsis.

    Science.gov (United States)

    Xu, Yangyang; Wu, Hanying; Zhao, Mingming; Wu, Wang; Xu, Yinong; Gu, Dan

    2016-04-21

    SHINE (SHN/WIN) clade proteins, transcription factors of the plant-specific APETALA 2/ethylene-responsive element binding factor (AP2/ERF) family, have been proven to be involved in wax and cutin biosynthesis. Glycine max is an important economic crop, but its molecular mechanism of wax biosynthesis is rarely characterized. In this study, 10 homologs of Arabidopsis SHN genes were identified from soybean. These homologs were different in gene structures and organ expression patterns. Constitutive expression of each of the soybean SHN genes in Arabidopsis led to different leaf phenotypes, as well as different levels of glossiness on leaf surfaces. Overexpression of GmSHN1 and GmSHN9 in Arabidopsis exhibited 7.8-fold and 9.9-fold up-regulation of leaf cuticle wax productions, respectively. C31 and C29 alkanes contributed most to the increased wax contents. Total cutin contents of leaves were increased 11.4-fold in GmSHN1 overexpressors and 5.7-fold in GmSHN9 overexpressors, mainly through increasing C16:0 di-OH and dioic acids. GmSHN1 and GmSHN9 also altered leaf cuticle membrane ultrastructure and increased water loss rate in transgenic Arabidopsis plants. Transcript levels of many wax and cutin biosynthesis and leaf development related genes were altered in GmSHN1 and GmSHN9 overexpressors. Overall, these results suggest that GmSHN1 and GmSHN9 may differentially regulate the leaf development process as well as wax and cutin biosynthesis.

  10. Overexpression of the Transcription Factors GmSHN1 and GmSHN9 Differentially Regulates Wax and Cutin Biosynthesis, Alters Cuticle Properties, and Changes Leaf Phenotypes in Arabidopsis

    Directory of Open Access Journals (Sweden)

    Yangyang Xu

    2016-04-01

    Full Text Available SHINE (SHN/WIN clade proteins, transcription factors of the plant-specific APETALA 2/ethylene-responsive element binding factor (AP2/ERF family, have been proven to be involved in wax and cutin biosynthesis. Glycine max is an important economic crop, but its molecular mechanism of wax biosynthesis is rarely characterized. In this study, 10 homologs of Arabidopsis SHN genes were identified from soybean. These homologs were different in gene structures and organ expression patterns. Constitutive expression of each of the soybean SHN genes in Arabidopsis led to different leaf phenotypes, as well as different levels of glossiness on leaf surfaces. Overexpression of GmSHN1 and GmSHN9 in Arabidopsis exhibited 7.8-fold and 9.9-fold up-regulation of leaf cuticle wax productions, respectively. C31 and C29 alkanes contributed most to the increased wax contents. Total cutin contents of leaves were increased 11.4-fold in GmSHN1 overexpressors and 5.7-fold in GmSHN9 overexpressors, mainly through increasing C16:0 di-OH and dioic acids. GmSHN1 and GmSHN9 also altered leaf cuticle membrane ultrastructure and increased water loss rate in transgenic Arabidopsis plants. Transcript levels of many wax and cutin biosynthesis and leaf development related genes were altered in GmSHN1 and GmSHN9 overexpressors. Overall, these results suggest that GmSHN1 and GmSHN9 may differentially regulate the leaf development process as well as wax and cutin biosynthesis.

  11. Arabidopsis STO/BBX24 negatively regulates UV-B signaling by interacting with COP1 and repressing HY5 transcriptional activity

    Institute of Scientific and Technical Information of China (English)

    Lei Jiang; Yan Wang; Qian-Feng Li; Lars Olof Bj(o)rn; Jun-Xian He; Shao-Shan Li

    2012-01-01

    UV-B (280-315 nm) is an integral part of solar radiation and can act either as a stress inducer or as a developmental signal.In recent years,increasing attention has been paid to the Iow-fluence UV-B-induced photomorphogenic response and several key players in this response have been identified,which include UVR8 (a UV-B-specific photoreceptor),COPI (a WD40-repeat-containing RING finger protein),HY5 (a basic zipper transcription factor),and RUP1/2 (two UVR8-interacting proteins).Here we report that Arabidopsis SALT TOLERANCE (STO/BBX24),a known regulator for light signaling in plants,defines a new signaling component in UV-B-mediated photomorphogenesis.The bbx24 mutant is hypersensitive to UV-B radiation and becomes extremely dwarfed under UV-B treatment.By contrast,BBX24 overexpression transgenic lines respond much more weakly to UV-B than the bbx24 and wild-type plants.BBX24 expression is UV-B-inducible and its accumulation under UV-B requires COP1.Co-immunoprecipitation experiments indicate that BBX24 interacts with COP1 in planta upon UV-B illumination.Moreover,BBX24 interacts with HY5 and acts antagonistically with HY5 in UV-B-induced inhibition of hypocotyl elongation.Furthermore,BBX24 attenuates UV-B-induced HY5 accumulation and suppresses its transcription-activation activity.Taken together,our results reveal a previously uncharacterized function of the light-regulated BBX24 in UV-B responses and demonstrate that BBX24 functions as a negative regulator of photomorphogenic UV-B responses by interacting with both COP1 and HY5.The UV-B-inducible expression pattern and its suppression of HY5 activity suggest that BBX24 could be a new component of the feedback regulatory module of UV-B signaling in plants.

  12. Characterization of three Arabidopsis AP2/EREBP family transcription factors involved in ABA sensitivity,freeze and salt tolerance

    Institute of Scientific and Technical Information of China (English)

    MEI WenQian; LEI Juan; Xu Yu; WEI Gang; ZHU YuXian

    2007-01-01

    AP2/EREBP transcription factors (TFs) play very important roles in plant development,hormonal regulation and stress response. Upon genome-wide cDNA cloning,phylogenetic and expression pattern analyses of this plant specific TF family,we found that three of the members including At1g71450,At1g50680 and At5g13910,were likely involved in responses to ABA,cold and salt. Complementary DNAs containing putative full-length ORFs of these three TFs were obtained and fused individually to the GAL4 DNA-binding domains. All the 3 genes functioned effectively as trans-activators using yeast one-hybrid assays. RT-PCR experiments showed that the At1g71450 gene was induced by ABA and low temperature; the At1g50680 gene was responsive to quite a few stress conditions,but especially to freezing temperature; and the At5g13910 gene was induced by high salt treatment,drought and ethylene. By searching the ABRC T-DNA insertion mutant stocks,we obtained knockout lines for these TFs. Homozygous ko1 (At1g71450) plants showed a hypersensitive response to ABA during seed germination and also in stomata movement. Homozygous ko2 (At1g50680) plants showed a significant reduction in plant freezing tolerance compared to the wild type after chilling treatment. Homozygous ko3 (At5g13910) were less tolerant to high salinity than wild type plants. Our data suggest that At1g71450 is a negative regulator in ABA signaling,while At1g50680 and At5g13910 are positive regulators in cold and salt stress responses,respectively.

  13. Ultraviolet-B-induced responses in Arabidopsis thaliana: role of salicylic acid and reactive oxygen species in the regulation of transcripts encoding photosynthetic and acidic pathogenesis-related proteins

    International Nuclear Information System (INIS)

    Supplementary UV-B was shown to lead to a decrease in transcripts encoding the photosynthetic genes Lhcb and psbA and a concomitant increase in transcripts encoding three acid-type pathogenesis-related proteins, PR-1, PR-2 and PR-5, in Arabidopsis thaliana. UV-B radiation has been reported to lead to the generation of reactive oxygen species (ROS). Here we report that ROS are required for UV-B-induced down-regulation of the photosynthetic genes and up-regulation of PR genes, as the addition of antioxidants before UV-B treatment resulted in a marked reduction in the effect of UV-B on both sets of genes. Rises in ROS are frequently accompanied by increases in salicylic acid (SA) accumulation. UV-B treatment of transgenic NahG Arabidopsis plants, which are unable to accumulate SA, showed that the increase in PR transcripts, but not the decrease in photosynthetic transcripts, was dependent on the increase in SA. In addition, a 3 d exposure to UV-B radiation resulted in a 7-fold increase in SA levels. Oxidant treatment of NahG plants indicated that ROS could not up-regulate PR genes in the absence of SA accumulation; however, the down-regulation of photosynthetic transcripts was unchanged from that in wild-type plants. The results indicate that the effects of UV-B on the two sets of genes are mediated through two distinct signal tranduction pathways. One pathway is ROS-dependent but SA-independent and mediates the down-regulation of photosynthetic genes. The other is SA- and ROS-dependent and mediates the up-regulation of the acidic-type PR genes

  14. Gravitational and magnetic field variations synergize to cause subtle variations in the global transcriptional state of Arabidopsis in vitro callus cultures

    Directory of Open Access Journals (Sweden)

    Manzano Ana I

    2012-03-01

    Full Text Available Abstract Background Biological systems respond to changes in both the Earth's magnetic and gravitational fields, but as experiments in space are expensive and infrequent, Earth-based simulation techniques are required. A high gradient magnetic field can be used to levitate biological material, thereby simulating microgravity and can also create environments with a reduced or an enhanced level of gravity (g, although special attention should be paid to the possible effects of the magnetic field (B itself. Results Using diamagnetic levitation, we exposed Arabidopsis thaliana in vitro callus cultures to five environments with different levels of effective gravity and magnetic field strengths. The environments included levitation, i.e. simulated μg* (close to 0 g* at B = 10.1 T, intermediate g* (0.1 g* at B = 14.7 T and enhanced gravity levels (1.9 g* at B = 14.7 T and 2 g* at B = 10.1 T plus an internal 1 g* control (B = 16.5 T. The asterisk denotes the presence of the background magnetic field, as opposed to the effective gravity environments in the absence of an applied magnetic field, created using a Random Position Machine (simulated μg and a Large Diameter Centrifuge (2 g. Microarray analysis indicates that changes in the overall gene expression of cultured cells exposed to these unusual environments barely reach significance using an FDR algorithm. However, it was found that gravitational and magnetic fields produce synergistic variations in the steady state of the transcriptional profile of plants. Transcriptomic results confirm that high gradient magnetic fields (i.e. to create μg* and 2 g* conditions have a significant effect, mainly on structural, abiotic stress genes and secondary metabolism genes, but these subtle gravitational effects are only observable using clustering methodologies. Conclusions A detailed microarray dataset analysis, based on clustering of similarly expressed genes (GEDI software, can detect underlying global

  15. Lhcb transcription is coordinated with cell size and chlorophyll accumulation. Studies on fluorescence-activated, cell-sorter-purified single cells from wild-type and immutans Arabidopsis thaliana

    Energy Technology Data Exchange (ETDEWEB)

    Meehan, L.; Harkins, K.; Rodermel, S. [Iowa State Univ., Ames, IA (United States)] [and others

    1996-11-01

    To study the mechanisms that integrate pigment and chlorophyll a/b-binding apoprotein biosynthesis during light-harvesting complex II assembly, we have examined {beta}-glucuronidase (GUS) enzyme activities, cell-sorting-separated single cells sizes in fluorescence activated, cell-sorting-separated single cells from transgenic Arabidopsis thaliana wild-type and immutans variegation mutant plants that express an Lhcb (photosystem II chlorophyll a/b-binding polypeptide gene)/GUS promoter fusion. We found that GUS activities are positively correlated with chlorophyll content and cell size in green cells from the control and immutans plants, indicating that Lhcb gene transcription is coordinated with cell size in this species. Compared with the control plants, however, chlorophyll production is enhanced in the green cells of immutans; this may represent part of a strategy to maximize photosynthesis in the white sectors of the mutant. Lhcb transcription is significantly higher in pure-white cells of the transgenic immutans plants than in pure-white cells from norflurazon-treated, photooxidized A. thaliana leaves. This suggests that immutans partially uncouples Lhcb transcription from its normal dependence on chlorophyll accumulation and chloroplast development. We conclude that immutans may play a role in regulating Lhcb transcription, and may be a key component in the signal transduction pathways that control chloroplast biogenesis. 58 refs., 5 figs., 2 tabs.

  16. Hydrogen Peroxide-induced Cell Death in Arabidopsis : Transcriptional and Mutant Analysis Reveals a Role of an Oxoglutarate-dependent Dioxygenase Gene in the Cell Death Process

    NARCIS (Netherlands)

    Gechev, Tsanko S.; Minkov, Ivan N.; Hille, Jacques

    2005-01-01

    Hydrogen peroxide is a major regulator of plant programmed cell death (PCD) but little is known about the downstream genes from the H2O2-signaling network that mediate the cell death. To address this question, a novel system for studying H2O2-induced programmed cell death in Arabidopsis thaliana was

  17. Post-Transcriptional Coordination of the Arabidopsis Iron Deficiency Response is Partially Dependent on the E3 Ligases RING DOMAIN LIGASE1 (RGLG1) and RING DOMAIN LIGASE2 (RGLG2).

    Science.gov (United States)

    Pan, I-Chun; Tsai, Huei-Hsuan; Cheng, Ya-Tan; Wen, Tuan-Nan; Buckhout, Thomas J; Schmidt, Wolfgang

    2015-10-01

    Acclimation to changing environmental conditions is mediated by proteins, the abundance of which is carefully tuned by an elaborate interplay of DNA-templated and post-transcriptional processes. To dissect the mechanisms that control and mediate cellular iron homeostasis, we conducted quantitative high-resolution iTRAQ proteomics and microarray-based transcriptomic profiling of iron-deficient Arabidopsis thaliana plants. A total of 13,706 and 12,124 proteins was identified with a quadrupole-Orbitrap hybrid mass spectrometer in roots and leaves, respectively. This deep proteomic coverage allowed accurate estimates of post-transcriptional regulation in response to iron deficiency. Similarly regulated transcripts were detected in only 13% (roots) and 11% (leaves) of the 886 proteins that differentially accumulated between iron-sufficient and iron-deficient plants, indicating that the majority of the iron-responsive proteins was post-transcriptionally regulated. Mutants harboring defects in the RING DOMAIN LIGASE1 (RGLG1)(1) and RING DOMAIN LIGASE2 (RGLG2) showed a pleiotropic phenotype that resembled iron-deficient plants with reduced trichome density and the formation of branched root hairs. Proteomic and transcriptomic profiling of rglg1 rglg2 double mutants revealed that the functional RGLG protein is required for the regulation of a large set of iron-responsive proteins including the coordinated expression of ribosomal proteins. This integrative analysis provides a detailed catalog of post-transcriptionally regulated proteins and allows the concept of a chiefly transcriptionally regulated iron deficiency response to be revisited. Protein data are available via ProteomeXchange with identifier PXD002126. PMID:26253232

  18. Overexpression of Grain Amaranth (Amaranthus hypochondriacus) AhERF or AhDOF Transcription Factors in Arabidopsis thaliana Increases Water Deficit- and Salt-Stress Tolerance, Respectively, via Contrasting Stress-Amelioration Mechanisms

    Science.gov (United States)

    Massange-Sánchez, Julio A.; Palmeros-Suárez, Paola A.; Espitia-Rangel, Eduardo; Rodríguez-Arévalo, Isaac; Sánchez-Segura, Lino; Martínez-Gallardo, Norma A.; Alatorre-Cobos, Fulgencio; Tiessen, Axel; Délano-Frier, John P.

    2016-01-01

    Two grain amaranth transcription factor (TF) genes were overexpressed in Arabidopsis plants. The first, coding for a group VII ethylene response factor TF (i.e., AhERF-VII) conferred tolerance to water-deficit stress (WS) in transgenic Arabidopsis without affecting vegetative or reproductive growth. A significantly lower water-loss rate in detached leaves coupled to a reduced stomatal opening in leaves of plants subjected to WS was associated with this trait. WS tolerance was also associated with an increased antioxidant enzyme activity and the accumulation of putative stress-related secondary metabolites. However, microarray and GO data did not indicate an obvious correlation between WS tolerance, stomatal closure, and abscisic acid (ABA)-related signaling. This scenario suggested that stomatal closure during WS in these plants involved ABA-independent mechanisms, possibly involving reactive oxygen species (ROS). WS tolerance may have also involved other protective processes, such as those employed for methyl glyoxal detoxification. The second, coding for a class A and cluster I DNA binding with one finger TF (i.e., AhDof-AI) provided salt-stress (SS) tolerance with no evident fitness penalties. The lack of an obvious development-related phenotype contrasted with microarray and GO data showing an enrichment of categories and genes related to developmental processes, particularly flowering. SS tolerance also correlated with increased superoxide dismutase activity but not with augmented stomatal closure. Additionally, microarray and GO data indicated that, contrary to AhERF-VII, SS tolerance conferred by AhDof-AI in Arabidopsis involved ABA-dependent and ABA-independent stress amelioration mechanisms. PMID:27749893

  19. Transcription profiling by array of Arabidopsis thaliana wild type (Col-0) and flowering time mutants to investigate synchronized induction of flowering

    OpenAIRE

    Valentim, F.L.; Mourik, van, J.A.; Posé, D.; Kim, M.C.; M. Schmid; van der Ham; Busscher, M.; Sanchez-Perez, G.F.; Molenaar, J.; Immink, G.H.; Dijk, van, G.

    2013-01-01

    Synchronized induction of flowering in Arabidopsis thaliana wild type (Col-0) and flowering time mutants (soc1, agl24, fd) by shifting from short day (8 hr light, 16 hr dark; 23C; 65% rel humidity) to long day (16 hr light, 8 hr dark; 23C; 65% rel humidity) for 0, 3, 5, and 7 days. Biotinylated probes were synthesized from RNA isolated from manually disseted shoot meristems and hybridized to Affymetrix ATH1 arrays.

  20. Ethylene Antagonizes Salt-Induced Growth Retardation and Cell Death Process via Transcriptional Controlling of Ethylene-, BAG- and Senescence-Associated Genes in Arabidopsis

    OpenAIRE

    Pan, Ya-Jie; Liu, Ling; Lin, Ying-Chao; Zu, Yuan-Gang; Li, Lei-Peng; Tang, Zhong-Hua

    2016-01-01

    The existing question whether ethylene is involved in the modulation of salt-induced cell death to mediate plant salt tolerance is important for understanding the salt tolerance mechanisms. Here, we employed Arabidopsis plants to study the possible role of ethylene in salt-induced growth inhibition and programmed cell death (PCD) profiles. The root length, DNA ladder and cell death indicated by Evan's blue detection were measured by compared to the control or salt-stressed seedlings. Secondly...

  1. Ethylene antagonizes salt-induced growth retardation and cell death process via transcriptional controlling of ethylene-, BAG- and senescence-associated genes in Arabidopsis

    OpenAIRE

    YaJie ePan; Ling eLiu; YingChao eLin; YuanGang eZu; Zhonghua eTang; LeiPeng eLi

    2016-01-01

    The existing question whether ethylene is involved in the modulation of salt-induced cell death to mediate plant salt tolerance is important for understanding the salt tolerance mechanisms. Here, we employed Arabidopsis plants to study the possible role of ethylene in salt-induced growth inhibition and programmed cell death (PCD) profiles. The root length, DNA ladder and cell death indicated by Evan’s blue detection were measured by compared to the control or salt-stressed seedlings. Secondly...

  2. The functional interplay between protein kinase CK2 and CCA1 transcriptional activity is essential for clock temperature compensation in Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Sergi Portolés

    2010-11-01

    Full Text Available Circadian rhythms are daily biological oscillations driven by an endogenous mechanism known as circadian clock. The protein kinase CK2 is one of the few clock components that is evolutionary conserved among different taxonomic groups. CK2 regulates the stability and nuclear localization of essential clock proteins in mammals, fungi, and insects. Two CK2 regulatory subunits, CKB3 and CKB4, have been also linked with the Arabidopsis thaliana circadian system. However, the biological relevance and the precise mechanisms of CK2 function within the plant clockwork are not known. By using ChIP and Double-ChIP experiments together with in vivo luminescence assays at different temperatures, we were able to identify a temperature-dependent function for CK2 modulating circadian period length. Our study uncovers a previously unpredicted mechanism for CK2 antagonizing the key clock regulator CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1. CK2 activity does not alter protein accumulation or subcellular localization but interferes with CCA1 binding affinity to the promoters of the oscillator genes. High temperatures enhance the CCA1 binding activity, which is precisely counterbalanced by the CK2 opposing function. Altering this balance by over-expression, mutation, or pharmacological inhibition affects the temperature compensation profile, providing a mechanism by which plants regulate circadian period at changing temperatures. Therefore, our study establishes a new model demonstrating that two opposing and temperature-dependent activities (CCA1-CK2 are essential for clock temperature compensation in Arabidopsis.

  3. Arabidopsis HIT4, a regulator involved in heat-triggered reorganization of chromatin and release of transcriptional gene silencing, relocates from chromocenters to the nucleolus in response to heat stress.

    Science.gov (United States)

    Wang, Lian-Chin; Wu, Jia-Rong; Hsu, Yi-Ju; Wu, Shaw-Jye

    2015-01-01

    Arabidopsis HIT4 is known to mediate heat-induced decondensation of chromocenters and release from transcriptional gene silencing (TGS) with no change in the level of DNA methylation. It is unclear whether HIT4 and MOM1, a well-known DNA methylation-independent transcriptional silencer, have overlapping regulatory functions. A hit4-1/mom1 double mutant strain was generated. Its nuclear morphology and TGS state were compared with those of wild-type, hit4-1, and mom1 plants. Fluorescent protein tagging was employed to track the fates of HIT4, hit4-1 and MOM1 in vivo under heat stress. HIT4- and MOM1-mediated TGS were distinguishable. Both HIT4 and MOM1 were localized normally to chromocenters. Under heat stress, HIT4 relocated to the nucleolus, whereas MOM1 dispersed with the chromocenters. hit4-1 was able to relocate to the nucleolus under heat stress, but its relocation was insufficient to trigger the decompaction of chromocenters. The hypersensitivity to heat associated with the impaired reactivation of TGS in hit4-1 was not alleviated by mom1-induced release from TGS. HIT4 delineates a novel and MOM1-independent TGS regulation pathway. The involvement of a currently unidentified component that links HIT4 relocation and the large-scale reorganization of chromatin, and which is essential for heat tolerance in plants is hypothesized.

  4. Physiological, biochemical, and genome-wide transcriptional analysis reveals that elevated CO2 mitigates the impact of combined heat wave and drought stress in Arabidopsis thaliana at multiple organizational levels.

    Science.gov (United States)

    Zinta, Gaurav; AbdElgawad, Hamada; Domagalska, Malgorzata A; Vergauwen, Lucia; Knapen, Dries; Nijs, Ivan; Janssens, Ivan A; Beemster, Gerrit T S; Asard, Han

    2014-12-01

    Climate changes increasingly threaten plant growth and productivity. Such changes are complex and involve multiple environmental factors, including rising CO2 levels and climate extreme events. As the molecular and physiological mechanisms underlying plant responses to realistic future climate extreme conditions are still poorly understood, a multiple organizational level analysis (i.e. eco-physiological, biochemical, and transcriptional) was performed, using Arabidopsis exposed to incremental heat wave and water deficit under ambient and elevated CO2 . The climate extreme resulted in biomass reduction, photosynthesis inhibition, and considerable increases in stress parameters. Photosynthesis was a major target as demonstrated at the physiological and transcriptional levels. In contrast, the climate extreme treatment induced a protective effect on oxidative membrane damage, most likely as a result of strongly increased lipophilic antioxidants and membrane-protecting enzymes. Elevated CO2 significantly mitigated the negative impact of a combined heat and drought, as apparent in biomass reduction, photosynthesis inhibition, chlorophyll fluorescence decline, H2 O2 production, and protein oxidation. Analysis of enzymatic and molecular antioxidants revealed that the stress-mitigating CO2 effect operates through up-regulation of antioxidant defense metabolism, as well as by reduced photorespiration resulting in lowered oxidative pressure. Therefore, exposure to future climate extreme episodes will negatively impact plant growth and production, but elevated CO2 is likely to mitigate this effect.

  5. Conserved cis-regulatory elements for DNA-binding-with-one-finger and homeo-domain-leucine-zipper transcription factors regulate companion cell-specific expression of the Arabidopsis thaliana SUCROSE TRANSPORTER 2 gene.

    Science.gov (United States)

    Schneidereit, Alexander; Imlau, Astrid; Sauer, Norbert

    2008-09-01

    The transition from young carbon-importing sink leaves of higher plants to mature carbon-exporting source leaves is paralleled by a complete reversal of phloem function. While sink-leaf phloem mediates the influx of reduced carbon from older source leaves and the release of this imported carbon to the sink-leaf mesophyll, source-leaf phloem catalyzes the uptake of photoassimilates into companion cells (CCs) and sieve elements (SEs) and the net carbon export from the leaf. Phloem loading in source leaves with sucrose, the main or exclusive transport form for fixed carbon in most higher plants, is catalyzed by plasma membrane-localized sucrose transporters. Consistent with the described physiological switch from sink to source, the promoter of the Arabidopsis AtSUC2 gene is active only in source-leaf CCs of Arabidopsis or of transgenic tobacco (Nicotiana tabacum). For the identification of regulatory elements involved in this companion cell-specific and source-specific gene expression, we performed detailed analyses of the AtSUC2 promoter by truncation and mutagenesis. A 126-bp promoter fragment was identified, which seems to contain these fragments and which drives AtSUC2-typical expression when combined with a 35S minimal promoter. Within this fragment, linker-scanning analyses revealed two cis-regulatory elements that were further characterized as putative binding sites for transcription factors of the DNA-binding-with-one-finger or the homeo-domain-leucine-zipper families. Similar or identical binding sites are found in other genes and in different plant species, suggesting an ancient regulatory mechanism for this important physiological switch. PMID:18551303

  6. The Metabolic Response of Arabidopsis Roots to Oxidative Stress is Distinct from that of Heterotrophic Cells in Culture and Highlights a Complex Relationship between the Levels of Transcripts,Metabolites,and Flux

    Institute of Scientific and Technical Information of China (English)

    Martin Lehmann; Markus Schwarzl(a)inder; Toshihiro Obata; Supaart Sirikantaramas; Meike Burow; Carl Erik Olsen; Takayuki Tohge; Mark D.Fricker; Birger Lindberg Mφller; Alisdair R.Fernie; Lee J.Sweetloveb; Miriam Laxa

    2009-01-01

    Metabolic adjustments are a significant,but poorly understood,part of the response of plants to oxidative stress.In a previous study (Baxter et al.,2007),the metabolic response of Arabidopsis cells in culture to induction of ox-idative stress by menadione was characterized.An emergency survival strategy was uncovered in which anabolic primary metabolism was largely down-regulated in favour of catabolic and antioxidant metabolism.The response in whole plant tissues may be different and we have therefore investigated the response of Arabidopsis roots to menadione treatment,analyzing the transcriptome,metabolome and key metabolic fluxes with focus on primary as well as secondary metab-olism.Using a redox-sensitive GFP,it was also shown that menadione causes redox perturbation,not just in the mitochon-drion,but also in the cytosol and plastids of roots.In the first 30 min of treatment,the response was similar to the cell culture:there was a decrease in metabolites of the TCA cycle and amino acid biosynthesis and the transcriptomic response was dominated by up-regulation of DNA regulatory proteins.After 2 and 6 h of treatment,the response of the roots was different to the cell culture.Metabolite levels did not remain depressed,but instead recovered and,in the case of pyruvate,some amino acids and aliphatic glucosinolates showed a steady increase above control levels.However,no major changes in fluxes of central carbon metabolism were observed and metabolic transcripts changed largely independently of the corresponding metabolites.Together,the results suggest that root tissues can recover metabolic activity after oxidative inhibition and highlight potentially important roles for glycolysis and the oxidative pentose phosphate pathway.

  7. Arabidopsis CDS blastp result: AK243230 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK243230 J100044L04 At1g19850.1 68414.m02490 transcription factor MONOPTEROS (MP) /... auxin-responsive protein (IAA24) / auxin response factor 5 (ARF5) identical to transcription factor MONOPTEROS (MP/IAA24/ARF5) SP:P93024 from [Arabidopsis thaliana] 2e-65 ...

  8. Arabidopsis CDS blastp result: AK103452 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK103452 J033129I11 At1g19850.1 transcription factor MONOPTEROS (MP) / auxin-respon...sive protein (IAA24) / auxin response factor 5 (ARF5) identical to transcription factor MONOPTEROS (MP/IAA24/ARF5) SP:P93024 from [Arabidopsis thaliana] 1e-166 ...

  9. Arabidopsis CDS blastp result: AK318617 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK318617 J100090H20 At1g19850.1 68414.m02490 transcription factor MONOPTEROS (MP) /... auxin-responsive protein (IAA24) / auxin response factor 5 (ARF5) identical to transcription factor MONOPTEROS (MP/IAA24/ARF5) SP:P93024 from [Arabidopsis thaliana] 2e-63 ...

  10. Arabidopsis CDS blastp result: AK243428 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK243428 J100067L15 At5g14750.1 68418.m01731 myb family transcription factor (MYB66) / werewolf...iption factor (MYB66) mRNA, partial cds GI:3941491; identical to GP:9755743 myb transcription factor werewolf (WER)/ MYB66 {Arabidopsis thaliana} 8e-36 ...

  11. Arabidopsis CDS blastp result: AK288699 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK288699 J090061C22 At5g14750.1 68418.m01731 myb family transcription factor (MYB66) / werewolf...iption factor (MYB66) mRNA, partial cds GI:3941491; identical to GP:9755743 myb transcription factor werewolf (WER)/ MYB66 {Arabidopsis thaliana} 8e-36 ...

  12. Arabidopsis CDS blastp result: AK243271 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK243271 J100049K04 At5g14750.1 68418.m01731 myb family transcription factor (MYB66) / werewolf...iption factor (MYB66) mRNA, partial cds GI:3941491; identical to GP:9755743 myb transcription factor werewolf (WER)/ MYB66 {Arabidopsis thaliana} 4e-35 ...

  13. Arabidopsis CDS blastp result: AK241812 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK241812 J065210K15 At5g14750.1 68418.m01731 myb family transcription factor (MYB66) / werewolf...iption factor (MYB66) mRNA, partial cds GI:3941491; identical to GP:9755743 myb transcription factor werewolf (WER)/ MYB66 {Arabidopsis thaliana} 1e-22 ...

  14. Arabidopsis CDS blastp result: AK241549 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK241549 J065176M15 At5g14750.1 68418.m01731 myb family transcription factor (MYB66) / werewolf...iption factor (MYB66) mRNA, partial cds GI:3941491; identical to GP:9755743 myb transcription factor werewolf (WER)/ MYB66 {Arabidopsis thaliana} 3e-32 ...

  15. Arabidopsis CDS blastp result: AK241615 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK241615 J065186D02 At5g14750.1 68418.m01731 myb family transcription factor (MYB66) / werewolf...iption factor (MYB66) mRNA, partial cds GI:3941491; identical to GP:9755743 myb transcription factor werewolf (WER)/ MYB66 {Arabidopsis thaliana} 8e-35 ...

  16. Arabidopsis CDS blastp result: AK288487 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK288487 J090040H24 At5g14750.1 68418.m01731 myb family transcription factor (MYB66) / werewolf...iption factor (MYB66) mRNA, partial cds GI:3941491; identical to GP:9755743 myb transcription factor werewolf (WER)/ MYB66 {Arabidopsis thaliana} 5e-37 ...

  17. Arabidopsis CDS blastp result: AK287469 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK287469 J043021L20 At5g14750.1 68418.m01731 myb family transcription factor (MYB66) / werewolf...iption factor (MYB66) mRNA, partial cds GI:3941491; identical to GP:9755743 myb transcription factor werewolf (WER)/ MYB66 {Arabidopsis thaliana} 2e-36 ...

  18. Arabidopsis CDS blastp result: AK241370 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK241370 J065154C10 At5g14750.1 68418.m01731 myb family transcription factor (MYB66) / werewolf...iption factor (MYB66) mRNA, partial cds GI:3941491; identical to GP:9755743 myb transcription factor werewolf (WER)/ MYB66 {Arabidopsis thaliana} 2e-31 ...

  19. Arabidopsis CDS blastp result: AK288415 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK288415 J090031E07 At5g14750.1 68418.m01731 myb family transcription factor (MYB66) / werewolf...iption factor (MYB66) mRNA, partial cds GI:3941491; identical to GP:9755743 myb transcription factor werewolf (WER)/ MYB66 {Arabidopsis thaliana} 3e-37 ...

  20. AtCCR4a and AtCCR4b are Involved in Determining the Poly(A) Length of Granule-bound starch synthase 1 Transcript and Modulating Sucrose and Starch Metabolism in Arabidopsis thaliana.

    Science.gov (United States)

    Suzuki, Yuya; Arae, Toshihiro; Green, Pamela J; Yamaguchi, Junji; Chiba, Yukako

    2015-05-01

    Removing the poly(A) tail is the first and rate-limiting step of mRNA degradation and apparently an effective step not only for modulating mRNA stability but also for translation of many eukaryotic transcripts. Carbon catabolite repressor 4 (CCR4) has been identified as a major cytoplasmic deadenylase in Saccharomyces cerevisiae. The Arabidopsis thaliana homologs of the yeast CCR4, AtCCR4a and AtCCR4b, were identified by sequence-based analysis; however, their role and physiological significance in plants remain to be elucidated. In this study, we revealed that AtCCR4a and AtCCR4b are localized to cytoplasmic mRNA processing bodies, which are specific granules consisting of many enzymes involved in mRNA turnover. Double mutants of AtCCR4a and AtCCR4b exhibited tolerance to sucrose application but not to glucose. The levels of sucrose in the seedlings of the atccr4a/4b double mutants were reduced, whereas no difference was observed in glucose levels. Further, amylose levels were slightly but significantly increased in the atccr4a/4b double mutants. Consistent with this observation, we found that the transcript encoding granule-bound starch synthase 1 (GBSS1), which is responsible for amylose synthesis, is accumulated to a higher level in the atccr4a/4b double mutant plants than in the control plants. Moreover, we revealed that GBSS1 has a longer poly(A) tail in the double mutant than in the control plant, suggesting that AtCCR4a and AtCCR4b can influence the poly(A) length of transcripts related to starch metabolism. Our results collectively suggested that AtCCR4a and AtCCR4b are involved in sucrose and starch metabolism in A. thaliana.

  1. Bioinformatic cis-element analyses performed in Arabidopsis and rice disclose bZIP- and MYB-related binding sites as potential AuxRE-coupling elements in auxin-mediated transcription

    Directory of Open Access Journals (Sweden)

    Berendzen Kenneth W

    2012-08-01

    Full Text Available Abstract Background In higher plants, a diverse array of developmental and growth-related processes is regulated by the plant hormone auxin. Recent publications have proposed that besides the well-characterized Auxin Response Factors (ARFs that bind Auxin Response Elements (AuxREs, also members of the bZIP- and MYB-transcription factor (TF families participate in transcriptional control of auxin-regulated genes via bZIP Response Elements (ZREs or Myb Response Elements (MREs, respectively. Results Applying a novel bioinformatic algorithm, we demonstrate on a genome-wide scale that singular motifs or composite modules of AuxREs, ZREs, MREs but also of MYC2 related elements are significantly enriched in promoters of auxin-inducible genes. Despite considerable, species-specific differences in the genome structure in terms of the GC content, this enrichment is generally conserved in dicot (Arabidopsis thaliana and monocot (Oryza sativa model plants. Moreover, an enrichment of defined composite modules has been observed in selected auxin-related gene families. Consistently, a bipartite module, which encompasses a bZIP-associated G-box Related Element (GRE and an AuxRE motif, has been found to be highly enriched. Making use of transient reporter studies in protoplasts, these findings were experimentally confirmed, demonstrating that GREs functionally interact with AuxREs in regulating auxin-mediated transcription. Conclusions Using genome-wide bioinformatic analyses, evolutionary conserved motifs have been defined which potentially function as AuxRE-dependent coupling elements to establish auxin-specific expression patterns. Based on these findings, experimental approaches can be designed to broaden our understanding of combinatorial, auxin-controlled gene regulation.

  2. A single amino acid substitution in IIIf subfamily of basic helix-loop-helix transcription factor AtMYC1 leads to trichome and root hair patterning defects by abolishing its interaction with partner proteins in Arabidopsis.

    Science.gov (United States)

    Zhao, Hongtao; Wang, Xiaoxue; Zhu, Dandan; Cui, Sujuan; Li, Xia; Cao, Ying; Ma, Ligeng

    2012-04-20

    Plant trichomes and root hairs are powerful models for the study of cell fate determination. In Arabidopsis thaliana, trichome and root hair initiation requires a combination of three groups of proteins, including the WD40 repeat protein transparent TESTA GLABRA1 (TTG1), R2R3 repeat MYB protein GLABRA1 (GL1), or werewolf (WER) and the IIIf subfamily of basic helix-loop-helix (bHLH) protein GLABRA3 (GL3) or enhancer of GLABRA3 (EGL3). The bHLH component acts as a docking site for TTG1 and MYB proteins. Here, we isolated a mutant showing defects in trichome and root hair patterning that carried a point mutation (R173H) in AtMYC1 that encodes the fourth member of IIIf bHLH family protein. Genetic analysis revealed partial redundant yet distinct function between AtMYC1 and GL3/EGL3. GLABRA2 (GL2), an important transcription factor involved in trichome and root hair control, was down-regulated in Atmyc1 plants, suggesting the requirement of AtMYC1 for appropriate GL2 transcription. Like its homologs, AtMYC1 formed a complex with TTG1 and MYB proteins but did not dimerized. In addition, the interaction of AtMYC1 with MYB proteins and TTG1 was abrogated by the R173H substitution in Atmyc1-1. We found that this amino acid (Arg) is conserved in the AtMYC1 homologs GL3/EGL3 and that it is essential for their interaction with MYB proteins and for their proper functions. Our findings indicate that AtMYC1 is an important regulator of trichome and root hair initiation, and they reveal a novel amino acid necessary for protein-protein interactions and gene function in IIIf subfamily bHLH transcription factors.

  3. MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for arabidopsis lateral root development.

    Science.gov (United States)

    Guo, Hui-Shan; Xie, Qi; Fei, Ji-Feng; Chua, Nam-Hai

    2005-05-01

    Although several plant microRNAs (miRNAs) have been shown to play a role in plant development, no phenotype has yet been associated with a reduction or loss of expression of any plant miRNA. Arabidopsis thaliana miR164 was predicted to target five NAM/ATAF/CUC (NAC) domain-encoding mRNAs, including NAC1, which transduces auxin signals for lateral root emergence. Here, we show that miR164 guides the cleavage of endogenous and transgenic NAC1 mRNA, producing 3'-specific fragments. Cleavage was blocked by NAC1 mutations that disrupt base pairing with miR164. Compared with wild-type plants, Arabidopsis mir164a and mir164b mutant plants expressed less miR164 and more NAC1 mRNA and produced more lateral roots. These mutant phenotypes can be complemented by expression of the appropriate MIR164a and MIR164b genomic sequences. By contrast, inducible expression of miR164 in wild-type plants led to decreased NAC1 mRNA levels and reduced lateral root emergence. Auxin induction of miR164 was mirrored by an increase in the NAC1 mRNA 3' fragment, which was not observed in the auxin-insensitive mutants auxin resistant1 (axr1-12), axr2-1, and transport inhibitor response1. Moreover, the cleavage-resistant form of NAC1 mRNA was unaffected by auxin treatment. Our results indicate that auxin induction of miR164 provides a homeostatic mechanism to clear NAC1 mRNA to downregulate auxin signals.

  4. Changing a conserved amino acid in R2R3-MYB transcription repressors results in cytoplasmic accumulation and abolishes their repressive activity in Arabidopsis.

    Science.gov (United States)

    Zhou, Meiliang; Sun, Zhanmin; Wang, Chenglong; Zhang, Xinquan; Tang, Yixiong; Zhu, Xuemei; Shao, Jirong; Wu, Yanmin

    2015-10-01

    Sub-group 4 R2R3-type MYB transcription factors, including MYB3, MYB4, MYB7 and MYB32, act as repressors in phenylpropanoid metabolism. These proteins contain the conserved MYB domain and the ethylene-responsive element binding factor-associated amphiphilic repression (EAR) repression domain. Additionally, MYB4, MYB7 and MYB32 possess a putative zinc-finger domain and a conserved GY/FDFLGL motif in their C-termini. The protein 'sensitive to ABA and drought 2' (SAD2) recognizes the nuclear pore complex, which then transports the SAD2-MYB4 complex into the nucleus. Here, we show that the conserved GY/FDFLGL motif contributes to the interaction between MYB factors and SAD2. The Asp → Asn mutation in the GY/FDFLGL motif abolishes the interaction between MYB transcription factors and SAD2, and therefore they cannot be transported into the nucleus and cannot repress their target genes. We found that MYB4(D261N) loses the capacity to repress expression of the cinnamate 4-hydroxylase (C4H) gene and biosynthesis of sinapoyl malate. Our results indicate conservation among MYB transcription factors in terms of their interaction with SAD2. Therefore, the Asp → Asn mutation may be used to engineer transcription factors. PMID:26332741

  5. Terpene Specialized Metabolism in Arabidopsis thaliana

    OpenAIRE

    Tholl, Dorothea; Lee, Sungbeom

    2011-01-01

    Terpenes constitute the largest class of plant secondary (or specialized) metabolites, which are compounds of ecological function in plant defense or the attraction of beneficial organisms. Using biochemical and genetic approaches, nearly all Arabidopsis thaliana (Arabidopsis) enzymes of the core biosynthetic pathways producing the 5-carbon building blocks of terpenes have been characterized and closer insight has been gained into the transcriptional and posttranscriptional/translational mech...

  6. Identification of a novel type of WRKY transcription factor binding site in elicitor-responsive cis-sequences from Arabidopsis thaliana.

    Science.gov (United States)

    Machens, Fabian; Becker, Marlies; Umrath, Felix; Hehl, Reinhard

    2014-03-01

    Using a combination of bioinformatics and synthetic promoters, novel elicitor-responsive cis-sequences were discovered in promoters of pathogen-upregulated genes from Arabidopsis thaliana. One group of functional sequences contains the conserved core sequence GACTTTT. This core sequence and adjacent nucleotides are essential for elicitor-responsive gene expression in a parsley protoplast system. By yeast one-hybrid screening, WRKY70 was selected with a cis-sequence harbouring the core sequence GACTTTT but no known WRKY binding site (W-box). Transactivation experiments, mutation analyses, and electrophoretic mobility shift assays demonstrate that the sequence CGACTTTT is the binding site for WRKY70 in the investigated cis-sequence and is required for WRKY70-activated gene expression. Using several cis-sequences in transactivation experiments and binding studies, the CGACTTTT sequence can be extended to propose YGACTTTT as WRKY70 binding site. This binding site, designated WT-box, is enriched in promoters of genes upregulated in a WRKY70 overexpressing line. Interestingly, functional WRKY70 binding sites are present in the promoter of WRKY30, supporting recent evidence that both factors play a role in the same regulatory network. PMID:24104863

  7. Transcriptome and metabolome analysis of plant sulphate starvation and resupply provides novel information on transcriptional regulation of metabolism associated with sulphur, nitrogen and phosphorus nutritional responses in Arabidopsis.

    OpenAIRE

    Monika eBielecka; Mutsumi eWatanabe; Wolf Rüdiger Scheible; Rosa eMorcuende; Malcolm John Hawkesford; Holger eHesse; Rainer eHoefgen

    2015-01-01

    Sulphur is an essential macronutrient for plant growth and development. Reaching a thorough understanding of the molecular basis for changes in plant metabolism depending on the sulphur-nutritional status at the systems level will advance our basic knowledge and help target future crop improvement. Although the transcriptional responses induced by sulphate starvation have been studied in the past, knowledge of the regulation of sulphur metabolism is still fragmentary. This work focuses on the...

  8. Transcriptome and metabolome analysis of plant sulfate starvation and resupply provides novel information on transcriptional regulation of metabolism associated with sulfur, nitrogen and phosphorus nutritional responses in Arabidopsis

    OpenAIRE

    Bielecka, Monika; Watanabe, Mutsumi; Morcuende, Rosa; Scheible, Wolf-Rüdiger; Hawkesford, Malcolm J.; Hesse, Holger; Hoefgen, Rainer

    2015-01-01

    Sulfur is an essential macronutrient for plant growth and development. Reaching a thorough understanding of the molecular basis for changes in plant metabolism depending on the sulfur-nutritional status at the systems level will advance our basic knowledge and help target future crop improvement. Although the transcriptional responses induced by sulfate starvation have been studied in the past, knowledge of the regulation of sulfur metabolism is still fragmentary. This work focuses on the dis...

  9. Transcriptome and metabolome analysis of plant sulphate starvation and resupply provides novel information on transcriptional regulation of metabolism associated with sulphur, nitrogen and phosphorus nutritional responses in Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Monika eBielecka

    2015-01-01

    Full Text Available Sulphur is an essential macronutrient for plant growth and development. Reaching a thorough understanding of the molecular basis for changes in plant metabolism depending on the sulphur-nutritional status at the systems level will advance our basic knowledge and help target future crop improvement. Although the transcriptional responses induced by sulphate starvation have been studied in the past, knowledge of the regulation of sulphur metabolism is still fragmentary. This work focuses on the discovery of candidates for regulatory genes such as transcription factors (TFs using ‘omics technologies. For this purpose a short term sulphate-starvation / re-supply approach was used. ATH1 microarray studies and metabolite determinations yielded 21 TFs which responded more than 2-fold at the transcriptional level to sulphate starvation. Categorization by response behaviors under sulphate-starvation / re-supply and other nutrient starvations such as nitrate and phosphate allowed determination of whether the TF genes are specific for or common between distinct mineral nutrient depletions. Extending this co-behavior analysis to the whole transcriptome data set enabled prediction of putative downstream genes. Additionally, combinations of transcriptome and metabolome data allowed identification of relationships between TFs and downstream responses, namely, expression changes in biosynthetic genes and subsequent metabolic responses. Effect chains on glucosinolate and polyamine biosynthesis are discussed in detail. The knowledge gained from this study provides a blueprint for an integrated analysis of transcriptomics and metabolomics and application for the identification of uncharacterized genes.

  10. Reactive oxygen species and transcript analysis upon excess light treatment in wild-type Arabidopsis thaliana vs a photosensitive mutant lacking zeaxanthin and lutein

    Directory of Open Access Journals (Sweden)

    Roncaglia Enrica

    2011-04-01

    Full Text Available Abstract Background Reactive oxygen species (ROS are unavoidable by-products of oxygenic photosynthesis, causing progressive oxidative damage and ultimately cell death. Despite their destructive activity they are also signalling molecules, priming the acclimatory response to stress stimuli. Results To investigate this role further, we exposed wild type Arabidopsis thaliana plants and the double mutant npq1lut2 to excess light. The mutant does not produce the xanthophylls lutein and zeaxanthin, whose key roles include ROS scavenging and prevention of ROS synthesis. Biochemical analysis revealed that singlet oxygen (1O2 accumulated to higher levels in the mutant while other ROS were unaffected, allowing to define the transcriptomic signature of the acclimatory response mediated by 1O2 which is enhanced by the lack of these xanthophylls species. The group of genes differentially regulated in npq1lut2 is enriched in sequences encoding chloroplast proteins involved in cell protection against the damaging effect of ROS. Among the early fine-tuned components, are proteins involved in tetrapyrrole biosynthesis, chlorophyll catabolism, protein import, folding and turnover, synthesis and membrane insertion of photosynthetic subunits. Up to now, the flu mutant was the only biological system adopted to define the regulation of gene expression by 1O2. In this work, we propose the use of mutants accumulating 1O2 by mechanisms different from those activated in flu to better identify ROS signalling. Conclusions We propose that the lack of zeaxanthin and lutein leads to 1O2 accumulation and this represents a signalling pathway in the early stages of stress acclimation, beside the response to ADP/ATP ratio and to the redox state of both plastoquinone pool. Chloroplasts respond to 1O2 accumulation by undergoing a significant change in composition and function towards a fast acclimatory response. The physiological implications of this signalling specificity are

  11. Comparative analysis of drought resistance genes in Arabidopsis and rice

    NARCIS (Netherlands)

    Trijatmiko, K.R.

    2005-01-01

    Keywords: rice, Arabidopsis, drought, genetic mapping,microarray, transcription factor, AP2/ERF, SHINE, wax, stomata, comparative genetics, activation tagging, Ac/Ds, En/IThis thesis describes the use of genomics information and tools from Arabidopsis and

  12. Transcriptional profiling of an Fd-GOGAT1/GLU1 mutant in Arabidopsis thaliana reveals a multiple stress response and extensive reprogramming of the transcriptome

    Directory of Open Access Journals (Sweden)

    Størseth Trond R

    2010-03-01

    Full Text Available Abstract Background Glutamate plays a central position in the synthesis of a variety of organic molecules in plants and is synthesised from nitrate through a series of enzymatic reactions. Glutamate synthases catalyse the last step in this pathway and two types are present in plants: NADH- or ferredoxin-dependent. Here we report a genome wide microarray analysis of the transcriptional reprogramming that occurs in leaves and roots of the A. thaliana mutant glu1-2 knocked-down in the expression of Fd-GOGAT1 (GLU1; At5g04140, one of the two genes of A. thaliana encoding ferredoxin-dependent glutamate synthase. Results Transcriptional profiling of glu1-2 revealed extensive changes with the expression of more than 5500 genes significantly affected in leaves and nearly 700 in roots. Both genes involved in glutamate biosynthesis and transformation are affected, leading to changes in amino acid compositions as revealed by NMR metabolome analysis. An elevated glutamine level in the glu1-2 mutant was the most prominent of these changes. An unbiased analysis of the gene expression datasets allowed us to identify the pathways that constitute the secondary response of an FdGOGAT1/GLU1 knock-down. Among the most significantly affected pathways, photosynthesis, photorespiratory cycle and chlorophyll biosynthesis show an overall downregulation in glu1-2 leaves. This is in accordance with their slight chlorotic phenotype. Another characteristic of the glu1-2 transcriptional profile is the activation of multiple stress responses, mimicking cold, heat, drought and oxidative stress. The change in expression of genes involved in flavonoid biosynthesis is also revealed. The expression of a substantial number of genes encoding stress-related transcription factors, cytochrome P450 monooxygenases, glutathione S-transferases and UDP-glycosyltransferases is affected in the glu1-2 mutant. This may indicate an induction of the detoxification of secondary metabolites in the

  13. STIFDB2: An Updated Version of Plant Stress-Responsive TranscrIption Factor DataBase with Additional Stress Signals, Stress-Responsive Transcription Factor Binding Sites and Stress-Responsive Genes in Arabidopsis and Rice

    OpenAIRE

    Naika, Mahantesha; Shameer, Khader; Mathew, Oommen K; Gowda, Ramanjini; Sowdhamini, Ramanathan

    2013-01-01

    Understanding the principles of abiotic and biotic stress responses, tolerance and adaptation remains important in plant physiology research to develop better varieties of crop plants. Better understanding of plant stress response mechanisms and application of knowledge derived from integrated experimental and bioinformatics approaches are gaining importance. Earlier, we showed that compiling a database of stress-responsive transcription factors and their corresponding target binding sites in...

  14. Transcription factor WRKY46 modulates the development of Arabidopsis lateral roots in osmotic/salt stress conditions via regulation of ABA signaling and auxin homeostasis.

    Science.gov (United States)

    Ding, Zhong Jie; Yan, Jing Ying; Li, Chun Xiao; Li, Gui Xin; Wu, Yun Rong; Zheng, Shao Jian

    2015-10-01

    The development of lateral roots (LR) is known to be severely inhibited by salt or osmotic stress. However, the molecular mechanisms underlying LR development in osmotic/salt stress conditions are poorly understood. Here we show that the gene encoding the WRKY transcription factor WRKY46 (WRKY46) is expressed throughout lateral root primordia (LRP) during early LR development and that expression is subsequently restricted to the stele of the mature LR. In osmotic/salt stress conditions, lack of WRKY46 (in loss-of-function wrky46 mutants) significantly reduces, while overexpression of WRKY46 enhances, LR development. We also show that exogenous auxin largely restores LR development in wrky46 mutants, and that the auxin transport inhibitor 2,3,5-triiodobenzoic acid (TIBA) inhibits LR development in both wild-type (WT; Col-0) and in a line overexpressing WRKY46 (OV46). Subsequent analysis of abscisic acid (ABA)-related mutants indicated that WRKY46 expression is down-regulated by ABA signaling, and up-regulated by an ABA-independent signal induced by osmotic/salt stress. Next, we show that expression of the DR5:GUS auxin response reporter is reduced in roots of wrky46 mutants, and that both wrky46 mutants and OV46 display altered root levels of free indole-3-acetic acid (IAA) and IAA conjugates. Subsequent RT-qPCR and ChIP-qPCR experiments indicated that WRKY46 directly regulates the expression of ABI4 and of genes regulating auxin conjugation. Finally, analysis of wrky46 abi4 double mutant plants confirms that ABI4 acts downstream of WRKY46. In summary, our results demonstrate that WRKY46 contributes to the feedforward inhibition of osmotic/salt stress-dependent LR inhibition via regulation of ABA signaling and auxin homeostasis.

  15. Arabidopsis CDS blastp result: AK287576 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK287576 J065037D19 At1g28300.1 68414.m03473 transcriptional factor B3 family protein / leaf...y cotyledon 2 (LEC2) nearly identical to LEAFY COTYLEDON 2 [Arabidopsis thaliana] GI:15987516; contains Pfam profile PF02362: B3 DNA binding domain 5e-13 ...

  16. Prokaryotic expression and inclusion body renaturation of the plant transcriptional factor Arabidopsis thaliana AGL47%拟南芥转录因子AGL47的原核表达与包涵体复性研究

    Institute of Scientific and Technical Information of China (English)

    乔帅; 王明凤; 杨文博; 许君; 郑文明

    2011-01-01

    AGL47 is a transcription factor coded by the At5g55690 gene on the fifth chromosome of Arabidopsis thaliana, belonging to MADS-box protein family. At5g55690 gene was reported to be upregulated by limited inorganic phosphate stress and may play an important role in plant phosphorus metabolism. To identify its function, At5g55690 gene' s full-length CDS was cloned to construct recombinant plasmid pET-28a-At5g55690. pET-28a-At5g55690 was then transformed into E. Coli BL21 ( DE3) cells to perform prokaryotic expression. AGL47 protein was obtained by induction of 1 mmol· L-1 IPTG but found to be in form of inclusion bodies. AGL47 soluble protein was isolated from purified inclusion bodies after denaturation with urea and renaturarion with dialysis.%AGL47是拟南芥第五染色体上AtSg55690基因编码的1个转录因子,属于MADS-box蛋白质家族,前期研究显示,At5g55690基因受磷胁迫特异诱导表达,极有可能在磷代谢调控中发挥重要的作用.为了进一步鉴定该基因的功能,本研究克隆At5g55690基因全长ORF,构建重组表达载体pPET-28a-At5g55690,转入表达宿主菌E.coli BL21( DE3),在1 mmol· L-1 IPTG诱导下,成功实现了AGL47蛋白的原核表达.可溶性鉴定结果显示,融合蛋白以包涵体的形式存在.对包涵体进行纯化,变性和复性后获得了可溶性目的蛋白.

  17. Transcriptional networks of TCP transcription factors in Arabidopsis development

    NARCIS (Netherlands)

    Danisman, S.D.

    2011-01-01

    Leaves are a plant’s main organs of photosynthesis and hence the development of this organ is under strict control. The different phases of leaf development are under the control of both endogenous and exogenous influences. In this work we were interested in a particular class of

  18. 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.

  19. Transcriptional and post-transcriptional regulation of a NAC1 transcription factor in Medicago truncatula roots.

    Science.gov (United States)

    D'haeseleer, Katrien; Den Herder, Griet; Laffont, Carole; Plet, Julie; Mortier, Virginie; Lelandais-Brière, Christine; De Bodt, Stefanie; De Keyser, Annick; Crespi, Martin; Holsters, Marcelle; Frugier, Florian; Goormachtig, Sofie

    2011-08-01

    • Legume roots develop two types of lateral organs, lateral roots and nodules. Nodules develop as a result of a symbiotic interaction with rhizobia and provide a niche for the bacteria to fix atmospheric nitrogen for the plant. • The Arabidopsis NAC1 transcription factor is involved in lateral root formation, and is regulated post-transcriptionally by miRNA164 and by SINAT5-dependent ubiquitination. We analyzed in Medicago truncatula the role of the closest NAC1 homolog in lateral root formation and in nodulation. • MtNAC1 shows a different expression pattern in response to auxin than its Arabidopsis homolog and no changes in lateral root number or nodulation were observed in plants affected in MtNAC1 expression. In addition, no interaction was found with SINA E3 ligases, suggesting that post-translational regulation of MtNAC1 does not occur in M. truncatula. Similar to what was found in Arabidopsis, a conserved miR164 target site was retrieved in MtNAC1, which reduced protein accumulation of a GFP-miR164 sensor. Furthermore, miR164 and MtNAC1 show an overlapping expression pattern in symbiotic nodules, and overexpression of this miRNA led to a reduction in nodule number. • This work suggests that regulatory pathways controlling a conserved transcription factor are complex and divergent between M. truncatula and Arabidopsis.

  20. Arabidopsis CDS blastp result: AK101133 [KOME

    Lifescience Database Archive (English)

    Full Text Available F|00847 AP2 domain; identical to cDNA enhancer of shoot regeneration ESR1 GI:18028939, enhancer of shoot regeneration ESR1 [Arabidopsis thaliana] GI:18028940 1e-10 ... ...eneration (ESR1) similar to gb|D38124 EREBP-3 from Nicotiana tabacum and contains P...AK101133 J033026F23 At1g12980.1 AP2 domain-containing transcription factor, putative / enhancer of shoot reg

  1. Arabidopsis CDS blastp result: AK119645 [KOME

    Lifescience Database Archive (English)

    Full Text Available PF|00847 AP2 domain; identical to cDNA enhancer of shoot regeneration ESR1 GI:18028939, enhancer of shoot regeneration ESR1 [Arabidopsis thaliana] GI:18028940 1e-10 ... ...ve / enhancer of shoot regeneration (ESR1) similar to gb|D38124 EREBP-3 from Nicotiana tabacum and contains ...AK119645 002-130-G05 At1g12980.1 AP2 domain-containing transcription factor, putati

  2. Analyzing Synthetic Promoters Using Arabidopsis Protoplasts.

    Science.gov (United States)

    Stracke, Ralf; Thiedig, Katharina; Kuhlmann, Melanie; Weisshaar, Bernd

    2016-01-01

    This chapter describes a transient protoplast co-transfection method that can be used to quantitatively study in vivo the activity and function of promoters and promoter elements (reporters), and their induction or repression by transcription factors (effectors), stresses, hormones, or metabolites. A detailed protocol for carrying out transient co-transfection assays with Arabidopsis At7 protoplasts and calculating the promoter activity is provided. PMID:27557761

  3. CAMTA 1 regulates drought responses in Arabidopsis thaliana

    OpenAIRE

    Pandey, Neha; Ranjan, Alok; Pant, Poonam; Tripathi, Rajiv K; Ateek, Farha; Pandey, Haushilla P; Patre, Uday V; Sawant, Samir V

    2013-01-01

    Background Transcription factors (TF) play a crucial role in regulating gene expression and are fit to regulate diverse cellular processes by interacting with other proteins. A TF named calmodulin binding transcription activator (CAMTA) was identified in Arabidopsis thaliana (AtCAMTA1-6). To explore the role of CAMTA1 in drought response, the phenotypic differences and gene expression was studied between camta1 and Col-0 under drought condition. Results In camta1, root development was abolish...

  4. NAC transcription factors in senescence

    DEFF Research Database (Denmark)

    Podzimska-Sroka, Dagmara; O'Shea, Charlotte; Gregersen, Per L.;

    2015-01-01

    Within the last decade, NAC transcription factors have been shown to play essential roles in senescence, which is the focus of this review. Transcriptome analyses associate approximately one third of Arabidopsis NAC genes and many crop NAC genes with senescence, thereby implicating NAC genes...... as important regulators of the senescence process. The consensus DNA binding site of the NAC domain is used to predict NAC target genes, and protein interaction sites can be predicted for the intrinsically disordered transcription regulatory domains of NAC proteins. The molecular characteristics...

  5. Regulation of Arabidopsis thaliana Em genes : role of AB15

    NARCIS (Netherlands)

    Carles, C.; Bies-Etheve, N.; Aspart, L.; Léon-Kloosterziel, K.M.; Koornneef, M.; Echeverria, M.; Delseny, M.

    2002-01-01

    In order to identify new factors involved in Em (a class I Late Embryogenesis Abundant protein) gene expression, Arabidopsis mutants with an altered expression of an Em promoter GUS fusion construct and a modified accumulation of Em transcripts and proteins were isolated. Germination tests on ABA sh

  6. AthaMap, integrating transcriptional and post-transcriptional data.

    Science.gov (United States)

    Bülow, Lorenz; Engelmann, Stefan; Schindler, Martin; Hehl, Reinhard

    2009-01-01

    The AthaMap database generates a map of predicted transcription factor binding sites (TFBS) for the whole Arabidopsis thaliana genome. AthaMap has now been extended to include data on post-transcriptional regulation. A total of 403,173 genomic positions of small RNAs have been mapped in the A. thaliana genome. These identify 5772 putative post-transcriptionally regulated target genes. AthaMap tools have been modified to improve the identification of common TFBS in co-regulated genes by subtracting post-transcriptionally regulated genes from such analyses. Furthermore, AthaMap was updated to the TAIR7 genome annotation, a graphic display of gene analysis results was implemented, and the TFBS data content was increased. AthaMap is freely available at http://www.athamap.de/. PMID:18842622

  7. Histone Deacetylase Genes in Arabidopsis Development

    Institute of Scientific and Technical Information of China (English)

    Courtney Hollender; Zhongchi Liu

    2008-01-01

    Histone acetylatlon and deacetylation are directly connected with transcriptional activation and silencing in eukaryotas.Gene families for enzymes that accomplish these histone modifications show surprising complexity in domain organization,tissue-specific expression, and function. This review is focused on the family of histone deacetylases (HDACs) that remove the acetyl group from core histone tails, resulting in a "closed" chromatin and transcriptional repression. In Arabidopsis,18 HDAC genes are divided in to three different types - RPD3-1ike, HD-tuin and sirtuin - with two or more members ineach type. The structural feature of each HDAC class, the expression profile of each HDAC gene during development and functional insights of important family members are summarized here. It is clear that HDACs are an important class of global transcriptional regulators that play crucial roles in plant development, defense, and adaptation.

  8. The arabidopsis cyclic nucleotide interactome

    KAUST Repository

    Donaldson, Lara

    2016-05-11

    Background Cyclic nucleotides have been shown to play important signaling roles in many physiological processes in plants including photosynthesis and defence. Despite this, little is known about cyclic nucleotide-dependent signaling mechanisms in plants since the downstream target proteins remain unknown. This is largely due to the fact that bioinformatics searches fail to identify plant homologs of protein kinases and phosphodiesterases that are the main targets of cyclic nucleotides in animals. Methods An affinity purification technique was used to identify cyclic nucleotide binding proteins in Arabidopsis thaliana. The identified proteins were subjected to a computational analysis that included a sequence, transcriptional co-expression and functional annotation analysis in order to assess their potential role in plant cyclic nucleotide signaling. Results A total of twelve cyclic nucleotide binding proteins were identified experimentally including key enzymes in the Calvin cycle and photorespiration pathway. Importantly, eight of the twelve proteins were shown to contain putative cyclic nucleotide binding domains. Moreover, the identified proteins are post-translationally modified by nitric oxide, transcriptionally co-expressed and annotated to function in hydrogen peroxide signaling and the defence response. The activity of one of these proteins, GLYGOLATE OXIDASE 1, a photorespiratory enzyme that produces hydrogen peroxide in response to Pseudomonas, was shown to be repressed by a combination of cGMP and nitric oxide treatment. Conclusions We propose that the identified proteins function together as points of cross-talk between cyclic nucleotide, nitric oxide and reactive oxygen species signaling during the defence response.

  9. The conserved splicing factor SUA controls alternative splicing of the developmental regulator ABI3 in Arabidopsis.

    NARCIS (Netherlands)

    Sugliani, M.; Brambilla, V.; Clerkx, E.J.M.; Koornneef, M.; Soppe, W.J.J.

    2010-01-01

    ABSCISIC ACID INSENSITIVE3 (ABI3) is a major regulator of seed maturation in Arabidopsis thaliana. We detected two ABI3 transcripts, ABI3- and ABI3-ß, which encode full-length and truncated proteins, respectively. Alternative splicing of ABI3 is developmentally regulated, and the ABI3-ß transcript a

  10. SAGE ANALYSIS OF TRANSCRIPTOME RESPONSES IN ARABIDOPSIS ROOTS EXPOSED TO 2,4,6-TRINITROTOLUENE

    Science.gov (United States)

    Serial Analysis of Gene Expression (SAGE) was used to profile transcript levels in Arabidopsis thaliana roots and assess their responses to 2,4,6-trinitrotoluene (TNT) exposure. SAGE libraries representing control and TNT-exposed seedling root transcripts were constructed, and ea...

  11. MASSUGU2 encodes Aux/IAA19, an auxin-regulated protein that functions together with the transcriptional activator NPH4/ARF7 to regulate differential growth responses of hypocotyl and formation of lateral roots in Arabidopsis thaliana.

    Science.gov (United States)

    Tatematsu, Kiyoshi; Kumagai, Satoshi; Muto, Hideki; Sato, Atsuko; Watahiki, Masaaki K; Harper, Reneé M; Liscum, Emmanuel; Yamamoto, Kotaro T

    2004-02-01

    We have isolated a dominant, auxin-insensitive mutant of Arabidopsis thaliana, massugu2 (msg2), that displays neither hypocotyl gravitropism nor phototropism, fails to maintain an apical hook as an etiolated seedling, and is defective in lateral root formation. Yet other aspects of growth and development of msg2 plants are almost normal. These characteristics of msg2 are similar to those of another auxin-insensitive mutant, non-phototropic hypocotyl4 (nph4), which is a loss-of-function mutant of AUXIN RESPONSE FACTOR7 (ARF7) (Harper et al., 2000). Map-based cloning of the MSG2 locus reveals that all four mutant alleles result in amino acid substitutions in the conserved domain II of an Auxin/Indole-3-Acetic Acid protein, IAA19. Interestingly, auxin inducibility of MSG2/IAA19 gene expression is reduced by 65% in nph4/arf7. Moreover, MSG2/IAA19 protein binds to the C-terminal domain of NPH4/ARF7 in a Saccharomyces cerevisiae (yeast) two-hybrid assay and to the whole latter protein in vitro by pull-down assay. These results suggest that MSG2/IAA19 and NPH4/ARF7 may constitute a negative feedback loop to regulate differential growth responses of hypocotyls and lateral root formation.

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

    OpenAIRE

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

    2013-01-01

    ML (MD2-related lipid recognition) proteins are known to enhance innate immune responses in mammals. This study reports the analysis of the putative ML gene family in Arabidopsis thaliana and suggests a role for the ML3 gene in herbivory-associated responses in plants. Feeding by larvae of the Lepidopteran generalist herbivore Spodoptera littoralis and larvae of the specialist herbivore Plutella xylostella activated ML3 transcription in leaf tissues. ML3 loss-of-function Arabidopsis plants we...

  13. Multisite light-induced phosphorylation of the transcription factor PIF3 is necessary for both its rapid degradation and concomitant negative feedback modulation of photoreceptor phyB levels in Arabidopsis.

    Science.gov (United States)

    Ni, Weimin; Xu, Shou-Ling; Chalkley, Robert J; Pham, Thao Nguyen D; Guan, Shenheng; Maltby, Dave A; Burlingame, Alma L; Wang, Zhi-Yong; Quail, Peter H

    2013-07-01

    Plants constantly monitor informational light signals using sensory photoreceptors, which include the phytochrome (phy) family (phyA to phyE), and adjust their growth and development accordingly. Following light-induced nuclear translocation, photoactivated phy molecules bind to and induce rapid phosphorylation and degradation of phy-interacting basic Helix Loop Helix (bHLH) transcription factors (PIFs), such as PIF3, thereby regulating the expression of target genes. However, the mechanisms underlying the signal-relay process are still not fully understood. Here, using mass spectrometry, we identify multiple, in vivo, light-induced Ser/Thr phosphorylation sites in PIF3. Using transgenic expression of site-directed mutants of PIF3, we provide evidence that a set of these phosphorylation events acts collectively to trigger rapid degradation of the PIF3 protein in response to initial exposure of dark-grown seedlings to light. In addition, we show that phyB-induced PIF3 phosphorylation is also required for the known negative feedback modulation of phyB levels in prolonged light, potentially through codegradation of phyB and PIF3. This mutually regulatory intermolecular transaction thus provides a mechanism with the dual capacity to promote early, graded, or threshold regulation of the primary, PIF3-controlled transcriptional network in response to initial light exposure, and later, to attenuate global sensitivity to the light signal through reductions in photoreceptor levels upon prolonged exposure. PMID:23903316

  14. Suppressor Screens in Arabidopsis.

    Science.gov (United States)

    Li, Xin; Zhang, Yuelin

    2016-01-01

    Genetic screens have proven to be a useful tool in the dissection of biological processes in plants. Specifically, suppressor screens have been widely used to study signal transduction pathways. Here we provide a detailed protocol for ethyl methanesulfonate (EMS) mutagenesis used in our suppressor screens in Arabidopsis and discuss the basic principles behind suppressor screen design and downstream analyses. PMID:26577776

  15. 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)

    Mortel, van de J.E.; Schat, H.; Moerland, P.D.; Loren van Themaat, Ver E.; Ent, van der S.; Blankestijn-de Vries, M.H.C.; Ghandilyan, A.; Tsiatsiani, S.; Aarts, M.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

  16. Prediction of anther-expressed gene resulation in Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    HUANG JiFeng; YANG JingJin; WANG Guan; YU QingBo; YANG ZhongNan

    2008-01-01

    Anther development in Arabidopsis, a popular model plant for plant biology and genetics, is controlled by a complex gene network. Despite the extensive use of this genus for genetic research, little is known about its regulatory network. In this paper, the direct transcriptional regulatory relationships between genes expressed in Arabidopsis anther development were predicted with an integrated bioinformatic method that combines mining of microarray data with promoter analysis. A total of 7710 transcription factor-gene pairs were obtained. The 80 direct regulatory relationships demonstrating the highest con-fidence were screened from the initial 7710 pairs; three of the 80 were validated by previous experi-ments. The results indicate that our predicted results were reliable. The regulatory relationships re-vealed by this research and described in this paper may facilitate further investigation of the molecular mechanisms of anther development. The bioinformatic method used in this work can also be applied to the prediction of gene regulatory relationships in other organisms.

  17. A Genetic Pathway for Tapetum Development and Function in Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    Jun Zhu; Yue Lou; Xiaofeng Xu; Zhong-Nan Yang

    2011-01-01

    In anther development,tapetal cells take part in complex processes,including endomitosis and apoptosis (programmed cell death).The tapetum provides many of the proteins,lipids,polysaccharides and other molecules necessary for pollen development.Several transcription factors,including DYT1,TDF1,AMS,MS188 and MS1,have been reported to be essential for tapetum development and function in Arabidopsis thaliana.Here,we present a detailed cytological analysis of knockout mutants for these genes,along with an in situ RNA hybridization experiment and double mutant analysis showing that these transcription factors form a genetic pathway in tapetum development.DYT1,TDF1 and AMS function in early tapetum development,while MS188 and MS1 are important for late tapetum development.The genetic pathway revealed in this work facilitates further investigation of the function and molecular mechanisms of tapetum development in Arabidopsis.

  18. 过表达转录因子 AhAREB1对拟南芥生长素分布的影响%Auxin Distribution in Arabidopsis Plants Over-Expressing AhAREB1 Encoding a Transcription Factor

    Institute of Scientific and Technical Information of China (English)

    林莹莹; 李晓云; 刘帅; 钟钰婷; 李玲

    2015-01-01

    本课题组前期研究表明,过表达AhAREB1(花生AREB转录因子基因)植株矮小,叶片卷曲,抗旱能力增强,体内IAA含量升高,推测AhAREB1可能影响植株体内IAA分布。该文采用携带3个重复IAA化学诱导启动子元件的pDR5:GUS植株与AhAREB1过表达拟南芥植株的杂交纯合后代,通过GUS组织化学染色方法,探讨AhAREB1转录因子对植株体内IAA分布的影响。结果表明,过表达AhAREB1植株体内IAA增加,主要分布在幼苗的根尖和成苗的叶片边缘;在过表达植株IAA响应基因IAA29和IAA运输蛋白基因LAX3表达均显著下调,而IAA响应蛋白基因ARF2和ARF9显著上调。过表达AhAREB1植株体内IAA分布不均衡是引起表型变化的原因之一。%Our previous study showed that Arabidopsis plants over-expressing AhAREB1 ( a peanut AREB transcrip-tion factor) displayed growth retardation, curly leaves, enhanced drought tolerance and increased IAA content.It is implied that auxin distribution may be affected by the expression of AhAREB1.In the present study, the homozy-gous transgenic Arabidopsis, generated by hybridizing the pDR5::GUS ( harboring GUS gene driven by a promoter with three repeat IAA-induced elements) plants with AhAREB1 over-expressing plants, was used to further investi-gate the effect of the expression of AhAREB1 transcription factor on auxin distribution through GUS histochemical staining .The results showed that the IAA content was increased in AhAREB1 over-expressing plants when compared with that in the controlled plants.The IAA mainly accumulated in the root tip of transgenic seedlings, instead on the edge of the leaves in mature plants.The expressions of IAA-responsive genes IAA29 and IAA-transport gene LAX3 in AhAREB1 over-expressing plants were significantly down-regulated, whereas The expressions of other two IAA-responsive genes ARF2 and ARF9 were significantly up-regulated.Take together, the unbalanced IAA distri

  19. Arabidopsis ferritin 1 (AtFer1) gene regulation by the phosphate starvation response 1 (AtPHR1) transcription factor reveals a direct molecular link between iron and phosphate homeostasis.

    Science.gov (United States)

    Bournier, Marc; Tissot, Nicolas; Mari, Stéphane; Boucherez, Jossia; Lacombe, Eric; Briat, Jean-François; Gaymard, Frédéric

    2013-08-01

    A yeast one-hybrid screening allowed the selection of PHR1 as a factor that interacted with the AtFer1 ferritin gene promoter. In mobility shift assays, PHR1 and its close homologue PHL1 (PHR1-like 1) interact with Element 2 of the AtFer1 promoter, containing a P1BS (PHR1 binding site). In a loss of function mutant for genes encoding PHR1 and PHL1 (phr1 phl1 mutant), the response of AtFer1 to phosphate starvation was completely lost, showing that the two transcription factors regulate AtFer1 expression upon phosphate starvation. This regulation does not involve the IDRS (iron-dependent regulatory sequence) present in the AtFer1 promoter and involved in the iron-dependent regulation. The phosphate starvation response of AtFer1 is not linked to the iron status of plants and is specifically initiated by phosphate deficiency. Histochemical localization of iron, visualized by Perls DAB staining, was strongly altered in a phr1 phl1 mutant, revealing that both PHR1 and PHL1 are major factors involved in the regulation of iron homeostasis.

  20. Heterologous expression of the BABY BOOM AP2/ERF transcription factor enhances the regeneration capacity of tobacco (Nicotiana tabacum L.)

    NARCIS (Netherlands)

    Srinivasan, C.; Liu, Z.; Heidmann, I.; Supena, E.D.J.; Fukuoka, H.; Joosen, R.V.L.; Lambalk, J.; Angenent, G.C.; Scorza, R.; Custers, J.B.M.; Boutilier, K.A.

    2007-01-01

    Gain-of-function studies have shown that ectopic expression of the BABY BOOM (BBM) AP2/ERF domain transcription factor is sufficient to induce spontaneous somatic embryogenesis in Arabidopsis (Arabidopsis thaliana (L.) Heynh) and Brassica napus (B. napus L.) seedlings. Here we examined the effect of

  1. Does Arabidopsis thaliana DREAM of cell cycle control?

    Science.gov (United States)

    Fischer, Martin; DeCaprio, James A

    2015-08-01

    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 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. PMID:26089020

  2. Arabidopsis in Wageningen

    OpenAIRE

    Koornneef, M

    2013-01-01

    Arabidopsis thaliana is the plant species that in the past 25 years has developed into the major model species in plant biology research. This was due to its properties such as short generation time, its small genome and its easiness to be transformed. Wageningen University has played an important role in the development of this model, based on interdisciplinary collaborations using genetics as a major tool to investigate aspects of physiology, development, plant-microbe interactions and evol...

  3. AtHSPR may function in salt-induced cell death and ER stress in Arabidopsis.

    Science.gov (United States)

    Yang, Tao; Zhang, Peng; Wang, Chongying

    2016-07-01

    Salt stress is a harmful and global abiotic stress to plants and has an adverse effect on all physiological processes of plants. Recently, we cloned and identified a novel AtHSPR (Arabidopsis thaliana Heat Shock Protein Related), which encodes a nuclear-localized protein with ATPase activity, participates in salt and drought tolerance in Arabidopsis. Transcript profiling analysis revealed a differential expression of genes involved in accumulation of reactive oxygen species (ROS), abscisic acid (ABA) signaling, stress response and photosynthesis between athspr mutant and WT under salt stress. Here, we provide further analysis of the data showing the regulation of salt-induced cell death and endoplasmic reticulum (ER) stress response in Arabidopsis and propose a hypothetical model for the role of AtHSPR in the regulation of the salt tolerance in Arabidopsis. PMID:27302034

  4. MTHFD1 controls DNA methylation in Arabidopsis

    Science.gov (United States)

    Groth, Martin; Moissiard, Guillaume; Wirtz, Markus; Wang, Haifeng; Garcia-Salinas, Carolina; Ramos-Parra, Perla A.; Bischof, Sylvain; Feng, Suhua; Cokus, Shawn J.; John, Amala; Smith, Danielle C.; Zhai, Jixian; Hale, Christopher J.; Long, Jeff A.; Hell, Ruediger; Díaz de la Garza, Rocío I.; Jacobsen, Steven E.

    2016-01-01

    DNA methylation is an epigenetic mechanism that has important functions in transcriptional silencing and is associated with repressive histone methylation (H3K9me). To further investigate silencing mechanisms, we screened a mutagenized Arabidopsis thaliana population for expression of SDCpro-GFP, redundantly controlled by DNA methyltransferases DRM2 and CMT3. Here, we identify the hypomorphic mutant mthfd1-1, carrying a mutation (R175Q) in the cytoplasmic bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase (MTHFD1). Decreased levels of oxidized tetrahydrofolates in mthfd1-1 and lethality of loss-of-function demonstrate the essential enzymatic role of MTHFD1 in Arabidopsis. Accumulation of homocysteine and S-adenosylhomocysteine, genome-wide DNA hypomethylation, loss of H3K9me and transposon derepression indicate that S-adenosylmethionine-dependent transmethylation is inhibited in mthfd1-1. Comparative analysis of DNA methylation revealed that the CMT3 and CMT2 pathways involving positive feedback with H3K9me are mostly affected. Our work highlights the sensitivity of epigenetic networks to one-carbon metabolism due to their common S-adenosylmethionine-dependent transmethylation and has implications for human MTHFD1-associated diseases. PMID:27291711

  5. Hormonal Regulation of Leaf Morphogenesis in Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    Lin-Chuan Li; Ding-Ming Kang; Zhang-Liang Chen; Li-Jia Qu

    2007-01-01

    Leaf morphogenesis is strictly controlled not only by intrinsic genetic factors, such as transcriptional factors, but also by environmental cues, such as light, water and pathogens. Nevertheless, the molecular mechanism of how leaf rnorphogenesis is regulated by genetic programs and environmental cues is far from clear. Numerous series of events demonstrate that plant hormones, mostly small and simple molecules,play crucial roles in plant growth and development, and in responses of plants to environmental cues such as light. With more and more genetics and molecular evidence obtained from the model plant Arabidopsis,several fundamental aspects of leaf rnorphogenesis including the initiation of leaf primordia, the determination of leaf axes, the regulation of cell division and expansion in leaves have been gradually unveiled.Among these phytohormones, auxin is found to be essential in the regulation of leaf morphogenesis.

  6. An Arabidopsis callose synthase

    DEFF Research Database (Denmark)

    Ostergaard, Lars; Petersen, Morten; Mattsson, Ole;

    2002-01-01

    in the Arabidopsis mpk4 mutant which exhibits systemic acquired resistance (SAR), elevated beta-1,3-glucan synthase activity, and increased callose levels. In addition, AtGsl5 is a likely target of salicylic acid (SA)-dependent SAR, since AtGsl5 mRNA accumulation is induced by SA in wild-type plants, while...... expression of the nahG salicylate hydroxylase reduces AtGsl5 mRNA levels in the mpk4 mutant. These results indicate that AtGsl5 is likely involved in callose synthesis in flowering tissues and in the mpk4 mutant....

  7. Genome-scale cold stress response regulatory networks in ten Arabidopsis thaliana ecotypes

    DEFF Research Database (Denmark)

    Barah, Pankaj; Jayavelu, Naresh Doni; Rasmussen, Simon;

    2013-01-01

    ontology (GO) categories were identified to delineate natural variation of cold stress regulated differential gene expression in the model plant A. thaliana. The predicted regulatory network model was able to identify new ecotype specific transcription factors and their regulatory interactions, which might...... using Arabidopsis NimbleGen ATH6 microarrays. In total 6061 transcripts were significantly cold regulated (p expression pattern. By using sequence data...

  8. Functional analysis of the theobroma cacao NPR1 gene in arabidopsis

    OpenAIRE

    Verica Joseph; Liu Yi; Maximova Siela N; Shi Zi; Guiltinan Mark J

    2010-01-01

    Abstract Background The Arabidopsis thaliana NPR1 gene encodes a transcription coactivator (NPR1) that plays a major role in the mechanisms regulating plant defense response. After pathogen infection and in response to salicylic acid (SA) accumulation, NPR1 translocates from the cytoplasm into the nucleus where it interacts with other transcription factors resulting in increased expression of over 2000 plant defense genes contributing to a pathogen resistance response. Results A putative Theo...

  9. Sucrose regulated translational control of bZip genes in Arabidopsis thaliana

    NARCIS (Netherlands)

    Rahmani, F.

    2007-01-01

    Sucrose can translationally regulate the expression of bZIP11 and four other S-class bZip transcription factors in Arabidopsis thaliana. Sequence encoding 28 amino acids (SC-peptide) in the leader of the bZIP11 is sufficient to mediate sucrose induced translational control. A model proposes that suc

  10. Arabidopsis CAPRICE (MYB and GLABRA3 (bHLH control tomato (Solanum lycopersicum anthocyanin biosynthesis.

    Directory of Open Access Journals (Sweden)

    Takuji Wada

    Full Text Available In Arabidopsis thaliana the MYB transcription factor CAPRICE (CPC and the bHLH transcription factor GLABRA3 (GL3 are central regulators of root-hair differentiation and trichome initiation. By transforming the orthologous tomato genes SlTRY (CPC and SlGL3 (GL3 into Arabidopsis, we demonstrated that these genes influence epidermal cell differentiation in Arabidopsis, suggesting that tomato and Arabidopsis partially use similar transcription factors for epidermal cell differentiation. CPC and GL3 are also known to be involved in anthocyanin biosynthesis. After transformation into tomato, 35S::CPC inhibited anthocyanin accumulation, whereas GL3::GL3 enhanced anthocyanin accumulation. Real-time reverse transcription PCR analyses showed that the expression of anthocyanin biosynthetic genes including Phe-ammonia lyase (PAL, the flavonoid pathway genes chalcone synthase (CHS, dihydroflavonol reductase (DFR, and anthocyanidin synthase (ANS were repressed in 35S::CPC tomato. In contrast, the expression levels of PAL, CHS, DFR, and ANS were significantly higher in GL3::GL3 tomato compared with control plants. These results suggest that CPC and GL3 also influence anthocyanin pigment synthesis in tomato.

  11. A microarray analysis of the rice transcriptome and its comparison to Arabidopsis

    DEFF Research Database (Denmark)

    Ma, Ligeng; Chen, Chen; Liu, Xigang;

    2005-01-01

    Arabidopsis and rice are the only two model plants whose finished phase genome sequence has been completed. Here we report the construction of an oligomer microarray based on the presently known and predicted gene models in the rice genome. This microarray was used to analyze the transcriptional ...

  12. Navigating the transcriptional roadmap regulating plant secondary cell wall deposition

    Directory of Open Access Journals (Sweden)

    Steven Grant Hussey

    2013-08-01

    Full Text Available The current status of lignocellulosic biomass as an invaluable resource in industry, agriculture and health has spurred increased interest in understanding the transcriptional regulation of secondary cell wall (SCW biosynthesis. The last decade of research has revealed an extensive network of NAC, MYB and other families of transcription factors regulating Arabidopsis SCW biosynthesis, and numerous studies have explored SCW-related transcription factors in other dicots and monocots. Whilst the general structure of the Arabidopsis network has been a topic of several reviews, they have not comprehensively represented the detailed protein-DNA and protein-protein interactions described in the literature, and an understanding of network dynamics and functionality has not yet been achieved for SCW formation. Furthermore the methodologies employed in studies of SCW transcriptional regulation have not received much attention, especially in the case of non-model organisms. In this review, we have reconstructed the most exhaustive literature-based network representations to date of SCW transcriptional regulation in Arabidopsis. We include a manipulable Cytoscape representation of the Arabidopsis SCW transcriptional network to aid in future studies, along with a list of supporting literature for each documented interaction. Amongst other topics, we discuss the various components of the network, its evolutionary conservation in plants, putative modules and dynamic mechanisms that may influence network function, and the approaches that have been employed in network inference. Future research should aim to better understand network function and its response to dynamic perturbations, whilst the development and application of genome-wide approaches such as ChIP-seq and systems genetics are in progress for the study of SCW transcriptional regulation in non-model organisms.

  13. Elucidating the germination transcriptional program using small molecules.

    Science.gov (United States)

    Bassel, George W; Fung, Pauline; Chow, Tsz-fung Freeman; Foong, Justin A; Provart, Nicholas J; Cutler, Sean R

    2008-05-01

    The transition from seed to seedling is mediated by germination, a complex process that starts with imbibition and completes with radicle emergence. To gain insight into the transcriptional program mediating germination, previous studies have compared the transcript profiles of dry, dormant, and germinating after-ripened Arabidopsis (Arabidopsis thaliana) seeds. While informative, these approaches did not distinguish the transcriptional responses due to imbibition, shifts in metabolism, or breaking of dormancy from those triggered by the initiation of germination. In this study, three mechanistically distinct small molecules that inhibit Arabidopsis seed germination (methotrexate, 2, 4-dinitrophenol, and cycloheximide) were identified using a small-molecule screen and used to probe the germination transcriptome. Germination-responsive transcripts were defined as those with significantly altered transcript abundance across all inhibitory treatments with respect to control germinating seeds, using data from ATH1 microarrays. This analysis identified numerous germination regulators as germination responsive, including the DELLA proteins GAI, RGA, and RGL3, the abscisic acid-insensitive proteins ABI4, ABI5, ABI8, and FRY1, and the gibberellin receptor GID1A. To help visualize these and other publicly available seed microarray data, we designed a seed mRNA expression browser using the electronic Fluorescent Pictograph platform. An overall decrease in gene expression and a 5-fold greater number of transcripts identified as statistically down-regulated in drug-inhibited seeds point to a role for mRNA degradation or turnover during seed germination. The genes identified in our study as responsive to germination define potential uncharacterized regulators of this process and provide a refined transcriptional signature for germinating Arabidopsis seeds.

  14. Overexpression of Arabidopsis AnnAt8 Alleviates Abiotic Stress in Transgenic Arabidopsis and Tobacco

    Science.gov (United States)

    Yadav, Deepanker; Ahmed, Israr; Shukla, Pawan; Boyidi, Prasanna; Kirti, Pulugurtha Bharadwaja

    2016-01-01

    Abiotic stress results in massive loss of crop productivity throughout the world. Because of our limited knowledge of the plant defense mechanisms, it is very difficult to exploit the plant genetic resources for manipulation of traits that could benefit multiple stress tolerance in plants. To achieve this, we need a deeper understanding of the plant gene regulatory mechanisms involved in stress responses. Understanding the roles of different members of plant gene families involved in different stress responses, would be a step in this direction. Arabidopsis, which served as a model system for the plant research, is also the most suitable system for the functional characterization of plant gene families. Annexin family in Arabidopsis also is one gene family which has not been fully explored. Eight annexin genes have been reported in the genome of Arabidopsis thaliana. Expression studies of different Arabidopsis annexins revealed their differential regulation under various abiotic stress conditions. AnnAt8 (At5g12380), a member of this family has been shown to exhibit ~433 and ~175 fold increase in transcript levels under NaCl and dehydration stress respectively. To characterize Annexin8 (AnnAt8) further, we have generated transgenic Arabidopsis and tobacco plants constitutively expressing AnnAt8, which were evaluated under different abiotic stress conditions. AnnAt8 overexpressing transgenic plants exhibited higher seed germination rates, better plant growth, and higher chlorophyll retention when compared to wild type plants under abiotic stress treatments. Under stress conditions transgenic plants showed comparatively higher levels of proline and lower levels of malondialdehyde compared to the wild-type plants. Real-Time PCR analyses revealed that the expression of several stress-regulated genes was altered in AnnAt8 over-expressing transgenic tobacco plants, and the enhanced tolerance exhibited by the transgenic plants can be correlated with altered expressions of

  15. Studies of epigenetic mechanisms affecting transcription in "Arabidopsis thaliana"

    OpenAIRE

    Caikovski, Marian

    2008-01-01

    Le gène MOM1 code une protéine de 2001 acides aminés qui ne présente d'homologie avec les séquences disponibles dans les bases de données qu'au niveau d'une région de 300 acides aminé, reliquat d'un domaine SNF2. La mutation mom1 entraîne la réactivation transcriptionnelle de transgènes et de loci endogènes silencés. Mes études ont permis de montrer que l'activité de MOM1 porte non seulement sur les transposons mais également sur des gènes impliqués dans le développement. MOM1 ne possède d'ho...

  16. Transgenic Arabidopsis Gene Expression System

    Science.gov (United States)

    Ferl, Robert; Paul, Anna-Lisa

    2009-01-01

    The Transgenic Arabidopsis Gene Expression System (TAGES) investigation is one in a pair of investigations that use the Advanced Biological Research System (ABRS) facility. TAGES uses Arabidopsis thaliana, thale cress, with sensor promoter-reporter gene constructs that render the plants as biomonitors (an organism used to determine the quality of the surrounding environment) of their environment using real-time nondestructive Green Fluorescent Protein (GFP) imagery and traditional postflight analyses.

  17. Identification of prior candidate genes for Sclerotinia local resistance in Brassica napus using Arabidopsis cDNA microarray and Brassica-Arabidopsis comparative mapping

    Institute of Scientific and Technical Information of China (English)

    LIU; Renhu; ZHAO; Jianwei; XIAO; Yong; MENG; Jinling

    2005-01-01

    Arabidopsis cDNA arrays were used to screen the local-defense-associated genes in oilseed rape (Brassica napus L.) at the challenge of Sclerotinia sclerotiorum. 61 genes with two-fold expression changes were screened out from the local tissue around the necrosis. Among them, 36 unique genes were up-regulated and 25 unique genes were down-regulated. RT-PCR and Northern blot results were consistent with the array results, suggesting Arabidopsis arrays were useful for transcriptional profiling of B. napus genes. Some of these genes were located in the interval of some QTLs for Sclerotinia resistance in B. napus by Brassica- Arabidopsis comparative mapping. These genes may have priority to be pursued for more intensive research.

  18. Trichoderma volatiles effecting Arabidopsis

    DEFF Research Database (Denmark)

    Ramadan, Metwaly; Gigolashvili, Tamara; Grosskinsky, Dominik Kilian;

    2015-01-01

    Trichoderma species are present in many ecosystems and some strains have the ability to reduce the severity of plant diseases by activating various defense pathways via specific biologically active signaling molecules. Hence we investigated the effects of low molecular weight volatile compounds...... of Trichoderma asperellum IsmT5 on Arabidopsis thaliana. During co-cultivation of T. asperellum IsmT5 without physical contact to A. thaliana we observed smaller but vital and robust plants. The exposed plants exhibit increased trichome numbers, accumulation of defense-related compounds such as H2O2, anthocyanin......, camalexin, and increased expression of defense-related genes. We conclude that A. thaliana perceives the Trichoderma volatiles as stress compounds and subsequently initiates multilayered adaptations including activation of signaling cascades to withstand this environmental influence. The prominent headspace...

  19. G2 Checkpoint Responses in Arabidopsis

    Energy Technology Data Exchange (ETDEWEB)

    Britt, Anne

    2013-03-18

    This project focused on the mechanism and biological significance of the G2 arrest response to replication stress in plants. We employed both forward and reverse genetic approaches to identify genes required for this response. A total of 3 different postdocs, 5 undergraduates, and 2 graduate students participated in the project. We identified several genes required for damage response in plants, including homologs of genes previously identified in animals (ATM and ATR), novel, a plant-specific genes (SOG1) and a gene known in animals but previously thought to be missing from the Arabidopsis genome (ATRIP). We characterized the transcriptome of gamma-irradiated plants, and found that plants, unlike animals, express a robust transcriptional response to damage, involving genes that regulate the cell cycle and DNA metabolism. This response requires both ATM and the transcription factor SOG1. We found that both ATM and ATR play a role in meiosis in plants. We also found that plants have a cell-type-specific programmed cell death response to ionizing radiation and UV light, and that this response requires ATR, ATM, and SOG1. These results were published in a series of 5 papers.

  20. Cell fate in the Arabidopsis root epidermis is determined by competition between WEREWOLF and CAPRICE.

    Science.gov (United States)

    Song, Sang-Kee; Ryu, Kook Hui; Kang, Yeon Hee; Song, Jae Hyo; Cho, Young-Hee; Yoo, Sang-Dong; Schiefelbein, John; Lee, Myeong Min

    2011-11-01

    The root hair and nonhair cells in the Arabidopsis (Arabidopsis thaliana) root epidermis are specified by a suite of transcriptional regulators. Two of these are WEREWOLF (WER) and CAPRICE (CPC), which encode MYB transcription factors that are required for promoting the nonhair cell fate and the hair cell fate, respectively. However, the precise function and relationship between these transcriptional regulators have not been fully defined experimentally. Here, we examine these issues by misexpressing the WER gene using the GAL4-upstream activation sequence transactivation system. We find that WER overexpression in the Arabidopsis root tip is sufficient to cause epidermal cells to adopt the nonhair cell fate through direct induction of GLABRA2 (GL2) gene expression. We also show that GLABRA3 (GL3) and ENHANCER OF GLABRA3 (EGL3), two closely related bHLH proteins, are required for the action of the overexpressed WER and that WER interacts with these bHLHs in plant cells. Furthermore, we find that CPC suppresses the WER overexpression phenotype quantitatively. These results show that WER acts together with GL3/EGL3 to induce GL2 expression and that WER and CPC compete with one another to define cell fates in the Arabidopsis root epidermis.

  1. Developmentally distinct MYB genes encode functionally equivalent proteins in Arabidopsis.

    Science.gov (United States)

    Lee, M M; Schiefelbein, J

    2001-05-01

    The duplication and divergence of developmental control genes is thought to have driven morphological diversification during the evolution of multicellular organisms. To examine the molecular basis of this process, we analyzed the functional relationship between two paralogous MYB transcription factor genes, WEREWOLF (WER) and GLABROUS1 (GL1), in Arabidopsis. The WER and GL1 genes specify distinct cell types and exhibit non-overlapping expression patterns during Arabidopsis development. Nevertheless, reciprocal complementation experiments with a series of gene fusions showed that WER and GL1 encode functionally equivalent proteins, and their unique roles in plant development are entirely due to differences in their cis-regulatory sequences. Similar experiments with a distantly related MYB gene (MYB2) showed that its product cannot functionally substitute for WER or GL1. Furthermore, an analysis of the WER and GL1 proteins shows that conserved sequences correspond to specific functional domains. These results provide new insights into the evolution of the MYB gene family in Arabidopsis, and, more generally, they demonstrate that novel developmental gene function may arise solely by the modification of cis-regulatory sequences.

  2. Comparative Proteomic Analysis of Arabidopsis Mature Pollen and Germinated Pollen

    Institute of Scientific and Technical Information of China (English)

    Junjie Zou; Lianfen Song; Wenzheng Zhang; Yi Wang; Songlin Ruan; Wei-Hua Wu

    2009-01-01

    Proteomic analysis was applied to generating the map of Arabidopsis mature pollen proteins and analyzing the differentially expressed proteins that are potentially involved in the regulation of Arabidopsis pollen germination. By applying 2-D electrophoresis and silver staining, we resolved 499 and 494 protein spots from protein samples extracted from pollen grains and pollen tubes, respectively. Using the matrix-assisted laser desorption ionization time-of-flight mass spectrometry method, we identified 189 distinct proteins from 213 protein spots expressed in mature pollen or pollen tubes, and 75 new identified proteins that had not been reported before in research into the Arabidopsis pollen proteome. Comparative analysis revealed that 40 protein spots exhibit reproducible significant changes between mature pollen and pollen tubes. And 21 proteins from 17 downregulated and six upregulated protein spots were identified. Functional category analysis indicated that these differentially expressed proteins mainly involved in signaling, cellular structure, transport, defense/stress responses, transcription, metabolism, and energy production. The patterns of changes at protein level suggested the important roles for energy metabolism-related proteins in pollen tube growth, accompanied by the activation of the stress response pathway and modifications to the cell wall.

  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. Arabidopsis phospholipase Dδ is involved in basal defense and nonhost resistance to powdery mildew fungi

    DEFF Research Database (Denmark)

    Pinosa, Francesco; Buhot, Nathalie; Kwaaitaal, Mark Adrianus Cornelis J;

    2013-01-01

    and biotic stress signaling. In this study, the involvement of PLD in the interaction between Arabidopsis (Arabidopsis thaliana) and the barley powdery mildew fungus Blumeria graminis f. sp. hordei (Bgh) was investigated. This nonadapted pathogen is normally resisted by a cell wall-based defense, which stops...... the fungal hyphae from penetrating the epidermal cell wall. Chemical inhibition of phosphatidic acid production by PLD increased the penetration rate of Bgh spores on wild-type leaves. The analysis of transfer DNA knockout lines for all Arabidopsis PLD genes revealed that PLDδ is involved in penetration...... fluorescent protein fusion of PLDδ localized to the plasma membrane at the Bgh attack site, where it surrounded the cell wall reinforcement. Furthermore, in the pldδ mutant, transcriptional up-regulation of early microbe-associated molecular pattern response genes was delayed after chitin stimulation...

  5. NAC Transcription Factors in Stress Responses and Senescence

    DEFF Research Database (Denmark)

    O'Shea, Charlotte

    of these studies have also revealed emerging gene regulatory networks and protein-protein interaction networks. However, structural studies relating structure to function are lagging behind. Structure-function analysis of the NAC transcription factors has therefore been the main focus of this PhD thesis....... A systematic analysis has been performed of protein intrinsic disorder (ID), referring to the lack of a fixed tertiary structure, in NAC transcription factors. The transcription regulatory domains (TRDs) from six phylogenetically representative Arabidopsis thaliana NAC transcription factors have a similarly......RF is a functional hotspot for both transcriptional activity and interaction with the cellular hub protein Radical Induced Cell Death1 (RCD1). Specific amino acid residues essential for the interaction were identified. These studies and structural analysis suggested that RCD1-ANAC046 complex formation does...

  6. The ROS Wheel: Refining ROS Transcriptional Footprints1[OPEN

    Science.gov (United States)

    Noctor, Graham

    2016-01-01

    In the last decade, microarray studies have delivered extensive inventories of transcriptome-wide changes in messenger RNA levels provoked by various types of oxidative stress in Arabidopsis (Arabidopsis thaliana). Previous cross-study comparisons indicated how different types of reactive oxygen species (ROS) and their subcellular accumulation sites are able to reshape the transcriptome in specific manners. However, these analyses often employed simplistic statistical frameworks that are not compatible with large-scale analyses. Here, we reanalyzed a total of 79 Affymetrix ATH1 microarray studies of redox homeostasis perturbation experiments. To create hierarchy in such a high number of transcriptomic data sets, all transcriptional profiles were clustered on the overlap extent of their differentially expressed transcripts. Subsequently, meta-analysis determined a single magnitude of differential expression across studies and identified common transcriptional footprints per cluster. The resulting transcriptional footprints revealed the regulation of various metabolic pathways and gene families. The RESPIRATORY BURST OXIDASE HOMOLOG F-mediated respiratory burst had a major impact and was a converging point among several studies. Conversely, the timing of the oxidative stress response was a determining factor in shaping different transcriptome footprints. Our study emphasizes the need to interpret transcriptomic data sets in a systematic context, where initial, specific stress triggers can converge to common, aspecific transcriptional changes. We believe that these refined transcriptional footprints provide a valuable resource for assessing the involvement of ROS in biological processes in plants. PMID:27246095

  7. Does Arabidopsis thaliana DREAM of cell cycle control?

    Science.gov (United States)

    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 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. PMID:26089020

  8. Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions.

    Science.gov (United States)

    Kawakatsu, Taiji; Huang, Shao-Shan Carol; Jupe, Florian; Sasaki, Eriko; Schmitz, Robert J; Urich, Mark A; Castanon, Rosa; Nery, Joseph R; Barragan, Cesar; He, Yupeng; Chen, Huaming; Dubin, Manu; Lee, Cheng-Ruei; Wang, Congmao; Bemm, Felix; Becker, Claude; O'Neil, Ryan; O'Malley, Ronan C; Quarless, Danjuma X; Schork, Nicholas J; Weigel, Detlef; Nordborg, Magnus; Ecker, Joseph R

    2016-07-14

    The epigenome orchestrates genome accessibility, functionality, and three-dimensional structure. Because epigenetic variation can impact transcription and thus phenotypes, it may contribute to adaptation. Here, we report 1,107 high-quality single-base resolution methylomes and 1,203 transcriptomes from the 1001 Genomes collection of Arabidopsis thaliana. Although the genetic basis of methylation variation is highly complex, geographic origin is a major predictor of genome-wide DNA methylation levels and of altered gene expression caused by epialleles. Comparison to cistrome and epicistrome datasets identifies associations between transcription factor binding sites, methylation, nucleotide variation, and co-expression modules. Physical maps for nine of the most diverse genomes reveal how transposons and other structural variants shape the epigenome, with dramatic effects on immunity genes. The 1001 Epigenomes Project provides a comprehensive resource for understanding how variation in DNA methylation contributes to molecular and non-molecular phenotypes in natural populations of the most studied model plant.

  9. Chromatin Remodeling in Stem Cell Maintenance in Arabidopsis thaliana

    Institute of Scientific and Technical Information of China (English)

    Lin Xu; Wen-Hui Shen

    2009-01-01

    Pluripotent stem cells are able to both self-renew and generate undifferentiated cells for the formation of new tissues and organs.In higher plants,stem cells found in the shoot apical meristem (SAM) and the root apical meristem (RAM) are origins of organogenesis occurring post-embryonically.It is important to understand how the regulation of stem cell fate is coordinated to enable the meristem to constantly generate different types of lateral organs.Much knowledge has accumulated on specific transcription factors controlling SAM and RAM activity.Here,we review recent evidences for a role of chromatin remodeling in the maintenance of stable expression states of transcription factor genes and the control of stem cell activity in Arabidopsis.

  10. 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.

    Science.gov (United States)

    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

    2008-03-01

    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 and zinc (Zn) are examined, with the main aim to determine the differences in gene expression between the Cd-tolerant Zn-hyperaccumulator T. caerulescens and the Cd-sensitive non-accumulator Arabidopsis. This comparative transcriptional analysis emphasized the role of genes involved in lignin, glutathione and sulphate metabolism. Furthermore the transcription factors MYB72 and bHLH100 were studied for their involvement in metal homeostasis, as they showed an altered expression after exposure to Cd. The Arabidopsis myb72 knockout mutant was more sensitive to excess Zn or iron (Fe) deficiency than wild type, while Arabidopsis transformants overexpressing bHLH100 showed increased tolerance to high Zn and nickel (Ni) compared to wild-type plants, confirming their role in metal homeostasis in Arabidopsis. PMID:18088336

  11. MADS on the move : a study on MADS domain protein function and movement during floral development in Arabidopsis thaliana

    NARCIS (Netherlands)

    Urbanus, S.L.

    2010-01-01

    In this thesis we investigated the behaviour of fluorescently-tagged MADS domain proteins during floral development in the model plant Arabidopsis thaliana, and explored the importance of intercellular transport via plasmodesmata for MADS domain transcription factor functioning. The MADS domain tran

  12. The Arabidopsis NIMIN proteins affect NPR1 differentially

    Directory of Open Access Journals (Sweden)

    Meike eHermann

    2013-04-01

    Full Text Available NON-EXPRESSOR OF PATHOGENESIS-RELATED GENES1 (NPR1 is the central regulator of the pathogen defense reaction systemic acquired resistance (SAR. NPR1 acts by sensing the SAR signal molecule salicylic acid (SA to induce expression of PATHOGENESIS-RELATED (PR genes. Mechanistically, NPR1 is the core of a transcription complex interacting with TGA transcription factors and NIM1 INTERACTING (NIMIN proteins. Arabidopsis NIMIN1 has been shown to suppress NPR1 activity in transgenic plants. The Arabidopsis NIMIN family comprises four structurally related, yet distinct members. Here, we show that NIMIN1, NIMIN2 and NIMIN3 are expressed differentially, and that the encoded proteins affect expression of the SAR marker PR-1 differentially. NIMIN3 is expressed constitutively at a low level, but NIMIN2 and NIMIN1 are both responsive to SA. While NIMIN2 is an immediate early SA-induced and NPR1-independent gene, NIMIN1 is activated after NIMIN2, but clearly before PR-1. Notably, NIMIN1, like PR-1, depends on NPR1. In a transient assay system, NIMIN3 suppresses SA-induced PR-1 expression, albeit to a lesser extent than NIMIN1, whereas NIMIN2 does not negatively affect PR-1 gene activation. Furthermore, although binding to the same domain in the C-terminus, NIMIN1 and NIMIN2 interact differentially with NPR1, thus providing a molecular basis for their opposing effects on NPR1. Together, our data suggest that the Arabidopsis NIMIN proteins are regulators of the SAR response. We propose that NIMINs act in a strictly consecutive and SA-regulated manner on the SA sensor protein NPR1, enabling NPR1 to monitor progressing threat by pathogens and to promote appropriate defense gene activation at distinct stages of SAR. In this scenario, the defense gene PR-1 is repressed at the onset of SAR by SA-induced, yet instable NIMIN1.

  13. Environmental History Modulates Arabidopsis Pattern-Triggered Immunity in a HISTONE ACETYLTRANSFERASE1-Dependent Manner.

    Science.gov (United States)

    Singh, Prashant; Yekondi, Shweta; Chen, Po-Wen; Tsai, Chia-Hong; Yu, Chun-Wei; Wu, Keqiang; Zimmerli, Laurent

    2014-06-24

    In nature, plants are exposed to a fluctuating environment, and individuals exposed to contrasting environmental factors develop different environmental histories. Whether different environmental histories alter plant responses to a current stress remains elusive. Here, we show that environmental history modulates the plant response to microbial pathogens. Arabidopsis thaliana plants exposed to repetitive heat, cold, or salt stress were more resistant to virulent bacteria than Arabidopsis grown in a more stable environment. By contrast, long-term exposure to heat, cold, or exposure to high concentrations of NaCl did not provide enhanced protection against bacteria. Enhanced resistance occurred with priming of Arabidopsis pattern-triggered immunity (PTI)-responsive genes and the potentiation of PTI-mediated callose deposition. In repetitively stress-challenged Arabidopsis, PTI-responsive genes showed enrichment for epigenetic marks associated with transcriptional activation. Upon bacterial infection, enrichment of RNA polymerase II at primed PTI marker genes was observed in environmentally challenged Arabidopsis. Finally, repetitively stress-challenged histone acetyltransferase1-1 (hac1-1) mutants failed to demonstrate enhanced resistance to bacteria, priming of PTI, and increased open chromatin states. These findings reveal that environmental history shapes the plant response to bacteria through the development of a HAC1-dependent epigenetic mark characteristic of a primed PTI response, demonstrating a mechanistic link between the primed state in plants and epigenetics.

  14. Cinnamate-4-hydroxylase expression in arabidopsis. Regulation in response to development and the environment

    Energy Technology Data Exchange (ETDEWEB)

    Bell-Lelong, D.A.; Cusumano, J.C.; Meyer, K.; Chapple, C. [Purdue Univ., West Lafayette, IN (United States)

    1997-03-01

    Cinnamate-r-hydroxylase (C4H) is the first Cyt P450-dependent monooxygenase of the phenylpropanoid pathway. To study the expression of this gene in Arabidopsis thaliana, a C4H cDNA clone from the Arabidopsis expressed sequence tag database was identified and used to isolate its corresponding genomic clone. The entire C4H coding sequence plus 2.9 kb of its promoter were isolated on a 5.4-kb HindIII fragment of this cosmid. Inspection of the promoter sequence revealed the presence of a number of putative regulatory motifs previously identified in the promoters of other phenylpropanoid pathway genes. The expression of C4H was analyzed by RNA blot hybridization analysis and in transgenic Arabidopsis carrying a C4H-{beta}-glucuronidase transcriptional fusion. C4H message accumulation was light-dependent, but was detectable even in dark-grown seedlings. Consistent with these data, C4H mRNA was accumulated to light-grown levels in etiolated det1-1 mutant seedlings. C4H is widely expressed in various Arabidopsis tissues, particularly in roots and cells undergoing lignification. The C4H-driven {beta}-glucuronidase expression accurately reflected the tissue-specificity and wound-inducibility of the C4H promoter indicated by RNA blot hybridization analysis. A modest increase in C4H expression was observed in the tt8 mutant of Arabidopsis. 77 refs., 5 figs.

  15. Exploiting Natural Variation in Arabidopsis

    NARCIS (Netherlands)

    Molenaar, J.A.; Keurentjes, J.J.B.

    2014-01-01

    Natural variation for many traits is present within the species Arabidopsis thaliana . This chapter describes the use of natural variation to elucidate genes underlying the regulation of quantitative traits. It deals with the development and use of mapping populations, the detection and handling of

  16. Exploiting natural variation in Arabidopsis

    NARCIS (Netherlands)

    J.A. Molenaar; J.J.B. Keurentjes

    2014-01-01

    Natural variation for many traits is present within the species Arabidopsis thaliana. This chapter describes the use of natural variation to elucidate genes underlying the regulation of quantitative traits. It deals with the development and use of mapping populations, the detection and handling of g

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

    Science.gov (United States)

    Qian, Dan; Jiang, Lin; Lu, Lu; Wei, Chunhong; Li, Yi

    2011-01-01

    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.

  18. Characterization of the Ubiquitin E2 Enzyme Variant Gene Family in Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    Yu Zhang; Pei Wen; On-Sun Lau; Xing-Wang Deng

    2007-01-01

    Ubiquitin E2 enzyme variant (UEV) proteins are similar to ubiquitin-conjugating enzyme (E2) in both sequence and structure, but the lack of a catalytic cysteine residue renders them incapable of forming a thiolester linkage with ubiquitin. While the functional roles of several UEVs have been defined in yeast and animal systems, Arabidopsis COP10, a photomorphogenesis repressor, is the only UEV characterized in plants. Phylogenetic analysis revealed that the eight Arabidopsis UEV genes belong to three subfamilies.The expression of those genes is supported by either the presence of ESTs or RT-PCR analysis. We also characterized the other members of the COP10 subfamily, UEV2. Semi-quantitative RT-PCR analysis indicated that the UEV2 transcripts can be detected in most organs of Arabidopsis. Analysis of UEV2::GUS transgenic lines also showed its ubiquitous expression in nearly all the developmental stages of Arabidopsis.Transient expression analysis indicated that the sGFP-UEV2 fusion protein can localize to both the cytoplasm and nucleus. A T-DNA insertion mutant, uev2-1, which abolished the transcription of UEV2, displays no visible phenotype. Further, the cop10-4 uev2-1 double mutant exhibits the same phenotype as the cop10-4mutant in darkness. UEV2 is therefore not functionally redundant with COP10.

  19. Mutations in a new Arabidopsis cyclophilin disrupt its interaction with protein phosphatase 2A

    Science.gov (United States)

    Jackson, K.; Soll, D.; Evans, M. L. (Principal Investigator)

    1999-01-01

    The heterotrimeric protein phosphatase 2A (PP2A) is a component of multiple signaling pathways in eukaryotes. Disruption of PP2A activity in Arabidopsis is known to alter auxin transport and growth response pathways. We demonstrated that the regulatory subunit A of an Arabidopsis PP2A interacts with a novel cyclophilin, ROC7. The gene for this cyclophilin encodes a protein that contains a unique 30-amino acid extension at the N-terminus, which distinguishes the gene product from all previously identified Arabidopsis cyclophilins. Altered forms of ROC7 cyclophilin with mutations in the conserved DENFKL domain did not bind to PP2A. Unlike protein phosphatase 2B, PP2A activity in Arabidopsis extracts was not affected by the presence of the cyclophilin-binding molecule cyclosporin. The ROC7 transcript was expressed to high levels in all tissues tested. Expression of an ROC7 antisense transcript gave rise to increased root growth. These results indicate that cyclophilin may have a role in regulating PP2A activity, by a mechanism that differs from that employed for cyclophilin regulation of PP2B.

  20. 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.

  1. Transcriptional Regulation and Signaling in Phosphorus Starvation: What About Legumes?

    Institute of Scientific and Technical Information of China (English)

    Oswaldo Valdés-Lóppez; Georgina Hernández

    2008-01-01

    The availability of soil phosphorus (P), an essential element, is one of the most important requirements for plant growth and crop production. The morphological and physiological adaptations evolved by plants to cope with P starvation have been well characterized. Several P deficiency plant responses are regulated at the transcriptional level. Microarray analysis has generated valuable information on global gene expression in Arabidopsis thaliana grown under P-stress. Despite the identification of P responsive genes, little is known about the regulation of gene expression changes. Four transcription factors, PHR1, WRKY75, ZAT6 and BHLH32, involved in P starvation signaling have been characterized in Arabidopsis, and signaling pathways are deciphered. This review analyzes the current knowledge of transcriptional regulation of P starvation responses in Arabidopsis vis-a-vis legumes such as lupine, common bean and Medicago truncatula. The knowledge on regulatory and signaling mechanisms involved in P acquisition and use in legumes will be useful for improvement of these crops, which account for a large proportion of the world's crop production, providing good nutritional quality feed and food.

  2. Programming of Plant Leaf Senescence with Temporal and Inter-Organellar Coordination of Transcriptome in Arabidopsis.

    Science.gov (United States)

    Woo, Hye Ryun; Koo, Hee Jung; Kim, Jeongsik; Jeong, Hyobin; Yang, Jin Ok; Lee, Il Hwan; Jun, Ji Hyung; Choi, Seung Hee; Park, Su Jin; Kang, Byeongsoo; Kim, You Wang; Phee, Bong-Kwan; Kim, Jin Hee; Seo, Chaehwa; Park, Charny; Kim, Sang Cheol; Park, Seongjin; Lee, Byungwook; Lee, Sanghyuk; Hwang, Daehee; Nam, Hong Gil; Lim, Pyung Ok

    2016-05-01

    Plant leaves, harvesting light energy and fixing CO2, are a major source of foods on the earth. Leaves undergo developmental and physiological shifts during their lifespan, ending with senescence and death. We characterized the key regulatory features of the leaf transcriptome during aging by analyzing total- and small-RNA transcriptomes throughout the lifespan of Arabidopsis (Arabidopsis thaliana) leaves at multidimensions, including age, RNA-type, and organelle. Intriguingly, senescing leaves showed more coordinated temporal changes in transcriptomes than growing leaves, with sophisticated regulatory networks comprising transcription factors and diverse small regulatory RNAs. The chloroplast transcriptome, but not the mitochondrial transcriptome, showed major changes during leaf aging, with a strongly shared expression pattern of nuclear transcripts encoding chloroplast-targeted proteins. Thus, unlike animal aging, leaf senescence proceeds with tight temporal and distinct interorganellar coordination of various transcriptomes that would be critical for the highly regulated degeneration and nutrient recycling contributing to plant fitness and productivity. PMID:26966169

  3. The WRKY57 Transcription Factor Affects the Expression of Jasmonate ZIM-Domain Genes Transcriptionally to Compromise Botrytis cinerea Resistance.

    Science.gov (United States)

    Jiang, Yanjuan; Yu, Diqiu

    2016-08-01

    Although necrotrophic pathogens cause many devastating plant diseases, our understanding of the plant defense response to them is limited. Here, we found that loss of function of WRKY57 enhanced the resistance of Arabidopsis (Arabidopsis thaliana) against Botrytis cinerea infection. Further investigation suggested that the negative regulation of WRKY57 against B cinerea depends on the jasmonic acid (JA) signaling pathway. Chromatin immunoprecipitation experiments revealed that WRKY57 directly binds to the promoters of JASMONATE ZIM-DOMAIN1 (JAZ1) and JAZ5, encoding two important repressors of the JA signaling pathway, and activates their transcription. In vivo and in vitro experiments demonstrated that WRKY57 interacts with nuclear-encoded SIGMA FACTOR BINDING PROTEIN1 (SIB1) and SIB2. Further experiments display that the same domain, the VQ motif, of SIB1 and SIB2 interact with WRKY33 and WRKY57. Moreover, transient transcriptional activity assays confirmed that WRKY57 and WRKY33 competitively regulate JAZ1 and JAZ5, SIB1 and SIB2 further enhance these competitions of WRKY57 to WRKY33. Therefore, coordinated regulation of Arabidopsis against B cinerea by transcription activators and repressors would benefit plants by allowing fine regulation of defense.

  4. Overexpression of VOZ2 confers biotic stress tolerance but decreases abiotic stress resistance in Arabidopsis

    OpenAIRE

    Nakai, Yusuke; Fujiwara, Sumire; Kubo, Yasuyuki; Sato, Masa H.

    2013-01-01

    VOZ (vascular plant one zinc-finger protein) is a plant specific one-zinc finger type transcriptional activator, which is highly conserved through land plant evolution. We have previously shown that loss-of-function mutations in VOZ1 and VOZ2 showed increased cold and drought stress tolerances whereas decreased biotic stress resistance in Arabidopsis. Here, we demonstrate that transgenic plants overexpressing VOZ2 impairs freezing and drought stress tolerances but increases resistance to a fu...

  5. Funktionsanalyse ausgewählter DOF-Transkriptionsfaktoren bei der Modellpflanze Arabidopsis thaliana

    OpenAIRE

    Skirycz, Aleksandra

    2008-01-01

    Transcription factors (TFs) are global regulators of gene expression playing essential roles in almost all biological processes, and are therefore of great scientific and biotechnological interest. This project focused on functional characterisation of three DNA-binding-with-one-zinc-finger (DOF) TFs from the genetic model plant Arabidopsis thaliana, namely OBP1, OBP2 and AtDOF4;2. These genes were selected due to severe growth phenotypes conferred upon their constitutive over-expression. To ...

  6. Identification of novel regulators of COP1-controlled morphogenesis in Arabidopsis thaliana

    OpenAIRE

    Schrader, Andrea

    2011-01-01

    In Arabidopsis thaliana, COP1 is an essential element of light signal transduction acting downstream of photoreceptors and upstream of light-regulated gene expression. The COP1 protein acts as part of an E3 ligase complex to suppress photomorphogenic gene expression by ubiquitin-dependent degradation of light-regulated transcription factors. In dark-grown seedlings, the repression of photomorphogenesis involves the inhibition of hypocotyl growth, anthocyanin accumulation, expre...

  7. Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis

    Directory of Open Access Journals (Sweden)

    Mount Stephen M

    2006-12-01

    Full Text Available Abstract Background Recently, genomic sequencing efforts were finished for Oryza sativa (cultivated rice and Arabidopsis thaliana (Arabidopsis. Additionally, these two plant species have extensive cDNA and expressed sequence tag (EST libraries. We employed the Program to Assemble Spliced Alignments (PASA to identify and analyze alternatively spliced isoforms in both species. Results A comprehensive analysis of alternative splicing was performed in rice that started with >1.1 million publicly available spliced ESTs and over 30,000 full length cDNAs in conjunction with the newly enhanced PASA software. A parallel analysis was performed with Arabidopsis to compare and ascertain potential differences between monocots and dicots. Alternative splicing is a widespread phenomenon (observed in greater than 30% of the loci with transcript support and we have described nine alternative splicing variations. While alternative splicing has the potential to create many RNA isoforms from a single locus, the majority of loci generate only two or three isoforms and transcript support indicates that these isoforms are generally not rare events. For the alternate donor (AD and acceptor (AA classes, the distance between the splice sites for the majority of events was found to be less than 50 basepairs (bp. In both species, the most frequent distance between AA is 3 bp, consistent with reports in mammalian systems. Conversely, the most frequent distance between AD is 4 bp in both plant species, as previously observed in mouse. Most alternative splicing variations are localized to the protein coding sequence and are predicted to significantly alter the coding sequence. Conclusion Alternative splicing is widespread in both rice and Arabidopsis and these species share many common features. Interestingly, alternative splicing may play a role beyond creating novel combinations of transcripts that expand the proteome. Many isoforms will presumably have negative

  8. Functional analysis of the theobroma cacao NPR1 gene in arabidopsis

    Directory of Open Access Journals (Sweden)

    Verica Joseph

    2010-11-01

    Full Text Available Abstract Background The Arabidopsis thaliana NPR1 gene encodes a transcription coactivator (NPR1 that plays a major role in the mechanisms regulating plant defense response. After pathogen infection and in response to salicylic acid (SA accumulation, NPR1 translocates from the cytoplasm into the nucleus where it interacts with other transcription factors resulting in increased expression of over 2000 plant defense genes contributing to a pathogen resistance response. Results A putative Theobroma cacao NPR1 cDNA was isolated by RT-PCR using degenerate primers based on homologous sequences from Brassica, Arabidopsis and Carica papaya. The cDNA was used to isolate a genomic clone from Theobroma cacao containing a putative TcNPR1 gene. DNA sequencing revealed the presence of a 4.5 kb coding region containing three introns and encoding a polypeptide of 591 amino acids. The predicted TcNPR1 protein shares 55% identity and 78% similarity to Arabidopsis NPR1, and contains each of the highly conserved functional domains indicative of this class of transcription factors (BTB/POZ and ankyrin repeat protein-protein interaction domains and a nuclear localization sequence (NLS. To functionally define the TcNPR1 gene, we transferred TcNPR1 into an Arabidopsis npr1 mutant that is highly susceptible to infection by the plant pathogen Pseudomonas syringae pv. tomato DC3000. Driven by the constitutive CaMV35S promoter, the cacao TcNPR1 gene partially complemented the npr1 mutation in transgenic Arabidopsis plants, resulting in 100 fold less bacterial growth in a leaf infection assay. Upon induction with SA, TcNPR1 was shown to translocate into the nucleus of leaf and root cells in a manner identical to Arabidopsis NPR1. Cacao NPR1 was also capable of participating in SA-JA signaling crosstalk, as evidenced by the suppression of JA responsive gene expression in TcNPR1 overexpressing transgenic plants. Conclusion Our data indicate that the TcNPR1 is a functional

  9. Expression of aberrant forms of AUXIN RESPONSE FACTOR8 stimulates parthenocarpy in Arabidopsis and tomato.

    Science.gov (United States)

    Goetz, Marc; Hooper, Lauren C; Johnson, Susan D; Rodrigues, Julio Carlyle Macedo; Vivian-Smith, Adam; Koltunow, Anna M

    2007-10-01

    Fruit initiation in Arabidopsis (Arabidopsis thaliana) is generally repressed until fertilization occurs. However, mutations in AUXIN RESPONSE FACTOR8 (ARF8) uncouple fruit initiation from fertilization, resulting in the formation of seedless, parthenocarpic fruit. Here we induced parthenocarpy in wild-type Arabidopsis by introducing either the mutant genomic (g) Atarf8-4 sequence or gAtARF8:beta-glucuronidase translational fusion constructs by plant transformation. Silencing of endogenous AtARF8 transcription was not observed, indicating that the introduced, aberrant ARF8 transcripts were compromising the function of endogenous ARF8 and/or associated factors involved in suppressing fruit initiation. To analyze the role of ARF8 in tomato (Solanum lycopersicum) we initially emasculated 23 tomato cultivars to test for background parthenocarpy. Surprisingly, all had a predisposition to initiate fertilization-independent fruit growth. Expression of gAtarf8-4 in transgenic tomato ('Monalbo') resulted in a significant increase in the number and size of parthenocarpic fruit. Isolation of tomato ARF8 cDNA indicated significant sequence conservation with AtARF8. SlARF8 may therefore control tomato fruit initiation in a similar manner as AtARF8 does in Arabidopsis. Two SlARF8 cDNAs differing in size by 5 bp were found, both arising from the same gene. The smaller cDNA is a splice variant and is also present in Arabidopsis. We propose that low endogenous levels of the splice variant products might interfere with efficient formation/function of a complex repressing fruit initiation, thereby providing an explanation for the observed ovary expansion in tomato and also Arabidopsis after emasculation. Increasing the levels of aberrant Atarf8-4 transcripts may further destabilize formation/function of the complex in a dosage-dependent manner enhancing tomato parthenocarpic fruit initiation frequency and size and mimicking the parthenocarpic dehiscent silique phenotype found in

  10. High-throughput identification of transcriptional start sites in Pseudomonas syringae

    Science.gov (United States)

    Pseudomonas syringae pv. tomato strain DC3000 is a bacterial plant pathogen capable of causing disease in tomatoes and Arabidopsis. The genome of this bacterium has been sequenced. However, little information is available regarding the transcriptional activity and regulation involved when this org...

  11. Asparagine Metabolic Pathways in Arabidopsis.

    Science.gov (United States)

    Gaufichon, Laure; Rothstein, Steven J; Suzuki, Akira

    2016-04-01

    Inorganic nitrogen in the form of ammonium is assimilated into asparagine via multiple steps involving glutamine synthetase (GS), glutamate synthase (GOGAT), aspartate aminotransferase (AspAT) and asparagine synthetase (AS) in Arabidopsis. The asparagine amide group is liberated by the reaction catalyzed by asparaginase (ASPG) and also the amino group of asparagine is released by asparagine aminotransferase (AsnAT) for use in the biosynthesis of amino acids. Asparagine plays a primary role in nitrogen recycling, storage and transport in developing and germinating seeds, as well as in vegetative and senescence organs. A small multigene family encodes isoenzymes of each step of asparagine metabolism in Arabidopsis, except for asparagine aminotransferase encoded by a single gene. The aim of this study is to highlight the structure of the genes and encoded enzyme proteins involved in asparagine metabolic pathways; the regulation and role of different isogenes; and kinetic and physiological properties of encoded enzymes in different tissues and developmental stages. PMID:26628609

  12. Manipulation of hemoglobin expression affects Arabidopsis shoot organogenesis.

    Science.gov (United States)

    Wang, Yaping; Elhiti, Mohamed; Hebelstrup, Kim H; Hill, Robert D; Stasolla, Claudio

    2011-10-01

    Over the past few years non-symbiotic plant hemoglobins have been described in a variety of plant species where they fulfill several functions ranging from detoxification processes to basic aspects of plant growth and post-embryonic development. To date no information is available on the role of hemoglobins during in vitro morphogenesis. Shoot organogenesis was induced in Arabidopsis lines constitutively expressing class 1, 2 and 3 hemoglobins (GLB1, 2 and 3) and lines in which the respective genes were either downregulated by RNAi (GLB1) or knocked out (GLB2 and GLB3). The process was executed by culturing root explants on an initial auxin-rich callus induction medium (CIM) followed by a transfer onto a cytokinin-containing shoot induction medium (SIM). While the repression of GLB2 inhibited organogenesis the over-expression of GLB1 or GLB2 enhanced the number of shoots produced in culture, and altered the transcript levels of genes participating in cytokinin perception and signalling. The up-regulation of GLB1 or GLB2 activated CKI1 and AHK3, genes encoding cytokinin receptors and affected the transcript levels of cytokinin responsive regulators (ARRs). The expression of Type-A ARRs (ARR4, 5, 7, 15, and 16), feed-back repressors of the cytokinin pathway, was repressed in both hemoglobin over-expressors whereas that of several Type-B ARRs (ARR2, 12, and 13), transcription activators of cytokinin-responsive genes, was induced. Such changes enhanced the sensitivity of the root explants to cytokinin allowing the 35S::GLB1 and 35S::GLB2 lines to produce shoots at low cytokinin concentrations which did not promote organogenesis in the WT line. These results show that manipulation of hemoglobin can modify shoot organogenesis in Arabidopsis and possibly in those systems partially or completely unresponsive to applications of exogenous cytokinins. PMID:21741261

  13. Arabidopsis thaliana—Aphid Interaction

    OpenAIRE

    Louis, Joe; Singh, Vijay,; Shah, Jyoti

    2012-01-01

    Aphids are important pests of plants that use their stylets to tap into the sieve elements to consume phloem sap. Besides the removal of photosynthates, aphid infestation also alters source-sink patterns. Most aphids also vector viral diseases. In this chapter, we will summarize on recent significant findings in plant-aphid interaction, and how studies involving Arabidopsis thaliana and Myzus persicae (Sülzer), more commonly known as the green peach aphid (GPA), are beginning to provide impor...

  14. Stem cell organization in Arabidopsis

    OpenAIRE

    Wendrich, J.R.

    2016-01-01

    Growth of plant tissues and organs depends on continuous production of new cells, by niches of stem cells. Stem cells typically divide to give rise to one differentiating daughter and one non-differentiating daughter. This constant process of self-renewal ensures that the niches of stem cells or meristems stay active throughout plant-life. Specification of stem cells occurs very early during development of the emrbyo and they are maintained during later stages. The Arabidopsis embryo is a hig...

  15. Analysis of metabolic alterations in Arabidopsis following changes in the carbon dioxide and oxygen partial pressures

    Institute of Scientific and Technical Information of China (English)

    Alexandra Florian; Stefan Timm; Zoran Nikoloski; Takayuki Tohge; Hermann Bauwe; Wagner LArajo; Alisdair RFernie

    2014-01-01

    As sessile organisms, plants are subject to a multitude of environmental variations including several which directly affect their interaction with the atmosphere. Given the indiscriminant nature of Rubisco, the relative rates of photosynthesis and photorespiration are known to be responsive to changes in gas composition. However, compre-hensive profiling methods have not yet been applied in order to characterize the wider consequences of these changes on primary metabolism in general. Moreover, although transcrip-tional profiling has revealed that a subset of photorespiratory enzymes are co-expressed, whether transcriptional responses play a role in short-term responses to atmospheric composi-tional changes remains unknown. To address these questions, plants Arabidopsis thaliana (Arabidopsis) ecotype Columbia (Col-O) grown under normal air conditions were transferred to different CO2 and O2 concentrations and characterized at the physiological, molecular, and metabolic levels fol owing this transition. The results reveal alterations in the components, which are directly involved in, or supporting, photorespiration, including transcripts and metabolite levels. The results further highlight that the majority of the regulation of these pathways is not mediated at the level of transcription and that the photorespiratory pathway is essential also in conditions in which flux through the pathway is minimized, yet suggest that flux through this pathway is not mediated at the level of transcription.

  16. Analysis of ripening-related gene expression in papaya using an Arabidopsis-based microarray

    Directory of Open Access Journals (Sweden)

    Fabi João Paulo

    2012-12-01

    Full Text Available Abstract Background Papaya (Carica papaya L. is a commercially important crop that produces climacteric fruits with a soft and sweet pulp that contain a wide range of health promoting phytochemicals. Despite its importance, little is known about transcriptional modifications during papaya fruit ripening and their control. In this study we report the analysis of ripe papaya transcriptome by using a cross-species (XSpecies microarray technique based on the phylogenetic proximity between papaya and Arabidopsis thaliana. Results Papaya transcriptome analyses resulted in the identification of 414 ripening-related genes with some having their expression validated by qPCR. The transcription profile was compared with that from ripening tomato and grape. There were many similarities between papaya and tomato especially with respect to the expression of genes encoding proteins involved in primary metabolism, regulation of transcription, biotic and abiotic stress and cell wall metabolism. XSpecies microarray data indicated that transcription factors (TFs of the MADS-box, NAC and AP2/ERF gene families were involved in the control of papaya ripening and revealed that cell wall-related gene expression in papaya had similarities to the expression profiles seen in Arabidopsis during hypocotyl development. Conclusion The cross-species array experiment identified a ripening-related set of genes in papaya allowing the comparison of transcription control between papaya and other fruit bearing taxa during the ripening process.

  17. Evidences for involvement of endogenous cAMP in Arabidopsis defense responses to Verticillium toxins

    Institute of Scientific and Technical Information of China (English)

    Jing JIANG; Ling Wen FAN; Wei Hua WU

    2005-01-01

    Although there were reports suggesting the involvement of endogenous cAMP in plant defense signaling cascades,there is no direct evidence supporting this notion yet and the detailed mechanism is unclear. In the present study, we have used pathogenic fungi Verticillium dahliae and Arabidopsis plants as a model system of plant-microb interaction to demonstrate the function of endogenous cAMP in Arabidopsis defense responses. Both V. dahliae inoculation and Verticillium toxins injection induced typical "wilt" symptoms in Arabidopsis seedlings. When either 8-Br-AMP (a membrane permeable cAMP analogue) or salicylic acid (SA) was applied to Arabidopsis, the plants became resistant to V. dahliae toxins. However, addition of 8-Br-AMP did not increase the resistance of Arabidopsis transgenic plants deficient in SA to the toxins, suggesting that cAMP might act upstream of SA in plant defense signaling pathway.Indeed, 8-Br-cAMP and forskolin, an activator of adenylyl cyclase, significantly stimulated the endogenous SA level in plants, whereas DDA, an inhibitor of adenylyl cyclase dramatically reduced toxin-induced SA increase. Both the endogenous cAMP and SA increased significantly in Arabidopsis seedlings treated with toxins. Furthermore, transcription level of pathogenesis-related protein 1 gene (PR1) was strongly induced by both 8-Br-cAMP and the toxin treatment. Taken together, our data demonstrate that endogenous cAMP is involved in plant defense responses against Verticilliumsecreted toxins by regulating the production of the known signal SA in plant defense pathway.

  18. 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.

  19. Arabidopsis CDS blastp result: AK240730 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK240730 J043030K09 At2g32440.1 68415.m03963 ent-kaurenoic acid hydroxylase, putati...ve / cytochrome P450, putative identical to ent-kaurenoic acid hydroxylase / cytochrome P450 CYP88A (GI:1302...1856) [Arabidopsis thaliana]; similar to ent-kaurenoic acid hydroxylase [Arabidopsis thaliana] GI:13021853 2e-11 ...

  20. Arabidopsis CDS blastp result: AK288052 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK288052 J075151I09 At2g32440.1 68415.m03963 ent-kaurenoic acid hydroxylase, putati...ve / cytochrome P450, putative identical to ent-kaurenoic acid hydroxylase / cytochrome P450 CYP88A (GI:1302...1856) [Arabidopsis thaliana]; similar to ent-kaurenoic acid hydroxylase [Arabidopsis thaliana] GI:13021853 6e-14 ...

  1. Arabidopsis CDS blastp result: AK240911 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK240911 J065037E05 At2g32440.1 68415.m03963 ent-kaurenoic acid hydroxylase, putati...ve / cytochrome P450, putative identical to ent-kaurenoic acid hydroxylase / cytochrome P450 CYP88A (GI:1302...1856) [Arabidopsis thaliana]; similar to ent-kaurenoic acid hydroxylase [Arabidopsis thaliana] GI:13021853 4e-22 ...

  2. Arabidopsis CDS blastp result: AK241119 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK241119 J065094C22 At2g32440.1 68415.m03963 ent-kaurenoic acid hydroxylase, putati...ve / cytochrome P450, putative identical to ent-kaurenoic acid hydroxylase / cytochrome P450 CYP88A (GI:1302...1856) [Arabidopsis thaliana]; similar to ent-kaurenoic acid hydroxylase [Arabidopsis thaliana] GI:13021853 2e-13 ...

  3. Arabidopsis CDS blastp result: AK243149 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK243149 J100032I21 At2g32440.1 68415.m03963 ent-kaurenoic acid hydroxylase, putati...ve / cytochrome P450, putative identical to ent-kaurenoic acid hydroxylase / cytochrome P450 CYP88A (GI:1302...1856) [Arabidopsis thaliana]; similar to ent-kaurenoic acid hydroxylase [Arabidopsis thaliana] GI:13021853 7e-12 ...

  4. Arabidopsis CDS blastp result: AK241581 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK241581 J065181K09 At2g32440.1 68415.m03963 ent-kaurenoic acid hydroxylase, putati...ve / cytochrome P450, putative identical to ent-kaurenoic acid hydroxylase / cytochrome P450 CYP88A (GI:1302...1856) [Arabidopsis thaliana]; similar to ent-kaurenoic acid hydroxylase [Arabidopsis thaliana] GI:13021853 4e-15 ...

  5. Arabidopsis CDS blastp result: AK287479 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK287479 J043023O14 At2g32440.1 68415.m03963 ent-kaurenoic acid hydroxylase, putati...ve / cytochrome P450, putative identical to ent-kaurenoic acid hydroxylase / cytochrome P450 CYP88A (GI:1302...1856) [Arabidopsis thaliana]; similar to ent-kaurenoic acid hydroxylase [Arabidopsis thaliana] GI:13021853 1e-17 ...

  6. Using "Arabidopsis" Genetic Sequences to Teach Bioinformatics

    Science.gov (United States)

    Zhang, Xiaorong

    2009-01-01

    This article describes a new approach to teaching bioinformatics using "Arabidopsis" genetic sequences. Several open-ended and inquiry-based laboratory exercises have been designed to help students grasp key concepts and gain practical skills in bioinformatics, using "Arabidopsis" leucine-rich repeat receptor-like kinase (LRR RLK) genetic…

  7. An International Bioinformatics Infrastructure to Underpin the Arabidopsis Community

    Science.gov (United States)

    The future bioinformatics needs of the Arabidopsis community as well as those of other scientific communities that depend on Arabidopsis resources were discussed at a pair of recent meetings held by the Multinational Arabidopsis Steering Committee (MASC) and the North American Arabidopsis Steering C...

  8. How salicylic acid takes transcriptional control over jasmonic acid signaling

    Directory of Open Access Journals (Sweden)

    Lotte eCaarls

    2015-03-01

    Full Text Available Transcriptional regulation is a central process in plant immunity. The induction or repression of defense genes is orchestrated by signaling networks that are directed by plant hormones of which salicylic acid (SA and jasmonic acid (JA are the major players. Extensive cross-communication between the hormone signaling pathways allows for fine tuning of transcriptional programs, determining resistance to invaders and trade-offs with plant development. Here, we give an overview of how SA can control transcriptional reprogramming of JA-induced genes in Arabidopsis thaliana. SA can influence activity and/or localization of transcriptional regulators by post-translational modifications of transcription factors and co-regulators. SA-induced redox changes, mediated by thioredoxins and glutaredoxins, modify transcriptional regulators that are involved in suppression of JA-dependent genes, such as NPR1 and TGA transcription factors, which affects their localization or DNA binding activity. Furthermore, SA can mediate sequestering of JA-responsive transcription factors away from their target genes by stalling them in the cytosol or in complexes with repressor proteins in the nucleus. SA also affects JA-induced transcription by inducing degradation of transcription factors with an activating role in JA signaling, as was shown for the ERF transcription factor ORA59. Additionally, SA can induce negative regulators, among which WRKY transcription factors, that can directly or indirectly inhibit JA-responsive gene expression. Finally, at the DNA level, modification of histones by SA-dependent factors can result in repression of JA-responsive genes. These diverse and complex regulatory mechanisms affect important signaling hubs in the integration of hormone signaling networks. Some pathogens have evolved effectors that highjack hormone crosstalk mechanisms for their own good, which are described in this review as well.

  9. Tape-Arabidopsis Sandwich - a simpler Arabidopsis protoplast isolation method

    Directory of Open Access Journals (Sweden)

    Lee Shu-Hong

    2009-11-01

    Full Text Available Abstract Background Protoplasts isolated from leaves are useful materials in plant research. One application, the transient expression of recombinant genes using Arabidopsis mesophyll protoplasts (TEAMP, is currently commonly used for studies of subcellular protein localization, promoter activity, and in vivo protein-protein interactions. This method requires cutting leaves into very thin slivers to collect mesophyll cell protoplasts, a procedure that often causes cell damage, may yield only a few good protoplasts, and is time consuming. In addition, this protoplast isolation method normally requires a large number of leaves derived from plants grown specifically under low-light conditions, which may be a concern when material availability is limited such as with mutant plants, or in large scale experiments. Results In this report, we present a new procedure that we call the Tape-Arabidopsis Sandwich. This is a simple and fast mesophyll protoplast isolation method. Two kinds of tape (Time tape adhered to the upper epidermis and 3 M Magic tape to the lower epidermis are used to make a "Tape-Arabidopsis Sandwich". The Time tape supports the top side of the leaf during manipulation, while tearing off the 3 M Magic tape allows easy removal of the lower epidermal layer and exposes mesophyll cells to cell wall digesting enzymes when the leaf is later incubated in an enzyme solution. The protoplasts released into solution are collected and washed for further use. For TEAMP, plasmids carrying a gene expression cassette for a fluorescent protein can be successfully delivered into protoplasts isolated from mature leaves grown under optimal conditions. Alternatively, these protoplasts may be used for bimolecular fluorescence complementation (BiFC to investigate protein-protein interactions in vivo, or for Western blot analysis. A significant advantage of this protocol over the current method is that it allows the generation of protoplasts in less than 1 hr

  10. Erasure of CpG methylation in Arabidopsis alters patterns of histone H3 methylation in heterochromatin

    DEFF Research Database (Denmark)

    Tariq, M.; Saze, H.; Probst, A.;

    2003-01-01

    DNA methylation to histone methylation, however, is less understood. Its recent examination in Arabidopsis with a partial loss of function in DNA methyltransferase 1 (responsible for maintenance of CpG methylation) yielded conflicting results. Here we report that complete removal of CpG methylation...... in an Arabidopsis mutant null for DNA maintenance methyltransferase results in a clear loss of histone H3 methylation at lysine 9 in heterochromatin and also at heterochromatic loci that remain transcriptionally silent. Surprisingly, these dramatic alterations are not reflected in heterochromatin relaxation.......In mammals and plants, formation of heterochromatin is associated with hypermethylation of DNA at CpG sites and histone H3 methylation at lysine 9. Previous studies have revealed that maintenance of DNA methylation in Neurospora and Arabidopsis requires histone H3 methylation. A feedback loop from...

  11. Methylation of Gibberellins by Arabidopsis GAMT1 and GAMT2

    Energy Technology Data Exchange (ETDEWEB)

    Varbanova,M.; Yamaguchi, S.; Yang, Y.; McKelvey, K.; Hanada, A.; Borochov, R.; Yu, F.; Jikumaru, Y.; Ross, J.; et al

    2007-01-01

    Arabidopsis thaliana GAMT1 and GAMT2 encode enzymes that catalyze formation of the methyl esters of gibberellins (GAs). Ectopic expression of GAMT1 or GAMT2 in Arabidopsis, tobacco (Nicotiana tabacum), and petunia (Petunia hybrida) resulted in plants with GA deficiency and typical GA deficiency phenotypes, such as dwarfism and reduced fertility. GAMT1 and GAMT2 are both expressed mainly in whole siliques (including seeds), with peak transcript levels from the middle until the end of silique development. Within whole siliques, GAMT2 was previously shown to be expressed mostly in developing seeds, and we show here that GAMT1 expression is also localized mostly to seed, suggesting a role in seed development. Siliques of null single GAMT1 and GAMT2 mutants accumulated high levels of various GAs, with particularly high levels of GA1 in the double mutant. Methylated GAs were not detected in wild-type siliques, suggesting that methylation of GAs by GAMT1 and GAMT2 serves to deactivate GAs and initiate their degradation as the seeds mature. Seeds of homozygous GAMT1 and GAMT2 null mutants showed reduced inhibition of germination, compared with the wild type, when placed on plates containing the GA biosynthesis inhibitor ancymidol, with the double mutant showing the least inhibition. These results suggest that the mature mutant seeds contained higher levels of active GAs than wild-type seeds.

  12. [Regulation pattern of the FRUITFULL (FUL) gene of Arabidopsis thaliana].

    Science.gov (United States)

    Chu, Tingting; Xie, Hua; Xu, Yong; Ma, Rongcai

    2010-11-01

    FRUITFULL (FUL) is an MADS box gene that functions early in controlling flowering time, meristem identity and cauline leaf morphology and later in carpel and fruit development in Arabidopsis thaliana. In order to clarify the regulation of FUL expression the upstream regulatory region, -2148 bp - +96 bp and the first intron of the FUL gene were cloned, and vectors with a series of deletion of FUL promoter, and the ones fused with the first intron were constructed. Vectors harboring the fusion of cis-acting elements with the constitutive promoters of TUBULIN and ACTIN were also constructed. Beta-Glucuronidase activity assays of the transgenic Arabidopsis plants showed that two cis-elements were involved in the repression of FUL expression, with one of the two being probably the binding site of the transcriptional factor AP1. And the two CArG boxes played a important role in FUL initiation particularly. Furthermore, the first intron of FUL was shown to participate in the development of carpel and stamen as an enhancer.

  13. Overexpression of Late Embryogenesis Abundant 14 enhances Arabidopsis salt stress tolerance

    Energy Technology Data Exchange (ETDEWEB)

    Jia, Fengjuan, E-mail: jfj.5566@163.com; Qi, Shengdong, E-mail: zisexanwu@163.com; Li, Hui, E-mail: 332453593@qq.com; Liu, Pu, E-mail: banbaokezhan@163.com; Li, Pengcheng, E-mail: lpcsdau@163.com; Wu, Changai, E-mail: cawu@sdau.edu.cn; Zheng, Chengchao, E-mail: cczheng@sdau.edu.cn; Huang, Jinguang, E-mail: jghuang@sdau.edu.cn

    2014-11-28

    Highlights: • It is the first time to investigate the biological function of AtLEA14 in salt stress response. • AtLEA14 enhances the salt stress tolerance both in Arabidopsis and yeast. • AtLEA14 responses to salt stress by stabilizing AtPP2-B11, an E3 ligase, under normal or salt stress conditions. - Abstract: Late embryogenesis abundant (LEA) proteins are implicated in various abiotic stresses in higher plants. In this study, we identified a LEA protein from Arabidopsis thaliana, AtLEA14, which was ubiquitously expressed in different tissues and remarkably induced with increased duration of salt treatment. Subcellular distribution analysis demonstrated that AtLEA14 was mainly localized in the cytoplasm. Transgenic Arabidopsis and yeast overexpressing AtLEA14 all exhibited enhanced tolerance to high salinity. The transcripts of salt stress-responsive marker genes (COR15a, KIN1, RD29B and ERD10) were overactivated in AtLEA14 overexpressing lines compared with those in wild type plants under normal or salt stress conditions. In vivo and in vitro analysis showed that AtLEA14 could effectively stabilize AtPP2-B11, an important E3 ligase. These results suggested that AtLEA14 had important protective functions under salt stress conditions in Arabidopsis.

  14. Overexpression of Nelumbo nucifera metallothioneins 2a and 3 enhances seed germination vigor in Arabidopsis.

    Science.gov (United States)

    Zhou, Yuliang; Chu, Pu; Chen, Huhui; Li, Yin; Liu, Jun; Ding, Yu; Tsang, Edward W T; Jiang, Liwen; Wu, Keqiang; Huang, Shangzhi

    2012-03-01

    Metallothioneins (MTs) are small, cysteine-rich and metal-binding proteins which are involved in metal homeostasis and scavenging of reactive oxygen species. Although plant MTs have been intensively studied, their roles in seeds remain to be clearly established. Here, we report the isolation and characterization of NnMT2a, NnMT2b and NnMT3 from sacred lotus (Nelumbo nucifera Gaertn.) and their roles in seed germination vigor. The transcripts of NnMT2a, NnMT2b and NnMT3 were highly expressed in developing and germinating sacred lotus seeds, and were dramatically up-regulated in response to high salinity, oxidative stresses and heavy metals. Analysis of transformed Arabidopsis protoplasts showed that NnMT2a-YFP and NnMT3-YFP were localized in cytoplasm and nucleoplasm. Transgenic Arabidopsis seeds overexpressing NnMT2a and NnMT3 displayed improved resistance to accelerated aging (AA) treatment, indicating their significant roles in seed germination vigor. These transgenic seeds also exhibited higher superoxide dismutase activity compared to wild-type seeds after AA treatment. In addition, we showed that NnMT2a and NnMT3 conferred improved germination ability to NaCl and methyl viologen on transgenic Arabidopsis seeds. Taken together, these data demonstrate that overexpression of NnMT2a and NnMT3 in Arabidopsis significantly enhances seed germination vigor after AA treatment and under abiotic stresses.

  15. Folic acid induces salicylic acid-dependent immunity in Arabidopsis and enhances susceptibility to Alternaria brassicicola.

    Science.gov (United States)

    Wittek, Finni; Kanawati, Basem; Wenig, Marion; Hoffmann, Thomas; Franz-Oberdorf, Katrin; Schwab, Wilfried; Schmitt-Kopplin, Philippe; Vlot, A Corina

    2015-08-01

    Folates are essential for one-carbon transfer reactions in all organisms and contribute, for example, to de novo DNA synthesis. Here, we detected the folate precursors 7,8-dihydropteroate (DHP) and 4-amino-4-deoxychorismate (ADC) in extracts from Arabidopsis thaliana plants by Fourier transform ion cyclotron resonance-mass spectrometry. The accumulation of DHP, but not ADC, was induced after infection of plants with Pseudomonas syringae delivering the effector protein AvrRpm1. Application of folic acid or the DHP precursor 7,8-dihydroneopterin (DHN) enhanced resistance in Arabidopsis to P. syringae and elevated the transcript accumulation of the salicylic acid (SA) marker gene pathogenesis-related1 in both the treated and systemic untreated leaves. DHN- and folic acid-induced systemic resistance was dependent on SA biosynthesis and signalling. Similar to SA, folic acid application locally enhanced Arabidopsis susceptibility to the necrotrophic fungus Alternaria brassicicola. Together, the data associate the folic acid pathway with innate immunity in Arabidopsis, simultaneously activating local and systemic SA-dependent resistance to P. syringae and suppressing local resistance to A. brassicicola.

  16. Arabidopsis thaliana is an asymptomatic host of Alfalfa mosaic virus.

    Science.gov (United States)

    Balasubramaniam, Muthukumar; Ibrahim, Amr; Kim, Bong-Suk; Loesch-Fries, L Sue

    2006-11-01

    The susceptibility of Arabidopsis thaliana ecotypes to infection by Alfalfa mosaic virus (AMV) was evaluated. Thirty-nine ecotypes supported both local and systemic infection, 26 ecotypes supported only local infection, and three ecotypes could not be infected. No obvious symptoms characteristic of virus infection developed on the susceptible ecotypes under standard conditions of culture. Parameters of AMV infection were characterized in ecotype Col-0, which supported systemic infection and accumulated higher levels of AMV than the symptomatic host Nicotiana tabacum. The formation of infectious AMV particles in infected Col-0 was confirmed by infectivity assays on a hypersensitive host and by electron microscopy of purified virions. Replication and transcription of AMV was confirmed by de novo synthesis of AMV subgenomic RNA in Col-0 protoplasts transfected with AMV RNA or plasmids harboring AMV cDNAs. PMID:16875753

  17. Manipulation of hemoglobin expression affects Arabidopsis shoot organogenesis

    DEFF Research Database (Denmark)

    Wang, Yaping; Elhiti, Mohamed; Hebelstrup, Kim;

    2011-01-01

    Over the past few years non-symbiotic plant hemoglobins have been described in a variety of plant species where they fulfill several functions ranging from detoxification processes to basic aspects of plant growth and post-embryonic development. To date no information is available on the role...... of hemoglobins during invitro morphogenesis. Shoot organogenesis was induced in Arabidopsis lines constitutively expressing class 1, 2 and 3 hemoglobins (GLB1, 2 and 3) and lines in which the respective genes were either downregulated by RNAi (GLB1) or knocked out (GLB2 and GLB3). The process was executed......, 15, and 16), feed-back repressors of the cytokinin pathway, was repressed in both hemoglobin over-expressors whereas that of several Type-B ARRs (ARR2, 12, and 13), transcription activators of cytokinin-responsive genes, was induced. Such changes enhanced the sensitivity of the root explants...

  18. Jasmonate Signal Pathway in Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    Xiao-Yi Shan; Zhi-Long Wang; Daoxin Xie

    2007-01-01

    Jasmonates (JAs), which include jasmonic acid and its cyclopentane derivatives are synthesized from the octadecanoid pathway and widely distributed throughout the plant kingdom. JAs modulate the expression of numerous genes and mediate responses to stress, wounding, insect attack, pathogen infection, and UV damage. They also affect a variety of processes in many plant developmental processes. The JA signal pathway involves two important events: the biosynthesis of JA and the transduction of JA signal. Several important Arabidopsis mutants in jasmonate signal pathway were described in this review.

  19. Overexpression of OsWRKY72 gene interferes in the abscisic acid signal and auxin transport pathway of Arabidopsis

    Indian Academy of Sciences (India)

    Song Yu; Chen Ligang; Zhang Liping; Yu Diqiu

    2010-09-01

    Through activating specific transcriptional programmes, plants can launch resistance mechanisms to stressful environments and acquire a new equilibrium between development and defence. To screen the rice WRKY transcription factor which functions in abiotic stress tolerance and modulates the abscisic acid (ABA) response, we generated a whole array of 35S-OsWRKY transgenic Arabidopsis. In this study, we report that 35S-OsWRKY72 transgenic Arabidopsis, whose seed germination was retarded under normal conditions, emerged more sensitive to mannitol, NaCl, ABA stresses and sugar starvation than vector plants. Meanwhile, 35S-OsWRKY72 transgenic Arabidopsis displayed early flowering, reduced apical dominance, lost high temperature-induced hypocotyl elongation response, and enhanced gravitropism response, which were similar to the auxin-related gene mutants aux1, axr1 and bud1. Further, semi-quantitative RT-PCR showed that the expression patterns of three auxin-related genes AUX1, AXR1 and BUD1 were significantly altered in rosette leaves and inflorescences of 35S-OsWRKY72 plants compared with control Arabidopsis, and two ABA-related genes ABA2 and ABI4 were induced in 35S-OsWRKY72 seedlings. In addition, northern blot analysis indicated that, in rice, OsWRKY72 was inducible by polyethylene glycol (PEG), NaCl, naphthalene acetic acid (NAA), ABA and 42°C, similar to its orthologue AtWRKY75 in Arabidopsis, implying that these two WRKY genes might be required for multiple physiological processes in their plants. Together, these results suggest that OsWRKY72 interferes in the signal cross-talk between the ABA signal and auxin transport pathway in transgenic Arabidopsis.

  20. The Clubroot Pathogen (Plasmodiophora brassicae Influences Auxin Signaling to Regulate Auxin Homeostasis in Arabidopsis

    Directory of Open Access Journals (Sweden)

    Linda Jahn

    2013-11-01

    Full Text Available The clubroot disease, caused by the obligate biotrophic protist Plasmodiophora brassicae, affects cruciferous crops worldwide. It is characterized by root swellings as symptoms, which are dependent on the alteration of auxin and cytokinin metabolism. Here, we describe that two different classes of auxin receptors, the TIR family and the auxin binding protein 1 (ABP1 in Arabidopsis thaliana are transcriptionally upregulated upon gall formation. Mutations in the TIR family resulted in more susceptible reactions to the root pathogen. As target genes for the different pathways we have investigated the transcriptional regulation of selected transcriptional repressors (Aux/IAA and transcription factors (ARF. As the TIR pathway controls auxin homeostasis via the upregulation of some auxin conjugate synthetases (GH3, the expression of selected GH3 genes was also investigated, showing in most cases upregulation. A double gh3 mutant showed also slightly higher susceptibility to P. brassicae infection, while all tested single mutants did not show any alteration in the clubroot phenotype. As targets for the ABP1-induced cell elongation the effect of potassium channel blockers on clubroot formation was investigated. Treatment with tetraethylammonium (TEA resulted in less severe clubroot symptoms. This research provides evidence for the involvement of two auxin signaling pathways in Arabidopsis needed for the establishment of the root galls by P. brassicae.

  1. Analysis of Arabidopsis JAZ gene expression during Pseudomonas syringae pathogenesis.

    Science.gov (United States)

    Demianski, Agnes J; Chung, Kwi Mi; Kunkel, Barbara N

    2012-01-01

    The jasmonates (JAs) comprise a family of plant hormones that regulate several developmental processes and mediate responses to various abiotic and biotic stresses, including pathogens. JA signalling is manipulated by several strains of the bacterial pathogen Pseudomonas syringae, including P. syringae strain DC3000, using the virulence factor coronatine (COR) as a mimic of jasmonyl-L-isoleucine (JA-Ile). To better understand the JA-Ile-mediated processes contributing to P. syringae disease susceptibility, it is important to investigate the regulation of JA signalling during infection. In Arabidopsis thaliana, JASMONATE ZIM-DOMAIN (JAZ) proteins are negative regulators of JA signalling. The transcription factor JASMONATE INSENSITIVE1 (JIN1/ATMYC2) has been implicated in the regulation of JAZ gene expression. To investigate the regulation of JAZ genes during P. syringae pathogenesis, we examined JAZ gene expression during infection of Arabidopsis by DC3000. We found that eight of the 12 JAZ genes are induced during infection in a COR-dependent manner. Unexpectedly, the induction of the majority of JAZ genes during infection was not dependent on JIN1, indicating that JIN1 is not the only transcription factor regulating JAZ genes. A T-DNA insertion mutant and an RNA interference line disrupted for the expression of JAZ10, one of the few JAZ genes regulated by JIN1 during infection, exhibited enhanced JA sensitivity and increased susceptibility to DC3000, with the primary effect being increased disease symptom severity. Thus, JAZ10 is a negative regulator of both JA signalling and disease symptom development. PMID:21726394

  2. Analysis of Arabidopsis JAZ gene expression during Pseudomonas syringae pathogenesis.

    Science.gov (United States)

    Demianski, Agnes J; Chung, Kwi Mi; Kunkel, Barbara N

    2012-01-01

    The jasmonates (JAs) comprise a family of plant hormones that regulate several developmental processes and mediate responses to various abiotic and biotic stresses, including pathogens. JA signalling is manipulated by several strains of the bacterial pathogen Pseudomonas syringae, including P. syringae strain DC3000, using the virulence factor coronatine (COR) as a mimic of jasmonyl-L-isoleucine (JA-Ile). To better understand the JA-Ile-mediated processes contributing to P. syringae disease susceptibility, it is important to investigate the regulation of JA signalling during infection. In Arabidopsis thaliana, JASMONATE ZIM-DOMAIN (JAZ) proteins are negative regulators of JA signalling. The transcription factor JASMONATE INSENSITIVE1 (JIN1/ATMYC2) has been implicated in the regulation of JAZ gene expression. To investigate the regulation of JAZ genes during P. syringae pathogenesis, we examined JAZ gene expression during infection of Arabidopsis by DC3000. We found that eight of the 12 JAZ genes are induced during infection in a COR-dependent manner. Unexpectedly, the induction of the majority of JAZ genes during infection was not dependent on JIN1, indicating that JIN1 is not the only transcription factor regulating JAZ genes. A T-DNA insertion mutant and an RNA interference line disrupted for the expression of JAZ10, one of the few JAZ genes regulated by JIN1 during infection, exhibited enhanced JA sensitivity and increased susceptibility to DC3000, with the primary effect being increased disease symptom severity. Thus, JAZ10 is a negative regulator of both JA signalling and disease symptom development.

  3. Arabidopsis PIZZA has the capacity to acylate brassinosteroids.

    Science.gov (United States)

    Schneider, Katja; Breuer, Christian; Kawamura, Ayako; Jikumaru, Yusuke; Hanada, Atsushi; Fujioka, Shozo; Ichikawa, Takanari; Kondou, Youichi; Matsui, Minami; Kamiya, Yuji; Yamaguchi, Shinjiro; Sugimoto, Keiko

    2012-01-01

    Brassinosteroids (BRs) affect a wide range of developmental processes in plants and compromised production or signalling of BRs causes severe growth defects. To identify new regulators of plant organ growth, we searched the Arabidopsis FOX (Full-length cDNA Over-eXpressor gene) collection for mutants with altered organ size and isolated two overexpression lines that display typical BR deficient dwarf phenotypes. The phenotype of these lines, caused by an overexpression of a putative acyltransferase gene PIZZA (PIZ), was partly rescued by supplying exogenous brassinolide (BL) and castasterone (CS), indicating that endogenous BR levels are rate-limiting for the growth of PIZ overexpression lines. Our transcript analysis further showed that PIZ overexpression leads to an elevated expression of genes involved in BR biosynthesis and a reduced expression of BR inactivating hydroxylases, a transcriptional response typical to low BR levels. Taking the advantage of relatively high endogenous BR accumulation in a mild bri1-301 background, we found that overexpression of PIZ results in moderately reduced levels of BL and CS and a strong reduction of typhasterol (TY) and 6-deoxocastasterone (6-deoxoCS), suggesting a role of PIZ in BR metabolism. We tested a set of potential substrates in vitro for heterologously expressed PIZ and confirmed its acyltransferase activity with BL, CS and TY. The PIZ gene is expressed in various tissues but as reported for other genes involved in BR metabolism, the loss-of-function mutants did not display obvious growth phenotypes under standard growth conditions. Together, our data suggest that PIZ can modify BRs by acylation and that these properties might help modulating endogenous BR levels in Arabidopsis.

  4. Arabidopsis PIZZA has the capacity to acylate brassinosteroids.

    Directory of Open Access Journals (Sweden)

    Katja Schneider

    Full Text Available Brassinosteroids (BRs affect a wide range of developmental processes in plants and compromised production or signalling of BRs causes severe growth defects. To identify new regulators of plant organ growth, we searched the Arabidopsis FOX (Full-length cDNA Over-eXpressor gene collection for mutants with altered organ size and isolated two overexpression lines that display typical BR deficient dwarf phenotypes. The phenotype of these lines, caused by an overexpression of a putative acyltransferase gene PIZZA (PIZ, was partly rescued by supplying exogenous brassinolide (BL and castasterone (CS, indicating that endogenous BR levels are rate-limiting for the growth of PIZ overexpression lines. Our transcript analysis further showed that PIZ overexpression leads to an elevated expression of genes involved in BR biosynthesis and a reduced expression of BR inactivating hydroxylases, a transcriptional response typical to low BR levels. Taking the advantage of relatively high endogenous BR accumulation in a mild bri1-301 background, we found that overexpression of PIZ results in moderately reduced levels of BL and CS and a strong reduction of typhasterol (TY and 6-deoxocastasterone (6-deoxoCS, suggesting a role of PIZ in BR metabolism. We tested a set of potential substrates in vitro for heterologously expressed PIZ and confirmed its acyltransferase activity with BL, CS and TY. The PIZ gene is expressed in various tissues but as reported for other genes involved in BR metabolism, the loss-of-function mutants did not display obvious growth phenotypes under standard growth conditions. Together, our data suggest that PIZ can modify BRs by acylation and that these properties might help modulating endogenous BR levels in Arabidopsis.

  5. Genome-Wide Analysis of Genes Encoding Methionine-Rich Proteins in Arabidopsis and Soybean Suggesting Their Roles in the Adaptation of Plants to Abiotic Stress.

    Science.gov (United States)

    Chu, Ha Duc; Le, Quynh Ngoc; Nguyen, Huy Quang; Le, Dung Tien

    2016-01-01

    Oxidation and reduction of methionine (Met) play important roles in scavenging reactive oxygen species (ROS) and signaling in living organisms. To understand the impacts of Met oxidation and reduction in plants during stress, we surveyed the genomes of Arabidopsis and soybean (Glycine max L.) for genes encoding Met-rich proteins (MRPs). We found 121 and 213 genes encoding MRPs in Arabidopsis and soybean, respectively. Gene annotation indicated that those with known function are involved in vital cellular processes such as transcriptional control, calcium signaling, protein modification, and metal transport. Next, we analyzed the transcript levels of MRP-coding genes under normal and stress conditions. We found that 57 AtMRPs were responsive either to drought or to high salinity stress in Arabidopsis; 35 GmMRPs were responsive to drought in the leaf of late vegetative or early reproductive stages of soybean. Among the MRP genes with a known function, the majority of the abiotic stress-responsive genes are involved in transcription control and calcium signaling. Finally, Arabidopsis plant which overexpressed an MRP-coding gene, whose transcripts were downregulated by abiotic stress, was more sensitive to paraquat than the control. Taken together, our report indicates that MRPs participate in various vital processes of plants under normal and stress conditions. PMID:27635394

  6. Rhizobacterial volatiles and photosynthesis-related signals coordinate MYB72 in Arabidopsis roots during onset of induced systemic resistance and iron deficiency responses

    NARCIS (Netherlands)

    Zamioudis, C.; Korteland, J.; Van Pelt, J.A.; Van Hamersveld, M.; Dombrowski, N.; Bai, Y.; Hanson, J.; Van Verk, M.C.; Ling, H.-Q.; Schulze-Lefert, P.; Pieterse, C.M.J.

    2015-01-01

    In Arabidopsis roots, the transcription factor MYB72 plays a dual role in the onset of rhizobacteria-induced systemic resistance (ISR) and plant survival under conditions of limited iron availability. Previously, it was shown that MYB72 coordinates the expression of a gene module that promotes synth

  7. An Arabidopsis thaliana knock-out mutant of the chloroplast triose phosphate/phosphate translocator is severely compromised only when starch synthesis, but not starch mobilisation is abolished

    DEFF Research Database (Denmark)

    Schneider, Anja; Häusler, Rainer E; Kolukisaoglu, Uner;

    2002-01-01

    The Arabidopsis thaliana tpt-1 mutant which is defective in the chloroplast triose phosphate/phosphate translocator (TPT) was isolated by reverse genetics. It contains a T-DNA insertion 24 bp upstream of the start ATG of the TPT gene. The mutant lacks TPT transcripts and triose phosphate (TP...

  8. Genome-Wide Analysis of Genes Encoding Methionine-Rich Proteins in Arabidopsis and Soybean Suggesting Their Roles in the Adaptation of Plants to Abiotic Stress

    Science.gov (United States)

    Chu, Ha Duc; Le, Quynh Ngoc; Nguyen, Huy Quang

    2016-01-01

    Oxidation and reduction of methionine (Met) play important roles in scavenging reactive oxygen species (ROS) and signaling in living organisms. To understand the impacts of Met oxidation and reduction in plants during stress, we surveyed the genomes of Arabidopsis and soybean (Glycine max L.) for genes encoding Met-rich proteins (MRPs). We found 121 and 213 genes encoding MRPs in Arabidopsis and soybean, respectively. Gene annotation indicated that those with known function are involved in vital cellular processes such as transcriptional control, calcium signaling, protein modification, and metal transport. Next, we analyzed the transcript levels of MRP-coding genes under normal and stress conditions. We found that 57 AtMRPs were responsive either to drought or to high salinity stress in Arabidopsis; 35 GmMRPs were responsive to drought in the leaf of late vegetative or early reproductive stages of soybean. Among the MRP genes with a known function, the majority of the abiotic stress-responsive genes are involved in transcription control and calcium signaling. Finally, Arabidopsis plant which overexpressed an MRP-coding gene, whose transcripts were downregulated by abiotic stress, was more sensitive to paraquat than the control. Taken together, our report indicates that MRPs participate in various vital processes of plants under normal and stress conditions.

  9. Molecular signatures in Arabidopsis thaliana in response to insect attack and bacterial infection.

    Directory of Open Access Journals (Sweden)

    Pankaj Barah

    Full Text Available BACKGROUND: Under the threat of global climatic change and food shortages, it is essential to take the initiative to obtain a comprehensive understanding of common and specific defence mechanisms existing in plant systems for protection against different types of biotic invaders. We have implemented an integrated approach to analyse the overall transcriptomic reprogramming and systems-level defence responses in the model plant species Arabidopsis thaliana (A. thaliana henceforth during insect Brevicoryne brassicae (B. brassicae henceforth and bacterial Pseudomonas syringae pv. tomato strain DC3000 (P. syringae henceforth attacks. The main aim of this study was to identify the attacker-specific and general defence response signatures in A. thaliana when attacked by phloem-feeding aphids or pathogenic bacteria. RESULTS: The obtained annotated networks of differentially expressed transcripts indicated that members of transcription factor families, such as WRKY, MYB, ERF, BHLH and bZIP, could be crucial for stress-specific defence regulation in Arabidopsis during aphid and P. syringae attack. The defence response pathways, signalling pathways and metabolic processes associated with aphid attack and P. syringae infection partially overlapped. Components of several important biosynthesis and signalling pathways, such as salicylic acid (SA, jasmonic acid (JA, ethylene (ET and glucosinolates, were differentially affected during the two the treatments. Several stress-regulated transcription factors were known to be associated with stress-inducible microRNAs. The differentially regulated gene sets included many signature transcription factors, and our co-expression analysis showed that they were also strongly co-expressed during 69 other biotic stress experiments. CONCLUSIONS: Defence responses and functional networks that were unique and specific to aphid or P. syringae stresses were identified. Furthermore, our analysis revealed a probable link between

  10. 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

  11. TINY, a DREB-Like Transcription Factor Binding to DRE Element

    Institute of Scientific and Technical Information of China (English)

    曹志方; 陈峰; 李洁; 李一勤; 周海梦; 张贵友; 刘强

    2001-01-01

    TINY isolated through a transposon-mutagenesis experiment designed to recover dominant gain-of-function alleles in Arabidopsis encodes a protein containing a putative DNA-binding domain which is conserved in AP2/EREBP transcription factors of plants. AP2/EREBP transcription factors play a variety of regulatory roles in several developmental processes and in response to biotic and environmental stresses. Using the yeast one-hybrid analysis system, we demonstrated that TINY could function as a DREB-like transcription factor specifically binding to the dehydration-responsive element (DRE) cis-acting element.

  12. DNA binding by the plant-specific NAC transcription factors in crystal and solution

    DEFF Research Database (Denmark)

    Welner, Ditte Hededam; Lindemose, Søren; Grossmann, J. Günter;

    2012-01-01

    NAC (NAM/ATAF/CUC) plant transcription factors regulate essential processes in development, stress responses and nutrient distribution in important crop and model plants (rice, Populus, Arabidopsis), which makes them highly relevant in the context of crop optimization and bioenergy production...... transcription factors and the mammalian GCM (Glial cell missing) transcription factors, which all use a ß-strand motif for DNA-binding. The structure shows that the NAC domain inserts the edge of its core ß-sheet into the major groove, while leaving the DNA largely undistorted. The structure of the NAC...

  13. Reciprocal responses in the interaction between Arabidopsis and the cell-content-feeding chelicerate herbivore spider mite.

    Science.gov (United States)

    Zhurov, Vladimir; Navarro, Marie; Bruinsma, Kristie A; Arbona, Vicent; Santamaria, M Estrella; Cazaux, Marc; Wybouw, Nicky; Osborne, Edward J; Ens, Cherise; Rioja, Cristina; Vermeirssen, Vanessa; Rubio-Somoza, Ignacio; Krishna, Priti; Diaz, Isabel; Schmid, Markus; Gómez-Cadenas, Aurelio; Van de Peer, Yves; Grbic, Miodrag; Clark, Richard M; Van Leeuwen, Thomas; Grbic, Vojislava

    2014-01-01

    Most molecular-genetic studies of plant defense responses to arthropod herbivores have focused on insects. However, plant-feeding mites are also pests of diverse plants, and mites induce different patterns of damage to plant tissues than do well-studied insects (e.g. lepidopteran larvae or aphids). The two-spotted spider mite (Tetranychus urticae) is among the most significant mite pests in agriculture, feeding on a staggering number of plant hosts. To understand the interactions between spider mite and a plant at the molecular level, we examined reciprocal genome-wide responses of mites and its host Arabidopsis (Arabidopsis thaliana). Despite differences in feeding guilds, we found that transcriptional responses of Arabidopsis to mite herbivory resembled those observed for lepidopteran herbivores. Mutant analysis of induced plant defense pathways showed functionally that only a subset of induced programs, including jasmonic acid signaling and biosynthesis of indole glucosinolates, are central to Arabidopsis's defense to mite herbivory. On the herbivore side, indole glucosinolates dramatically increased mite mortality and development times. We identified an indole glucosinolate dose-dependent increase in the number of differentially expressed mite genes belonging to pathways associated with detoxification of xenobiotics. This demonstrates that spider mite is sensitive to Arabidopsis defenses that have also been associated with the deterrence of insect herbivores that are very distantly related to chelicerates. Our findings provide molecular insights into the nature of, and response to, herbivory for a representative of a major class of arthropod herbivores.

  14. Cis-regulatory element-based genome-wide identification of DREB1/CBF targets in Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    Huan Zhao; Weizhong Liu; Yong Hu; Xianglin Liu; Yikun He

    2008-01-01

    Microarray analysis is used to identify transcriptional targets.However,the direct targets of transcription factors cannot be distin guished from indirect ones;further,genes with low-expression levels cannot be identified by this method.In the present study,we exploi the cis-element dehydration-responsive element(DRE)that is known to be responsible for the transcription of DRE binding factor](DREB1)targets in the promoter region of all Arabidopsis genes.Putative targets whose promoters contain the elements were verified by both microarray and reverse transcription-polymerase chain reaction(RT-PCR)analysis.Five new DREB 1/CBF direct targets were identified.Compared with traditional microarray analysis,our method is convenient and cost-effective for identifying the downstream targets of transcription factors.

  15. Polyploidy in the Arabidopsis genus.

    Science.gov (United States)

    Bomblies, Kirsten; Madlung, Andreas

    2014-06-01

    Whole genome duplication (WGD), which gives rise to polyploids, is a unique type of mutation that duplicates all the genetic material in a genome. WGD provides an evolutionary opportunity by generating abundant genetic "raw material," and has been implicated in diversification, speciation, adaptive radiation, and invasiveness, and has also played an important role in crop breeding. However, WGD at least initially challenges basic biological functions by increasing cell size, altering relationships between cell volume and DNA content, and doubling the number of homologous chromosome copies that must be sorted during cell division. Newly polyploid lineages often have extensive changes in gene regulation, genome structure, and may suffer meiotic or mitotic chromosome mis-segregation. The abundance of species that persist in nature as polyploids shows that these problems are surmountable and/or that advantages of WGD might outweigh drawbacks. The molecularly especially tractable Arabidopsis genus has several ancient polyploidy events in its history and contains several independent more recent polyploids. This genus can thus provide important insights into molecular aspects of polyploid formation, establishment, and genome evolution. The ability to integrate ecological and evolutionary questions with molecular and genetic understanding makes comparative analyses in this genus particularly attractive and holds promise for advancing our general understanding of polyploid biology. Here, we highlight some of the findings from Arabidopsis that have given us insights into the origin and evolution of polyploids. PMID:24788061

  16. The Function of the Early Trichomes Gene in Arabidopsis and Maize.

    Energy Technology Data Exchange (ETDEWEB)

    Scott Poethig

    2011-12-05

    Lateral organ polarity in Arabidopsis is regulated by antagonistic interactions between genes that promote either adaxial or abaxial identity, but the molecular basis of this interaction is largely unknown. We show that the adaxial regulator ASYMMETRIC LEAVES2 (AS2) is a direct target of the abaxial regulator KANADI1 (KAN1), and that KAN1 represses the transcription of AS2 in abaxial cells. Mutation of a single nucleotide in a KAN1 binding site in the AS2 promoter causes AS2 to be ectopically expressed in abaxial cells, resulting in a dominant, adaxialized phenotype. We also show that the abaxial expression of KAN1 is mediated directly or indirectly by AS2. These results demonstrate that KAN1 acts as a transcriptional repressor and that mutually repressive interactions between KAN1 and AS2 contribute to the establishment of adaxial-abaxial polarity in plants. A screen for mutations that affect the expression of a GFP reporter for KANADI2 produced mutations in two genes, CENTER CITY (CCT) and GRAND CENTRAL (GCT). Mutations in GCT and CCT delay the specification of central and peripheral identity and the globular-to-heart transition, but have little or no effect on the initial growth rate of the embryo. Mutant embryos eventually recover and undergo relatively normal patterning, albeit at an inappropriate size. GCT and CCT were identified as the Arabidopsis orthologs of MED12 and MED13--evolutionarily conserved proteins that act in association with the Mediator complex to negatively regulate transcription. The predicted function of these proteins combined with the effect of gct and cct on embryo development suggests that MED12 and MED13 regulate pattern formation during Arabidopsis embryogenesis by transiently repressing a transcriptional program that interferes with this process. Their mutant phenotype reveals the existence of a previously unknown temporal regulatory mechanism in plant embryogenesis.

  17. 莲瓣兰转录因子 MADS 家族 DEF 基因克隆及拟南芥遗传转化%Clone Transcription Factor of DEF-Like MADS Family Gene from Cymbidium lianpan and Its Transformation in Arabidopsis thaliana

    Institute of Scientific and Technical Information of China (English)

    李琼洁; 朱芮; 王小巧; 朱永平; 赵兴富; 肖靖译; 贾茸; 秦晓杰; 和凤美

    2014-01-01

    For research DEF gene function, DEF gene with open reading frame from petals of Cymbidium lianpan cv.‘Yutu Caidie’was cloned using primers which had been designed based on Cymbidium goeringii DEF gene sequences logged in GenBank (HM106982.1), the expression vector was constructed, Arabidopsis thaliana was transformed. The results showed that DEF gene with open reading frame was 669 bp and encoded a protein of 222 amino acids and had 25.560 kD predicted protein molecules. The gene had a typical MADS-box gene structure. Homology analysis showed that DEF shared 99% similarity with Cymbidium goeringii and above 90% similarity with other orchids. Plant over expression vector was constructed by enzyme digestion of DEF gene and pCAMBIA2300 and successive ligation, and transferred into Arabidopsis thaliana by floral dip. Transgenic plants with DEF gene were obtained successfully after molecular identification.%本研究以莲瓣兰‘玉兔彩蝶’花瓣为材料,根据 GenBank 中已经登录的春兰 DEF 基因序列(HM106982.1)设计引物,克隆 DEF 基因开放阅读框,构建表达载体,转化‘拟南芥’,并验证基因功能。研究结果表明:所扩增的 DEF 基因开放阅读框大小为669 bp,编码222个氨基酸,预测蛋白质分子质量为25.560 kD。该基因具有典型的植物 MADS-box 基因结构域,与春兰开放阅读框同源性达99%,与其它兰花同源性都在90%以上。将 DEF 基因构建到植物真核表达载体 pCAMBIA2300中,利用农杆菌花序法转化拟南芥,经 PCR 分子鉴定,获得含 DEF 转基因拟南芥植株。

  18. 莲瓣兰转录因子 MADS 家族 DEF 基因克隆及拟南芥遗传转化%Clone Transcription Factor of DEF-Like MADS Family Gene from Cymbidium lianpan and Its Transformation in Arabidopsis thaliana

    Institute of Scientific and Technical Information of China (English)

    李琼洁; 朱芮; 王小巧; 朱永平; 赵兴富; 肖靖译; 贾茸; 秦晓杰; 和凤美

    2014-01-01

    本研究以莲瓣兰‘玉兔彩蝶’花瓣为材料,根据 GenBank 中已经登录的春兰 DEF 基因序列(HM106982.1)设计引物,克隆 DEF 基因开放阅读框,构建表达载体,转化‘拟南芥’,并验证基因功能。研究结果表明:所扩增的 DEF 基因开放阅读框大小为669 bp,编码222个氨基酸,预测蛋白质分子质量为25.560 kD。该基因具有典型的植物 MADS-box 基因结构域,与春兰开放阅读框同源性达99%,与其它兰花同源性都在90%以上。将 DEF 基因构建到植物真核表达载体 pCAMBIA2300中,利用农杆菌花序法转化拟南芥,经 PCR 分子鉴定,获得含 DEF 转基因拟南芥植株。%For research DEF gene function, DEF gene with open reading frame from petals of Cymbidium lianpan cv.‘Yutu Caidie’was cloned using primers which had been designed based on Cymbidium goeringii DEF gene sequences logged in GenBank (HM106982.1), the expression vector was constructed, Arabidopsis thaliana was transformed. The results showed that DEF gene with open reading frame was 669 bp and encoded a protein of 222 amino acids and had 25.560 kD predicted protein molecules. The gene had a typical MADS-box gene structure. Homology analysis showed that DEF shared 99% similarity with Cymbidium goeringii and above 90% similarity with other orchids. Plant over expression vector was constructed by enzyme digestion of DEF gene and pCAMBIA2300 and successive ligation, and transferred into Arabidopsis thaliana by floral dip. Transgenic plants with DEF gene were obtained successfully after molecular identification.

  19. The EDLL motif: a potent plant transcriptional activation domain from AP2/ERF transcription factors.

    Science.gov (United States)

    Tiwari, Shiv B; Belachew, Alemu; Ma, Siu Fong; Young, Melinda; Ade, Jules; Shen, Yu; Marion, Colleen M; Holtan, Hans E; Bailey, Adina; Stone, Jeffrey K; Edwards, Leslie; Wallace, Andreah D; Canales, Roger D; Adam, Luc; Ratcliffe, Oliver J; Repetti, Peter P

    2012-06-01

    In plants, the ERF/EREBP family of transcriptional regulators plays a key role in adaptation to various biotic and abiotic stresses. These proteins contain a conserved AP2 DNA-binding domain and several uncharacterized motifs. Here, we describe a short motif, termed 'EDLL', that is present in AtERF98/TDR1 and other clade members from the same AP2 sub-family. We show that the EDLL motif, which has a unique arrangement of acidic amino acids and hydrophobic leucines, functions as a strong activation domain. The motif is transferable to other proteins, and is active at both proximal and distal positions of target promoters. As such, the EDLL motif is able to partly overcome the repression conferred by the AtHB2 transcription factor, which contains an ERF-associated amphiphilic repression (EAR) motif. We further examined the activation potential of EDLL by analysis of the regulation of flowering time by NF-Y (nuclear factor Y) proteins. Genetic evidence indicates that NF-Y protein complexes potentiate the action of CONSTANS in regulation of flowering in Arabidopsis; we show that the transcriptional activation function of CONSTANS can be substituted by direct fusion of the EDLL activation motif to NF-YB subunits. The EDLL motif represents a potent plant activation domain that can be used as a tool to confer transcriptional activation potential to heterologous DNA-binding proteins.

  20. Transcriptional control of fleshy fruit development and ripening.

    Science.gov (United States)

    Karlova, Rumyana; Chapman, Natalie; David, Karine; Angenent, Gerco C; Seymour, Graham B; de Maagd, Ruud A

    2014-08-01

    Fleshy fruits have evolved to be attractive to frugivores in order to enhance seed dispersal, and have become an indispensable part of the human diet. Here we review the recent advances in the understanding of transcriptional regulation of fleshy fruit development and ripening with a focus on tomato. While aspects of fruit development are probably conserved throughout the angiosperms, including the model plant Arabidopsis thaliana, it is shown that the likely orthologues of Arabidopsis genes have distinct functions in fleshy fruits. The model for the study of fleshy fruit development is tomato, because of the availability of single gene mutants and transgenic knock-down lines. In other species, our knowledge is often incomplete or absent. Tomato fruit size and shape are co-determined by transcription factors acting during formation of the ovary. Other transcription factors play a role in fruit chloroplast formation, and upon ripening impact quality aspects such as secondary metabolite content. In tomato, the transcription factors NON-RIPENING (NOR), COLORLESS NON-RIPENING (CNR), and RIPENING INHIBITOR (MADS-RIN) in concert with ethylene signalling regulate ripening, possibly in response to a developmental switch. Additional components include TOMATO AGAMOUS-LIKE1 (TAGL1), APETALA2a (AP2a), and FRUITFULL (FUL1 and FUL2). The links between this highly connected regulatory network and downstream effectors modulating colour, texture, and flavour are still relatively poorly understood. Intertwined with this network is post-transcriptional regulation by fruit-expressed microRNAs targeting several of these transcription factors. This important developmental process is also governed by changes in DNA methylation levels and possibly chromatin remodelling.

  1. Analysis of mRNA translation states in Arabidopsis over the diurnal cycle by polysome microarray.

    Science.gov (United States)

    Missra, Anamika; von Arnim, Albrecht G

    2014-01-01

    Gene regulation at the level of translation occurs in response to environmental perturbation and is increasingly recognized as a factor affecting plant development. Despite extensive knowledge of transcriptional control, very little is known about translational regulation of genes in response to the daily light/dark cycles. Here we describe the experimental layout designed to address how the translation states of genes change at various times during a diurnal cycle in Arabidopsis thaliana seedlings. We have adopted a strategy combining sucrose-gradient profiling of ribosomes and high-throughput microarray analysis of the ribosome-associated mRNA to investigate the translational landscape of the Arabidopsis genome. This is a powerful technique that can be easily extended to study translation regulation in different genetic backgrounds and under various environmental conditions. PMID:24792050

  2. Functional interconnection of MYC2 and SPA1 in the photomorphogenic seedling development of Arabidopsis.

    Science.gov (United States)

    Gangappa, Sreeramaiah N; Prasad, V Babu Rajendra; Chattopadhyay, Sudip

    2010-11-01

    MYC2 is a basic helix-loop-helix transcription factor that cross talks with light, abscisic acid (ABA), and jasmonic acid (JA) signaling pathways. Here, we have shown that Arabidopsis (Arabidopsis thaliana) MYC2 directly binds to the G-box present in the SUPPRESSOR OF PHYTOCHROME A1 (SPA1) promoter and that it controls the expression of SPA1 in a COP1-dependent manner. Analyses of atmyc2 spa1 double mutants suggest that whereas MYC2 and SPA1 act redundantly to suppress photomorphogenic growth in the dark, they function synergistically for the suppression of photomorphogenic growth in the light. Our studies have also revealed that MYC2-mediated ABA and JA responses are further modulated by SPA1. Taken together, this study demonstrates the molecular and physiological interrelations of MYC2 and SPA1 in light, ABA, and JA signaling pathways.

  3. Molecular and structural analyses of a novel temperature stress-induced lipocalin from wheat and Arabidopsis.

    Science.gov (United States)

    Frenette Charron, Jean Benoit; Breton, Ghislain; Badawi, Mohamed; Sarhan, Fathey

    2002-04-24

    Two cDNAs corresponding to a novel lipocalin were identified from wheat and Arabidopsis. The two cDNAs designated Tatil for Triticum aestivum L. temperature-induced lipocalin and Attil for Arabidopsis thaliana temperature-induced lipocalin encode polypeptides of 190 and 186 amino acids respectively. Structure analyses indicated the presence of the three structurally conserved regions that characterize lipocalins. Sequence analyses revealed that this novel class of plant lipocalin shares homology with three evolutionarily related lipocalins: the mammalian apolipoprotein D (ApoD), the bacterial lipocalin and the insect Lazarillo. The comparison of the putative tertiary structures of both the human ApoD and the wheat TaTIL suggest that the two proteins differ in membrane attachment and ligand interaction. Northern analyses demonstrated that Tatil and Attil transcripts are upregulated during cold acclimation and heat-shock treatment. The putative functions of this novel class of plant lipocalins during temperature stresses are discussed.

  4. Structure and function of centromeric and pericentromeric heterochromatin in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Lauriane eSimon

    2015-11-01

    Full Text Available The centromere is a specific chromosomal region where the kinetochore assembles to ensure the faithful segregation of sister chromatids during mitosis and meiosis. Centromeres are defined by a local enrichment of the specific histone variant CenH3 mostly at repetitive satellite sequences. A larger pericentromeric region containing repetitive sequences and transposable elements surrounds the centromere that adopts a particular chromatin state characterized by specific histone variants and post-translational modifications and forms a transcriptionally repressive chromosomal environment. In the model organism Arabidopsis thaliana centromeric and pericentromeric domains form conspicuous heterochromatin clusters called chromocenters in interphase. Here we discuss, using Arabidopsis as example, recent insight into mechanisms involved in maintenance and establishment of centromeric and pericentromeric chromatin signatures as well as in chromocenter formation.

  5. Phytoremediation potential of Arabidopsis with reference to acrylamide and microarray analysis of acrylamide-response genes.

    Science.gov (United States)

    Gao, Jian-Jie; Peng, Ri-He; Zhu, Bo; Wang, Bo; Wang, Li-Juan; Xu, Jing; Sun, Miao; Yao, Quan-Hong

    2015-10-01

    Acrylamide (ACR) is a widely used industrial chemical. However, it is a dangerous compound because it showed neurotoxic effects in humans and act as reproductive toxicant and carcinogen in many animal species. In the environment, acrylamide has high soil mobility and may travel via groundwater. Phytoremediation is an effective method to remove the environmental pollutants, but the mechanism of plant response to acrylamide remains unknown. With the purpose of assessing remediation potentials of plants for acrylamide, we have examined acrylamide uptake by the model plant Arabidopsis grown on contaminated substrates with high performance liquid chromatography (HPLC) analysis. The result revealed that acrylamide could be absorbed and degraded by Arabidopsis. Further microarray analysis showed that 527 transcripts were up-regulated within 2-days under acrylamide exposure condition. We have found many potential acrylamide-induced genes playing a major role in plant metabolism and phytoremediation.

  6. Programming of Plant Leaf Senescence with Temporal and Inter-Organellar Coordination of Transcriptome in Arabidopsis1[OPEN

    Science.gov (United States)

    Koo, Hee Jung; Kim, Jeongsik; Jeong, Hyobin; Yang, Jin Ok; Lee, Il Hwan; Jun, Ji Hyung; Choi, Seung Hee; Park, Su Jin; Kang, Byeongsoo; Kim, You Wang; Phee, Bong-Kwan; Kim, Jin Hee; Seo, Chaehwa; Park, Charny; Kim, Sang Cheol; Park, Seongjin; Lee, Byungwook; Lee, Sanghyuk; Hwang, Daehee; Lim, Pyung Ok

    2016-01-01

    Plant leaves, harvesting light energy and fixing CO2, are a major source of foods on the earth. Leaves undergo developmental and physiological shifts during their lifespan, ending with senescence and death. We characterized the key regulatory features of the leaf transcriptome during aging by analyzing total- and small-RNA transcriptomes throughout the lifespan of Arabidopsis (Arabidopsis thaliana) leaves at multidimensions, including age, RNA-type, and organelle. Intriguingly, senescing leaves showed more coordinated temporal changes in transcriptomes than growing leaves, with sophisticated regulatory networks comprising transcription factors and diverse small regulatory RNAs. The chloroplast transcriptome, but not the mitochondrial transcriptome, showed major changes during leaf aging, with a strongly shared expression pattern of nuclear transcripts encoding chloroplast-targeted proteins. Thus, unlike animal aging, leaf senescence proceeds with tight temporal and distinct interorganellar coordination of various transcriptomes that would be critical for the highly regulated degeneration and nutrient recycling contributing to plant fitness and productivity. PMID:26966169

  7. Arabidopsis RAV1 is down-regulated by brassinosteroid and may act as a negative regulator during plant development

    Institute of Scientific and Technical Information of China (English)

    Yu Xin HU; Yong Hong WANG; Xin Fang LIU; Jia Yang LI

    2004-01-01

    RAV1 is a novel DNA-binding protein with two distinct DNA-binding domains unique in higher plants,but its role in plant growth and development remains unknown. Using cDNA array,we found that transcription of RAV1 is downregulated by epibrassinolide (epiBL) in Arabidopsis suspension cells. RNA gel blot analysis revealed that epiBL-regulated RAV1 transcription involves neither protein phosphorylation/dephosphorylation nor newly synthesized protein,and does not require the functional BRI1,suggesting that this regulation might be through a new BR signaling pathway.Overexpressing RAV1 in Arabidopsis results in a retardation of lateral root and rosette leaf development,and the underexpression causes an earlier flowering phenotype,implying that RAV1 may function as a negative regulatory component of growth and development.

  8. Involvement of C2H2 zinc finger proteins in the regulation of epidermal cell fate determination in Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    An Yan; Minjie Wu; Yongqin Zhao; Aidong Zhang; Bohan Liu; John Schiefelbein; Yinbo Gan

    2014-01-01

    Cell fate determination is a basic developmental process during the growth of multicellular organisms. Trichomes and root hairs of Arabidopsis are both readily accessible structures originating from the epidermal cells of the aerial tissues and roots respectively, and they serve as excellent models for understanding the molecular mecha-nisms controlling cell fate determination and cell morphogen-esis. The regulation of trichome and root hair formation is a complex program that consists of the integration of hormonal signals with a large number of transcriptional factors, including MYB and bHLH transcriptional factors. Studies during recent years have uncovered an important role of C2H2 type zinc finger proteins in the regulation of epidermal cell fate determination. Here in this minireview we briefly summarize the involvement of C2H2 zinc finger proteins in the control of trichome and root hair formation in Arabidopsis.

  9. Activation of the Arabidopsis B class homeotic genes by APETALA1.

    Science.gov (United States)

    Ng, M; Yanofsky, M F

    2001-04-01

    Proper development of petals and stamens in Arabidopsis flowers requires the activities of APETALA3 (AP3) and PISTILLATA (PI), whose transcripts can be detected in the petal and stamen primordia. Localized expression of AP3 and PI requires the activities of at least three genes: APETALA1 (AP1), LEAFY (LFY), and UNUSUAL FLORAL ORGANS (UFO). It has been proposed that UFO provides spatial cues and that LFY specifies competence for AP3 and PI expression in the developing flower. To understand the epistatic relationship among AP1, LFY, and UFO in regulating AP3 and PI expression, we generated two versions of AP1 that have strong transcriptional activation potential. Genetic and molecular analyses of transgenic plants expressing these activated AP1 proteins show that the endogenous AP1 protein acts largely as a transcriptional activator in vivo and that AP1 specifies petals by regulating the spatial domains of AP3 and PI expression through UFO.

  10. Arabidopsis CDS blastp result: AK288065 [KOME

    Lifescience Database Archive (English)

    Full Text Available al to sulfate tansporter Sultr1;3 [Arabidopsis thaliana] GI:10716805; contains Pfam profile PF00916: Sulfate... transporter family; contains Pfam profile PF01740: STAS domain; contains TIGRfam profile TIGR00815: sulfate permease 1e-145 ...

  11. Arabidopsis CDS blastp result: AK061395 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK061395 006-305-E02 At2g02180.1 tobamovirus multiplication protein 3 (TOM3) identical to tobamovirus multip...lication protein (TOM3) GI:15425641 from [Arabidopsis thaliana] 1e-125 ...

  12. Arabidopsis CDS blastp result: AK104882 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK104882 001-044-H04 At2g02180.1 tobamovirus multiplication protein 3 (TOM3) identical to tobamovirus multip...lication protein (TOM3) GI:15425641 from [Arabidopsis thaliana] 1e-119 ...

  13. Arabidopsis CDS blastp result: AK066854 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK066854 J013075C10 At2g02180.1 tobamovirus multiplication protein 3 (TOM3) identical to tobamovirus multipl...ication protein (TOM3) GI:15425641 from [Arabidopsis thaliana] 1e-119 ...

  14. Arabidopsis CDS blastp result: AK101318 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK101318 J033034D12 At2g02180.1 tobamovirus multiplication protein 3 (TOM3) identical to tobamovirus multipl...ication protein (TOM3) GI:15425641 from [Arabidopsis thaliana] 1e-125 ...

  15. Arabidopsis CDS blastp result: AK069960 [KOME

    Lifescience Database Archive (English)

    Full Text Available thyltransferase 1 / caffeic acid/5-hydroxyferulic acid O-methyltransferase (OMT1) identical to O-methyltrans...T1) (Flavonol 3- O-methyltransferase 1) (Caffeic acid/5-hydroxyferulic acid O- methyltransferase) {Arabidopsis thaliana} 5e-60 ...

  16. Arabidopsis CDS blastp result: AK064768 [KOME

    Lifescience Database Archive (English)

    Full Text Available thyltransferase 1 / caffeic acid/5-hydroxyferulic acid O-methyltransferase (OMT1) identical to O-methyltrans...T1) (Flavonol 3- O-methyltransferase 1) (Caffeic acid/5-hydroxyferulic acid O- methyltransferase) {Arabidopsis thaliana} 1e-112 ...

  17. Arabidopsis CDS blastp result: AK061551 [KOME

    Lifescience Database Archive (English)

    Full Text Available ethyltransferase 1 / caffeic acid/5-hydroxyferulic acid O-methyltransferase (OMT1) identical to O-methyltran...MT1) (Flavonol 3- O-methyltransferase 1) (Caffeic acid/5-hydroxyferulic acid O- methyltransferase) {Arabidopsis thaliana} 2e-67 ...

  18. Arabidopsis CDS blastp result: AK104764 [KOME

    Lifescience Database Archive (English)

    Full Text Available ethyltransferase 1 / caffeic acid/5-hydroxyferulic acid O-methyltransferase (OMT1) identical to O-methyltran...MT1) (Flavonol 3- O-methyltransferase 1) (Caffeic acid/5-hydroxyferulic acid O- methyltransferase) {Arabidopsis thaliana} 2e-67 ...

  19. Arabidopsis CDS blastp result: AK098998 [KOME

    Lifescience Database Archive (English)

    Full Text Available thyltransferase 1 / caffeic acid/5-hydroxyferulic acid O-methyltransferase (OMT1) identical to O-methyltrans...T1) (Flavonol 3- O-methyltransferase 1) (Caffeic acid/5-hydroxyferulic acid O- methyltransferase) {Arabidopsis thaliana} 8e-57 ...

  20. Arabidopsis CDS blastp result: AK061859 [KOME

    Lifescience Database Archive (English)

    Full Text Available ethyltransferase 1 / caffeic acid/5-hydroxyferulic acid O-methyltransferase (OMT1) identical to O-methyltran...MT1) (Flavonol 3- O-methyltransferase 1) (Caffeic acid/5-hydroxyferulic acid O- methyltransferase) {Arabidopsis thaliana} 1e-100 ...

  1. Arabidopsis CDS blastp result: AK102695 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK102695 J033103F21 At5g16910.1 cellulose synthase family protein similar to gi:2827143 cellulose... synthase catalytic subunit, Arabidopsis thaliana, gi:9622886 cellulose synthase-7 from Zea mays 0.0 ...

  2. Arabidopsis CDS blastp result: AK102134 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK102134 J033085F12 At5g16910.1 cellulose synthase family protein similar to gi:2827143 cellulose... synthase catalytic subunit, Arabidopsis thaliana, gi:9622886 cellulose synthase-7 from Zea mays 0.0 ...

  3. Arabidopsis CDS blastp result: AK066835 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK066835 J013087I16 At5g16910.1 cellulose synthase family protein similar to gi:2827143 cellulose... synthase catalytic subunit, Arabidopsis thaliana, gi:9622886 cellulose synthase-7 from Zea mays 1e-171 ...

  4. Arabidopsis CDS blastp result: AK065259 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK065259 J013002J18 At5g16910.1 cellulose synthase family protein similar to gi:2827143 cellulose... synthase catalytic subunit, Arabidopsis thaliana, gi:9622886 cellulose synthase-7 from Zea mays 0.0 ...

  5. Arabidopsis CDS blastp result: AK100523 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK100523 J023100P04 At5g16910.1 cellulose synthase family protein similar to gi:2827143 cellulose... synthase catalytic subunit, Arabidopsis thaliana, gi:9622886 cellulose synthase-7 from Zea mays 0.0 ...

  6. Arabidopsis CDS blastp result: AK242550 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242550 J080319D10 At2g35630.1 68415.m04369 microtubule organization 1 protein (MO...R1) identical to microtubule organization 1 protein GI:14317953 from [Arabidopsis thaliana] 5e-44 ...

  7. Arabidopsis CDS blastp result: AK241043 [KOME

    Lifescience Database Archive (English)

    Full Text Available upted by a stop codon, creating non-consensus donor and acceptor splice sites. 2e-41 ... ...tical to SP|P92997 Germin-like protein subfamily 1 member 13 precursor {Arabidopsis thaliana}; exon 2 interr

  8. Arabidopsis CDS blastp result: AK243135 [KOME

    Lifescience Database Archive (English)

    Full Text Available upted by a stop codon, creating non-consensus donor and acceptor splice sites. 7e-43 ... ...tical to SP|P92997 Germin-like protein subfamily 1 member 13 precursor {Arabidopsis thaliana}; exon 2 interr

  9. The fifth international conference on Arabidopsis research

    Energy Technology Data Exchange (ETDEWEB)

    Hangarter, R.; Scholl, R.; Davis, K.; Feldmann, K.

    1993-12-31

    This volume contains abstracts of oral and poster presentations made in conjunction with the Fifth International Conference on Arabidopsis Research held August 19--22, 1993 at the Ohio State University, Columbus, Ohio.

  10. Arabidopsis CDS blastp result: AK101526 [KOME

    Lifescience Database Archive (English)

    Full Text Available ucosaminyltransferase, putative similar to N-acetylglucosaminyltransferase I from Arabidopsis thaliana [gi:5139335]; contains AT-AC non-consensus splice sites at intron 13 1e-179 ...

  11. Arabidopsis CDS blastp result: AK119708 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK119708 002-157-E08 At1g28330.1 dormancy-associated protein, putative (DRM1) identical to dormancy...-associated protein [Arabidopsis thaliana] GI:2995990; similar to dormancy-associated protei

  12. Arabidopsis CDS blastp result: AK060981 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK060981 006-202-H08 At1g28330.1 dormancy-associated protein, putative (DRM1) identical to dormancy...-associated protein [Arabidopsis thaliana] GI:2995990; similar to dormancy-associated protei

  13. Arabidopsis CDS blastp result: AK111576 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK111576 J013075J23 At1g01510.1 C-terminal binding protein (ANGUSTIFOLIA) nearly id...entical to C-terminal binding protein ANGUSTIFOLIA [Arabidopsis thaliana] GI:15408535; contains Pfam profile

  14. Arabidopsis CDS blastp result: AK120838 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK120838 J023022B11 At1g01510.1 C-terminal binding protein (ANGUSTIFOLIA) nearly id...entical to C-terminal binding protein ANGUSTIFOLIA [Arabidopsis thaliana] GI:15408535; contains Pfam profile

  15. Arabidopsis CDS blastp result: AK111921 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK111921 001-013-A10 At1g01510.1 C-terminal binding protein (ANGUSTIFOLIA) nearly i...dentical to C-terminal binding protein ANGUSTIFOLIA [Arabidopsis thaliana] GI:15408535; contains Pfam profil

  16. Arabidopsis CDS blastp result: AK064342 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK064342 002-107-H07 At5g58270.1 mitochondrial half-ABC transporter (STA1) identical to half...-molecule ABC transporter ATM3 GI:9964121 from [Arabidopsis thaliana]; almost identical to mitochondrial half...-ABC transporter STA1 GI:9187883 from [Arabidopsis thaliana]; identical to cDNA mitochondrial half-ABC transporter (STA1 gene)GI:9187882 0.0 ...

  17. Arabidopsis CDS blastp result: AK287662 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK287662 J065112L10 At5g58270.1 68418.m07295 mitochondrial half-ABC transporter (STA1) identical to half...-molecule ABC transporter ATM3 GI:9964121 from [Arabidopsis thaliana]; almost identical to mitochondrial half...-ABC transporter STA1 GI:9187883 from [Arabidopsis thaliana]; identical to cDNA mitochondrial half-ABC transporter (STA1 gene)GI:9187882 1e-65 ...

  18. Arabidopsis CDS blastp result: AK242094 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK242094 J075142E09 At5g58270.1 68418.m07295 mitochondrial half-ABC transporter (STA1) identical to half...-molecule ABC transporter ATM3 GI:9964121 from [Arabidopsis thaliana]; almost identical to mitochondrial half...-ABC transporter STA1 GI:9187883 from [Arabidopsis thaliana]; identical to cDNA mitochondrial half-ABC transporter (STA1 gene)GI:9187882 2e-33 ...

  19. Arabidopsis CDS blastp result: AK102879 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK102879 J033112G11 At5g58270.1 mitochondrial half-ABC transporter (STA1) identical to half...-molecule ABC transporter ATM3 GI:9964121 from [Arabidopsis thaliana]; almost identical to mitochondrial half...-ABC transporter STA1 GI:9187883 from [Arabidopsis thaliana]; identical to cDNA mitochondrial half-ABC transporter (STA1 gene)GI:9187882 1e-122 ...

  20. Arabidopsis CDS blastp result: AK287488 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK287488 J043029O04 At5g58270.1 68418.m07295 mitochondrial half-ABC transporter (STA1) identical to half...-molecule ABC transporter ATM3 GI:9964121 from [Arabidopsis thaliana]; almost identical to mitochondrial half...-ABC transporter STA1 GI:9187883 from [Arabidopsis thaliana]; identical to cDNA mitochondrial half-ABC transporter (STA1 gene)GI:9187882 4e-27 ...

  1. Transcriptomic Analysis of Soil-Grown Arabidopsis thaliana Roots and Shoots in Response to a Drought Stress

    OpenAIRE

    Sultana eRasheed; Khurram eBashir; Akihiro eMatsui; Maho eTanaka; Motoaki eSeki

    2016-01-01

    Drought stress has a negative impact on crop yield. Thus, understanding the molecular mechanisms responsible for plant drought stress tolerance is essential for improving this beneficial trait in crops. In the current study, a transcriptional analysis was conducted of gene regulatory networks in roots of soil-grown Arabidopsis plants in response to a drought stress treatment. A microarray analysis of drought-stressed roots and shoots was performed at 0, 1, 3, 5, 7 and 9 days. Results indicat...

  2. The Arabidopsis thaliana homeobox gene ATHB12 is involved in symptom development caused by geminivirus infection.

    Directory of Open Access Journals (Sweden)

    Jungan Park

    Full Text Available BACKGROUND: Geminiviruses are single-stranded DNA viruses that infect a number of monocotyledonous and dicotyledonous plants. Arabidopsis is susceptible to infection with the Curtovirus, Beet severe curly top virus (BSCTV. Infection of Arabidopsis with BSCTV causes severe symptoms characterized by stunting, leaf curling, and the development of abnormal inflorescence and root structures. BSCTV-induced symptom development requires the virus-encoded C4 protein which is thought to interact with specific plant-host proteins and disrupt signaling pathways important for controlling cell division and development. Very little is known about the specific plant regulatory factors that participate in BSCTV-induced symptom development. This study was conducted to identify specific transcription factors that are induced by BSCTV infection. METHODOLOGY/PRINCIPAL FINDINGS: Arabidopsis plants were inoculated with BSCTV and the induction of specific transcription factors was monitored using quantitative real-time polymerase chain reaction assays. We found that the ATHB12 and ATHB7 genes, members of the homeodomain-leucine zipper family of transcription factors previously shown to be induced by abscisic acid and water stress, are induced in symptomatic tissues of Arabidopsis inoculated with BSCTV. ATHB12 expression is correlated with an array of morphological abnormalities including leaf curling, stunting, and callus-like structures in infected Arabidopsis. Inoculation of plants with a BSCTV mutant with a defective c4 gene failed to induce ATHB12. Transgenic plants expressing the BSCTV C4 gene exhibited increased ATHB12 expression whereas BSCTV-infected ATHB12 knock-down plants developed milder symptoms and had lower ATHB12 expression compared to the wild-type plants. Reporter gene studies demonstrated that the ATHB12 promoter was responsive to BSCTV infection and the highest expression levels were observed in symptomatic tissues where cell cycle genes also were

  3. The SLO1 PPR protein is required for RNA editing at multiple sites with similar upstream sequences in Arabidopsis mitochondria.

    Science.gov (United States)

    Sung, Tzu-Ying; Tseng, Ching-Chih; Hsieh, Ming-Hsiun

    2010-08-01

    In Arabidopsis, RNA editing changes more than 500 cytidines to uridines in mitochondrial transcripts. The editing enzyme and co-factors involved in these processes are largely unknown. We have identified a nuclear gene SLOW GROWTH1 (SLO1) encoding an E motif-containing pentatricopeptide repeat protein that is required for RNA editing of nad4 and nad9 in Arabidopsis mitochondria. The SLO1 protein is localized to the mitochondrion, and its absence gives rise to small plants with slow growth and delayed development. A survey of approximately 500 mitochondrial RNA editing sites in Arabidopsis reveals that the editing of two sites, nad4-449 and nad9-328, is abolished in the slo1 mutants. Sequence comparison in the upstream (from -1 to -15 bp) of nad4-449 and nad9-328 editing sites shows that nine of the 15 nucleotides are identical. In addition to RNA editing, we used RNA gel blot analysis to compare the abundance and banding patterns of mitochondrial transcripts between the wild type and slo1 mutants. Of the 79 genes and open reading frames examined, steady-state levels of 56 mitochondrial transcripts are increased in the slo1 mutants. These results suggest that the SLO1 protein may indirectly regulate plant growth and development via affecting mitochondrial RNA editing and gene expression.

  4. Dissection of miRNA pathways using arabidopsis mesophyll protoplasts.

    Science.gov (United States)

    Martinho, Cláudia; Confraria, Ana; Elias, Carlos Alexandre; Crozet, Pierre; Rubio-Somoza, Ignacio; Weigel, Detlef; Baena-González, Elena

    2015-02-01

    MicroRNAs (miRNAs) control gene expression mostly post-transcriptionally by guiding transcript cleavage and/or translational repression of complementary mRNA targets, thereby regulating developmental processes and stress responses. Despite the remarkable expansion of the field, the mechanisms underlying miRNA activity are not fully understood. In this article, we describe a transient expression system in Arabidopsis mesophyll protoplasts, which is highly amenable for the dissection of miRNA pathways. We show that by transiently overexpressing primary miRNAs and target mimics, we can manipulate miRNA levels and consequently impact on their targets. Furthermore, we developed a set of luciferase-based sensors for quantifying miRNA activity that respond specifically to both endogenous and overexpressed miRNAs and target mimics. We demonstrate that these miRNA sensors can be used to test the impact of putative components of the miRNA pathway on miRNA activity, as well as the impact of specific mutations, by either overexpression or the use of protoplasts from the corresponding mutants. We further show that our miRNA sensors can be used for investigating the effect of chemicals on miRNA activity. Our cell-based transient expression system is fast and easy to set up, and generates quantitative results, being a powerful tool for assaying miRNA activity in vivo.

  5. Epidermal patterning genes are active during embryogenesis in Arabidopsis.

    Science.gov (United States)

    Costa, Silvia; Dolan, Liam

    2003-07-01

    Epidermal cells in the root of Arabidopsis seedling differentiate either as hair or non-hair cells, while in the hypocotyl they become either stomatal or elongated cells. WEREWOLF (WER) and GLABRA2 (GL2) are positive regulators of non-hair and elongated cell development. CAPRICE (CPC) is a positive regulator of hair cell development in the root. We show that WER, GL2 and CPC are expressed and active during the stages of embryogenesis when the pattern of cells in the epidermis of the root-hypocotyl axis forms. GL2 is first expressed in the future epidermis in the heart stage embryo and its expression is progressively restricted to those cells that will acquire a non-hair identity in the transition between torpedo and mature stage. The expression of GL2 at the heart stage requires WER function. WER and CPC are transiently expressed throughout the root epidermal layer in the torpedo stage embryo when the cell-specific pattern of GL2 expression is being established in the epidermis. We also show that WER positively regulates CPC transcription and GL2 negatively regulates WER transcription in the mature embryo. We propose that the restriction of GL2 to the future non-hair cells in the root epidermis can be correlated with the activities of WER and CPC during torpedo stage. In the embryonic hypocotyl we show that WER controls GL2 expression. We also provide evidence indicating that CPC may also regulate GL2 expression in the hypocotyl.

  6. Temporal evolution of the Arabidopsis oxidative stress response.

    Science.gov (United States)

    Mahalingam, Ramamurthy; Shah, Nigam; Scrymgeour, Alexandra; Fedoroff, Nina

    2005-03-01

    We have carried out a detailed analysis of the changes in gene expression levels in Arabidopsis thaliana ecotype Columbia (Col-0) plants during and for 6 h after exposure to ozone (O3) at 350 parts per billion (ppb) for 6 h. This O3 exposure is sufficient to induce a marked transcriptional response and an oxidative burst, but not to cause substantial tissue damage in Col-0 wild-type plants and is within the range encountered in some major metropolitan areas. We have developed analytical and visualization tools to automate the identification of expression profile groups with common gene ontology (GO) annotations based on the sub-cellular localization and function of the proteins encoded by the genes, as well as to automate promoter analysis for such gene groups. We describe application of these methods to identify stress-induced genes whose transcript abundance is likely to be controlled by common regulatory mechanisms and summarized our findings in a temporal model of the stress response. PMID:15988565

  7. Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions.

    Science.gov (United States)

    Kawakatsu, Taiji; Huang, Shao-Shan Carol; Jupe, Florian; Sasaki, Eriko; Schmitz, Robert J; Urich, Mark A; Castanon, Rosa; Nery, Joseph R; Barragan, Cesar; He, Yupeng; Chen, Huaming; Dubin, Manu; Lee, Cheng-Ruei; Wang, Congmao; Bemm, Felix; Becker, Claude; O'Neil, Ryan; O'Malley, Ronan C; Quarless, Danjuma X; Schork, Nicholas J; Weigel, Detlef; Nordborg, Magnus; Ecker, Joseph R

    2016-07-14

    The epigenome orchestrates genome accessibility, functionality, and three-dimensional structure. Because epigenetic variation can impact transcription and thus phenotypes, it may contribute to adaptation. Here, we report 1,107 high-quality single-base resolution methylomes and 1,203 transcriptomes from the 1001 Genomes collection of Arabidopsis thaliana. Although the genetic basis of methylation variation is highly complex, geographic origin is a major predictor of genome-wide DNA methylation levels and of altered gene expression caused by epialleles. Comparison to cistrome and epicistrome datasets identifies associations between transcription factor binding sites, methylation, nucleotide variation, and co-expression modules. Physical maps for nine of the most diverse genomes reveal how transposons and other structural variants shape the epigenome, with dramatic effects on immunity genes. The 1001 Epigenomes Project provides a comprehensive resource for understanding how variation in DNA methylation contributes to molecular and non-molecular phenotypes in natural populations of the most studied model plant. PMID:27419873

  8. Comprehensive Transcriptome Analysis of Auxin Responses in Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    Ivan A.Paponov; Martina Paponov; William Teale; Margit Menges; Sohini Chakrabortee; James A.H.Murray; Klaus Palme

    2008-01-01

    In plants,the hormone auxin shapes gene expression to regulate growth and development.Despite the detailed characterization of auxin-inducible genes,a comprehensive overview of the temporal and spatial dynamics of auxinregulated gene expression is lacking.Here,we analyze transcriptome data from many publicly available Arabidopsis profiling experiments and assess tissue-specific gene expression both in response to auxin concentration and exposure time and in relation to other plant growth regulators.Our analysis shows that the primary response to auxin over a wide range of auxin application conditions and in specific tissues comprises almost exclusively the up-regulation of genes and identifies the most robust auxin marker genes.Tissue-specific auxin responses correlate with differential expression of Aux/IAA genes and the subsequent regulation of context- and sequence-specific patterns of gene expression.Changes in transcript levels were consistent with a distinct sequence of conjugation,increased transport capacity and down-regulation of biosynthesis in the temperance of high cellular auxin concentrations.Our data show that auxin regulates genes associated with the biosynthesis,catabolism and signaling pathways of other phytohormones.We present a transcriptional overview of the auxin response.Specific interactions between auxin and other phytohormones are highlighted,particularly the regulation of their metabolism.Our analysis provides a roadmap for auxin-dependent processes that underpins the concept of an 'auxin code'-a tissue-specific fingerprint of gene expression that initiates specific developmental processes.

  9. The Transcriptomic Response of Arabidopsis thaliana to Zinc Oxide: A Comparison of the Impact of Nanoparticle, Bulk, and Ionic Zinc

    OpenAIRE

    Landa, P.; Přerostová, S. (Sylva); Petrová, Š. (Šárka); V. Knirsch; Vaňková, R. (Radomíra); Vaněk, T. (Tomáš)

    2015-01-01

    The impact of nanosize was evaluated by comparing of the transcriptomic response of Arabidopsis thaliana roots to ZnO nanopartides (nZnO), bulk ZnO, and ionic Zn2+. Microarray analyses revealed 416 up- and 961 down-regulated transcripts (expression difference >2-fold, p [FDR] < 0.01) after a seven-day treatment with nZnO (average particle size 20 nm, concentration 4 mg L-1). Exposure to bulk ZnO resulted in 816 up- and 2179 down-regulated transcripts. The most dramatic changes (1711 transcrip...

  10. ABI3 mediates dehydration stress recovery response in Arabidopsis thaliana by regulating expression of downstream genes.

    Science.gov (United States)

    Bedi, Sonia; Sengupta, Sourabh; Ray, Anagh; Nag Chaudhuri, Ronita

    2016-09-01

    ABI3, originally discovered as a seed-specific transcription factor is now implicated to act beyond seed physiology, especially during abiotic stress. In non-seed plants, ABI3 is known to act in desiccation stress signaling. Here we show that ABI3 plays a role in dehydration stress response in Arabidopsis. ABI3 gene was upregulated during dehydration stress and its expression was maintained during subsequent stress recovery phases. Comparative gene expression studies in response to dehydration stress and stress recovery were done with genes which had potential ABI3 binding sites in their upstream regulatory regions. Such studies showed that several genes including known seed-specific factors like CRUCIFERIN1, CRUCIFERIN3 and LEA-group of genes like LEA76, LEA6, DEHYDRIN LEA and LEA-LIKE got upregulated in an ABI3-dependent manner, especially during the stress recovery phase. ABI3 got recruited to regions upstream to the transcription start site of these genes during dehydration stress response through direct or indirect DNA binding. Interestingly, ABI3 also binds to its own promoter region during such stress signaling. Nucleosomes covering potential ABI3 binding sites in the upstream sequences of the above-mentioned genes alter positions, and show increased H3 K9 acetylation during stress-induced transcription. ABI3 thus mediates dehydration stress signaling in Arabidopsis through regulation of a group of genes that play a role primarily during stress recovery phase. PMID:27457990

  11. Conserved noncoding sequences are associated with rates of mRNA decay in Arabidopsis

    Directory of Open Access Journals (Sweden)

    Jacob B Spangler

    2013-05-01

    Full Text Available Steady-state mRNA levels are tightly regulated through a combination of transcriptional and post-transcriptional control mechanisms. The discovery of cis-acting DNA elements that encode these control mechanisms is of high importance. We have investigated the influence of conserved non-coding sequences (CNSs, DNA patterns retained after an ancient whole genome duplication event, on the breadth of gene expression and the rates of mRNA decay in Arabidopsis thaliana. The absence of CNSs near α duplicate genes was associated with a decrease in breadth of gene expression and slower mRNA decay rates while the presence CNSs near α duplicates was associated with an increase in breadth of gene expression and faster mRNA decay rates. The observed difference in mRNA decay rate was fastest in genes with CNSs in both nontranscribed and transcribed regions, albeit through an unknown mechanism. This study supports the notion that some Arabidopsis CNSs regulate the steady-state mRNA levels through post-transcriptional control mechanisms and that CNSs also play a role in controlling the breadth of gene expression.

  12. Identification of Novel Components of the Unfolded Protein Response in Arabidopsis

    Science.gov (United States)

    Hossain, Md. Amir; Henríquez-Valencia, Carlos; Gómez-Páez, Marcela; Medina, Joaquín; Orellana, Ariel; Vicente-Carbajosa, Jesús; Zouhar, Jan

    2016-01-01

    Unfavorable environmental and developmental conditions may cause disturbances in protein folding in the endoplasmic reticulum (ER) that are recognized and counteracted by components of the Unfolded Protein Response (UPR) signaling pathways. The early cellular responses include transcriptional changes to increase the folding and processing capacity of the ER. In this study, we systematically screened a collection of inducible transgenic Arabidopsis plants expressing a library of transcription factors for resistance toward UPR-inducing chemicals. We identified 23 candidate genes that may function as novel regulators of the UPR and of which only three genes (bZIP10, TBF1, and NF-YB3) were previously associated with the UPR. The putative role of identified candidate genes in the UPR signaling is supported by favorable expression patterns in both developmental and stress transcriptional analyses. We demonstrated that WRKY75 is a genuine regulator of the ER-stress cellular responses as its expression was found to be directly responding to ER stress-inducing chemicals. In addition, transgenic Arabidopsis plants expressing WRKY75 showed resistance toward salt stress, connecting abiotic and ER-stress responses. PMID:27242851

  13. The role of the SCRAMBLED receptor-like kinase in patterning the Arabidopsis root epidermis.

    Science.gov (United States)

    Kwak, Su-Hwan; Schiefelbein, John

    2007-02-01

    Cell-type patterning in the Arabidopsis root epidermis is achieved by a network of transcription factors and influenced by a position-dependent mechanism. The SCRAMBLED receptor-like kinase is required for the normal pattern to arise, but its precise role is not understood. Here we describe genetic and molecular studies to define the spatial and temporal role of SCM in epidermal patterning and its relationship to the transcriptional network. Our results suggest that SCM helps unspecified epidermal cells interpret their position in relation to the underlying cortical cells and establish distinct cell identities. Furthermore, SCM loss-of-function and overexpression analyses suggest that SCM influences cell fate through its negative transcriptional regulation of the WEREWOLF MYB gene in epidermal cells at the H position. We also find that SCM function is specifically required for patterning the post-embryonic root epidermis and not for the analogous epidermal cell-type patterning during embryogenesis or hypocotyl development. In addition, we show that two closely related SCM-like genes in Arabidopsis (SRF1 and SRF3) are not required alone or together with SCM for proper epidermal patterning. These findings help define the developmental and mechanistic role of SCM and suggest a new model for its action in root epidermal cell patterning.

  14. Autophagy contributes to regulation of the hypoxia response during submergence in Arabidopsis thaliana.

    Science.gov (United States)

    Chen, Liang; Liao, Bin; Qi, Hua; Xie, Li-Juan; Huang, Li; Tan, Wei-Juan; Zhai, Ning; Yuan, Li-Bing; Zhou, Ying; Yu, Lu-Jun; Chen, Qin-Fang; Shu, Wensheng; Xiao, Shi

    2015-01-01

    Autophagy involves massive degradation of intracellular components and functions as a conserved system that helps cells to adapt to adverse conditions. In mammals, hypoxia rapidly stimulates autophagy as a cell survival response. Here, we examine the function of autophagy in the regulation of the plant response to submergence, an abiotic stress that leads to hypoxia and anaerobic respiration in plant cells. In Arabidopsis thaliana, submergence induces the transcription of autophagy-related (ATG) genes and the formation of autophagosomes. Consistent with this, the autophagy-defective (atg) mutants are hypersensitive to submergence stress and treatment with ethanol, the end product of anaerobic respiration. Upon submergence, the atg mutants have increased levels of transcripts of anaerobic respiration genes (alcohol dehydrogenase 1, ADH1 and pyruvate decarboxylase 1, PDC1), but reduced levels of transcripts of other hypoxia- and ethylene-responsive genes. Both submergence and ethanol treatments induce the accumulation of reactive oxygen species (ROS) in the rosettes of atg mutants more than in the wild type. Moreover, the production of ROS by the nicotinamide adenine dinucleotide phosphate (NADPH) oxidases is necessary for plant tolerance to submergence and ethanol, submergence-induced expression of ADH1 and PDC1, and activation of autophagy. The submergence- and ethanol-sensitive phenotypes in the atg mutants depend on a complete salicylic acid (SA) signaling pathway. Together, our findings demonstrate that submergence-induced autophagy functions in the hypoxia response in Arabidopsis by modulating SA-mediated cellular homeostasis.

  15. Characterization of Putative cis-Regulatory Elements in Genes Preferentially Expressed in Arabidopsis Male Meiocytes

    Directory of Open Access Journals (Sweden)

    Junhua Li

    2014-01-01

    Full Text Available Meiosis is essential for plant reproduction because it is the process during which homologous chromosome pairing, synapsis, and meiotic recombination occur. The meiotic transcriptome is difficult to investigate because of the size of meiocytes and the confines of anther lobes. The recent development of isolation techniques has enabled the characterization of transcriptional profiles in male meiocytes of Arabidopsis. Gene expression in male meiocytes shows unique features. The direct interaction of transcription factors (TFs with DNA regulatory sequences forms the basis for the specificity of transcriptional regulation. Here, we identified putative cis-regulatory elements (CREs associated with male meiocyte-expressed genes using in silico tools. The upstream regions (1 kb of the top 50 genes preferentially expressed in Arabidopsis meiocytes possessed conserved motifs. These motifs are putative binding sites of TFs, some of which share common functions, such as roles in cell division. In combination with cell-type-specific analysis, our findings could be a substantial aid for the identification and experimental verification of the protein-DNA interactions for the specific TFs that drive gene expression in meiocytes.

  16. Tight interconnection and multi-level control of Arabidopsis MYB44 in MAPK cascade signalling.

    Science.gov (United States)

    Persak, Helene; Pitzschke, Andrea

    2013-01-01

    Abiotic stress poses a huge, ever-increasing problem to plants and agriculture. The dissection of signalling pathways mediating stress tolerance is a prerequisite to develop more resistant plant species. Mitogen-activated protein kinase (MAPK) cascades are universal signalling modules. In Arabidopsis, the MAPK MPK3 and its upstream regulator MAPK kinase MKK4 initiate the adaptation response to numerous abiotic and biotic stresses. Yet, molecular steps directly linked with MKK4-MPK3 activation are largely unknown. Starting with a yeast-two-hybrid screen for interacting partners of MKK4, we identified a transcription factor, MYB44. MYB44 is controlled at multiple levels by and strongly inter-connected with MAPK signalling. As we had shown earlier, stress-induced expression of the MYB44 gene is regulated by a MPK3-targeted bZIP transcription factor VIP1. At the protein level, MYB44 interacts with MPK3 in vivo. MYB44 is phosphorylated by MPK3 in vitro at a single residue, Ser145. Although replacement of Ser145 by a non-phosphorylatable (S145A) or phosphomimetic (S145D) residue did not alter MYB44 subcellular localisation, dimerization behaviour nor DNA-binding characteristics, abiotic stress tolerance tests in stable transgenic Arabidopsis plants clearly related S145 phosphorylation to MYB44 function: Compared to Arabidopsis wild type plants, MYB44 overexpressing lines exhibit an enhanced tolerance to osmotic stress and are slightly more sensitive to abscisic acid. Interestingly, overexpression of the S145A variant revealed that impaired phosphorylation does not render the MYB44 protein non-functional. Instead, S145A lines are highly sensitive to abiotic stress, and thereby remarkably similar to mpk3-deficient plants. Its in vivo interaction with the nuclear sub-pools of both MPK3 and MKK4 renders MYB44 the first plant transcription factor to have a second function as putative MAPK cascade scaffolding protein.

  17. Wrinkled1, a ubiquitous regulator in oil accumulating tissues from Arabidopsis embryos to oil palm mesocarp.

    Directory of Open Access Journals (Sweden)

    Wei Ma

    Full Text Available Wrinkled1 (AtWRI1 is a key transcription factor in the regulation of plant oil synthesis in seed and non-seed tissues. The structural features of WRI1 important for its function are not well understood. Comparison of WRI1 orthologs across many diverse plant species revealed a conserved 9 bp exon encoding the amino acids "VYL". Site-directed mutagenesis of amino acids within the 'VYL' exon of AtWRI1 failed to restore the full oil content of wri1-1 seeds, providing direct evidence for an essential role of this small exon in AtWRI1 function. Arabidopsis WRI1 is predicted to have three alternative splice forms. To understand expression of these splice forms we performed RNASeq of Arabidopsis developing seeds and queried other EST and RNASeq databases from several tissues and plant species. In all cases, only one splice form was detected and VYL was observed in transcripts of all WRI1 orthologs investigated. We also characterized a phylogenetically distant WRI1 ortholog (EgWRI1 as an example of a non-seed isoform that is highly expressed in the mesocarp tissue of oil palm. The C-terminal region of EgWRI1 is over 90 amino acids shorter than AtWRI1 and has surprisingly low sequence conservation. Nevertheless, the EgWRI1 protein can restore multiple phenotypes of the Arabidopsis wri1-1 loss-of-function mutant, including reduced seed oil, the "wrinkled" seed coat, reduced seed germination, and impaired seedling establishment. Taken together, this study provides an example of combining phylogenetic analysis with mutagenesis, deep-sequencing technology and computational analysis to examine key elements of the structure and function of the WRI1 plant transcription factor.

  18. Wrinkled1, a ubiquitous regulator in oil accumulating tissues from Arabidopsis embryos to oil palm mesocarp.

    Science.gov (United States)

    Ma, Wei; Kong, Que; Arondel, Vincent; Kilaru, Aruna; Bates, Philip D; Thrower, Nicholas A; Benning, Christoph; Ohlrogge, John B

    2013-01-01

    Wrinkled1 (AtWRI1) is a key transcription factor in the regulation of plant oil synthesis in seed and non-seed tissues. The structural features of WRI1 important for its function are not well understood. Comparison of WRI1 orthologs across many diverse plant species revealed a conserved 9 bp exon encoding the amino acids "VYL". Site-directed mutagenesis of amino acids within the 'VYL' exon of AtWRI1 failed to restore the full oil content of wri1-1 seeds, providing direct evidence for an essential role of this small exon in AtWRI1 function. Arabidopsis WRI1 is predicted to have three alternative splice forms. To understand expression of these splice forms we performed RNASeq of Arabidopsis developing seeds and queried other EST and RNASeq databases from several tissues and plant species. In all cases, only one splice form was detected and VYL was observed in transcripts of all WRI1 orthologs investigated. We also characterized a phylogenetically distant WRI1 ortholog (EgWRI1) as an example of a non-seed isoform that is highly expressed in the mesocarp tissue of oil palm. The C-terminal region of EgWRI1 is over 90 amino acids shorter than AtWRI1 and has surprisingly low sequence conservation. Nevertheless, the EgWRI1 protein can restore multiple phenotypes of the Arabidopsis wri1-1 loss-of-function mutant, including reduced seed oil, the "wrinkled" seed coat, reduced seed germination, and impaired seedling establishment. Taken together, this study provides an example of combining phylogenetic analysis with mutagenesis, deep-sequencing technology and computational analysis to examine key elements of the structure and function of the WRI1 plant transcription factor. PMID:23922666

  19. Advances in Arabidopsis research in China from 2006 to 2007

    Institute of Scientific and Technical Information of China (English)

    LIANG Yan; ZUO JianRu; YANG WeiCai

    2007-01-01

    @@ Arabidopsis thaliana, a model plant species, has a number of advantages over other plant species as an experimental organism due to many of its genetic and genomic features. The Chinese Arabidopsis community has made significant contributions to plant biology research in recent years[1,2]. In 2006, studies of plant biology in China received more attention than ever before, especially those pertaining to Arabidopsis research. Here we briefly summarize recent advances in Arabidopsis research in China.

  20. Morphology of nuclear transcription.

    Science.gov (United States)

    Weipoltshammer, Klara; Schöfer, Christian

    2016-04-01

    Gene expression control is a fundamental determinant of cellular life with transcription being the most important step. The spatial nuclear arrangement of the transcription process driven by RNA polymerases II and III is nonrandomly organized in foci, which is believed to add another regulatory layer on gene expression control. RNA polymerase I transcription takes place within a specialized organelle, the nucleolus. Transcription of ribosomal RNA directly responds to metabolic requirements, which in turn is reflected in the architecture of nucleoli. It differs from that of the other polymerases with respect to the gene template organization, transcription rate, and epigenetic expression control, whereas other features are shared like the formation of DNA loops bringing genes and components of the transcription machinery in close proximity. In recent years, significant advances have been made in the understanding of the structural prerequisites of nuclear transcription, of the arrangement in the nuclear volume, and of the dynamics of these entities. Here, we compare ribosomal RNA and mRNA transcription side by side and review the current understanding focusing on structural aspects of transcription foci, of their constituents, and of the dynamical behavior of these components with respect to foci formation, disassembly, and cell cycle. PMID:26847177

  1. A Nonnatural Transcriptional Coactivator

    Science.gov (United States)

    Nyanguile, Origene; Uesugi, Motonari; Austin, David J.; Verdine, Gregory L.

    1997-12-01

    In eukaryotes, sequence-specific DNA-binding proteins activate gene expression by recruiting the transcriptional apparatus and chromatin remodeling proteins to the promoter through protein-protein contacts. In many instances, the connection between DNA-binding proteins and the transcriptional apparatus is established through the intermediacy of adapter proteins known as coactivators. Here we describe synthetic molecules with low molecular weight that act as transcriptional coactivators. We demonstrate that a completely nonnatural activation domain in one such molecule is capable of stimulating transcription in vitro and in vivo. The present strategy provides a means of gaining external control over gene activation through intervention using small molecules.

  2. Identification and structural analysis of a novel snoRNA gene cluster from Arabidopsis thaliana

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A Z2 snoRNA gene cluster,consisting of four antisense snoRNA genes, was identified from Arabidopsis thaliana. The sequence and structural analysis showed that the Z2 snoRNA gene cluster might be transcribed as a polycistronic precursor from an upstream promoter, and the intergenic spacers of the gene cluster encode the 'hairpin' structures similar to the processing recognition signals of yeast Saccharomyces cerevisiae polycistronic snoRNA precursor. The results also revealed that plant snoRNA gene with multiple copies is a characteristic in common, and provides a good system for further revealing the transcription and expression mechanism of plant snoRNA gene cluster.

  3. TOBFAC: the database of tobacco transcription factors

    Directory of Open Access Journals (Sweden)

    Brannock Jennifer F

    2008-01-01

    Full Text Available Abstract Background Regulation of gene expression at the level of transcription is a major control point in many biological processes. Transcription factors (TFs can activate and/or repress the transcriptional rate of target genes and vascular plant genomes devote approximately 7% of their coding capacity to TFs. Global analysis of TFs has only been performed for three complete higher plant genomes – Arabidopsis (Arabidopsis thaliana, poplar (Populus trichocarpa and rice (Oryza sativa. Presently, no large-scale analysis of TFs has been made from a member of the Solanaceae, one of the most important families of vascular plants. To fill this void, we have analysed tobacco (Nicotiana tabacum TFs using a dataset of 1,159,022 gene-space sequence reads (GSRs obtained by methylation filtering of the tobacco genome. An analytical pipeline was developed to isolate TF sequences from the GSR data set. This involved multiple (typically 10–15 independent searches with different versions of the TF family-defining domain(s (normally the DNA-binding domain followed by assembly into contigs and verification. Our analysis revealed that tobacco contains a minimum of 2,513 TFs representing all of the 64 well-characterised plant TF families. The number of TFs in tobacco is higher than previously reported for Arabidopsis and rice. Results TOBFAC: the database of tobacco transcription factors, is an integrative database that provides a portal to sequence and phylogeny data for the identified TFs, together with a large quantity of other data concerning TFs in tobacco. The database contains an individual page dedicated to each of the 64 TF families. These contain background information, domain architecture via Pfam links, a list of all sequences and an assessment of the minimum number of TFs in this family in tobacco. Downloadable phylogenetic trees of the major families are provided along with detailed information on the bioinformatic pipeline that was used to find

  4. Transgenerational stress memory is not a general response in Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Ales Pecinka

    Full Text Available Adverse conditions can trigger DNA damage as well as DNA repair responses in plants. A variety of stress factors are known to stimulate homologous recombination, the most accurate repair pathway, by increasing the concentration of necessary enzymatic components and the frequency of events. This effect has been reported to last into subsequent generations not exposed to the stress. To establish a basis for a genetic analysis of this transgenerational stress memory, a broad range of treatments was tested for quantitative effects on homologous recombination in the progeny. Several Arabidopsis lines, transgenic for well-established recombination traps, were exposed to 10 different physical and chemical stress treatments, and scored for the number of somatic homologous recombination (SHR events in the treated generation as well as in the two subsequent generations that were not treated. These numbers were related to the expression level of genes involved in homologous recombination and repair. SHR was enhanced after the majority of treatments, confirming previous data and adding new effective stress types, especially interference with chromatin. Compounds that directly modify DNA stimulated SHR to values exceeding previously described induction rates, concomitant with an induction of genes involved in SHR. In spite of the significant stimulation in the stressed generations, the two subsequent non-treated generations only showed a low and stochastic increase in SHR that did not correlate with the degree of stimulation in the parental plants. Transcripts coding for SHR enzymes generally returned to pre-treatment levels in the progeny. Thus, transgenerational effects on SHR frequency are not a general response to abiotic stress in Arabidopsis and may require special conditions.

  5. Regulation of Arabidopsis defense responses against Spodoptera littoralis by CPK-mediated calcium signaling

    Directory of Open Access Journals (Sweden)

    Ishihama Nobuaki

    2010-05-01

    Full Text Available Abstract Background Plant Ca2+ signals are involved in a wide array of intracellular signaling pathways after pest invasion. Ca2+-binding sensory proteins such as Ca2+-dependent protein kinases (CPKs have been predicted to mediate the signaling following Ca2+ influx after insect herbivory. However, until now this prediction was not testable. Results To investigate the roles CPKs play in a herbivore response-signaling pathway, we screened the characteristics of Arabidopsis CPK mutants damaged by a feeding generalist herbivore, Spodoptera littoralis. Following insect attack, the cpk3 and cpk13 mutants showed lower transcript levels of plant defensin gene PDF1.2 compared to wild-type plants. The CPK cascade was not directly linked to the herbivory-induced signaling pathways that were mediated by defense-related phytohormones such as jasmonic acid and ethylene. CPK3 was also suggested to be involved in a negative feedback regulation of the cytosolic Ca2+ levels after herbivory and wounding damage. In vitro kinase assays of CPK3 protein with a suite of substrates demonstrated that the protein phosphorylates transcription factors (including ERF1, HsfB2a and CZF1/ZFAR1 in the presence of Ca2+. CPK13 strongly phosphorylated only HsfB2a, irrespective of the presence of Ca2+. Furthermore, in vivo agroinfiltration assays showed that CPK3-or CPK13-derived phosphorylation of a heat shock factor (HsfB2a promotes PDF1.2 transcriptional activation in the defense response. Conclusions These results reveal the involvement of two Arabidopsis CPKs (CPK3 and CPK13 in the herbivory-induced signaling network via HsfB2a-mediated regulation of the defense-related transcriptional machinery. This cascade is not involved in the phytohormone-related signaling pathways, but rather directly impacts transcription factors for defense responses.

  6. Grasses use an alternatively wired bHLH transcription factor network to establish stomatal identity.

    Science.gov (United States)

    Raissig, Michael T; Abrash, Emily; Bettadapur, Akhila; Vogel, John P; Bergmann, Dominique C

    2016-07-19

    Stomata, epidermal valves facilitating plant-atmosphere gas exchange, represent a powerful model for understanding cell fate and pattern in plants. Core basic helix-loop-helix (bHLH) transcription factors regulating stomatal development were identified in Arabidopsis, but this dicot's developmental pattern and stomatal morphology represent only one of many possibilities in nature. Here, using unbiased forward genetic screens, followed by analysis of reporters and engineered mutants, we show that stomatal initiation in the grass Brachypodium distachyon uses orthologs of stomatal regulators known from Arabidopsis but that the function and behavior of individual genes, the relationships among genes, and the regulation of their protein products have diverged. Our results highlight ways in which a kernel of conserved genes may be alternatively wired to produce diversity in patterning and morphology and suggest that the stomatal transcription factor module is a prime target for breeding or genome modification to improve plant productivity. PMID:27382177

  7. Grasses use an alternatively wired bHLH transcription factor network to establish stomatal identity

    Science.gov (United States)

    Raissig, Michael T.; Abrash, Emily; Bettadapur, Akhila; Bergmann, Dominique C.

    2016-01-01

    Stomata, epidermal valves facilitating plant–atmosphere gas exchange, represent a powerful model for understanding cell fate and pattern in plants. Core basic helix–loop–helix (bHLH) transcription factors regulating stomatal development were identified in Arabidopsis, but this dicot’s developmental pattern and stomatal morphology represent only one of many possibilities in nature. Here, using unbiased forward genetic screens, followed by analysis of reporters and engineered mutants, we show that stomatal initiation in the grass Brachypodium distachyon uses orthologs of stomatal regulators known from Arabidopsis but that the function and behavior of individual genes, the relationships among genes, and the regulation of their protein products have diverged. Our results highlight ways in which a kernel of conserved genes may be alternatively wired to produce diversity in patterning and morphology and suggest that the stomatal transcription factor module is a prime target for breeding or genome modification to improve plant productivity. PMID:27382177

  8. Bioavailability of nanoparticulate hematite to Arabidopsis thaliana

    International Nuclear Information System (INIS)

    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

  9. 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

  10. SUPERKILLER Complex Components Are Required for the RNA Exosome-Mediated Control of Cuticular Wax Biosynthesis in Arabidopsis Inflorescence Stems.

    Science.gov (United States)

    Zhao, Lifang; Kunst, Ljerka

    2016-06-01

    ECERIFERUM7 (CER7)/AtRRP45B core subunit of the exosome, the main cellular 3'-to-5' exoribonuclease, is a positive regulator of cuticular wax biosynthesis in Arabidopsis (Arabidopsis thaliana) inflorescence stems. CER7-dependent exosome activity determines stem wax load by controlling transcript levels of the wax-related gene CER3 Characterization of the second-site suppressors of the cer7 mutant revealed that small interfering RNAs (siRNAs) are direct effectors of CER3 expression. To explore the relationship between the exosome and posttranscriptional gene silencing (PTGS) in regulating CER3 transcript levels, we investigated two additional suppressor mutants, wax restorer1 (war1) and war7. We show that WAR1 and WAR7 encode Arabidopsis SUPERKILLER3 (AtSKI3) and AtSKI2, respectively, components of the SKI complex that associates with the exosome during cytoplasmic 3'-to-5' RNA degradation, and that CER7-dependent regulation of wax biosynthesis also requires participation of AtSKI8. Our study further reveals that it is the impairment of the exosome-mediated 3'-5' decay of CER3 transcript in the cer7 mutant that triggers extensive production of siRNAs and efficient PTGS of CER3. This identifies PTGS as a general mechanism for eliminating highly abundant endogenous transcripts that is activated when 3'-to-5' mRNA turnover by the exosome is disrupted. Diminished efficiency of PTGS in ski mutants compared with cer7, as evidenced by lower accumulation of CER3-related siRNAs, suggests that reduced amounts of CER3 transcript are available for siRNA synthesis, possibly because CER3 mRNA that does not interact with SKI is degraded by 5'-to-3' XRN4 exoribonuclease.

  11. The transcriptional landscape

    DEFF Research Database (Denmark)

    Nielsen, Henrik

    2011-01-01

    The application of new and less biased methods to study the transcriptional output from genomes, such as tiling arrays and deep sequencing, has revealed that most of the genome is transcribed and that there is substantial overlap of transcripts derived from the two strands of DNA. In protein codi...

  12. The Transcription Factor Encyclopedia

    DEFF Research Database (Denmark)

    Yusuf, Dimas; Butland, Stefanie L; Swanson, Magdalena I;

    2012-01-01

    ABSTRACT: Here we present the Transcription Factor Encyclopedia (TFe), a new web-based compendium of mini review articles on transcription factors (TFs) that is founded on the principles of open access and collaboration. Our consortium of over 100 researchers has collectively contributed over 130...

  13. The Arabidopsis Mediator Complex Subunit16 Is a Key Component of Basal Resistance against the Necrotrophic Fungal Pathogen Sclerotinia sclerotiorum.

    Science.gov (United States)

    Wang, Chenggang; Yao, Jin; Du, Xuezhu; Zhang, Yanping; Sun, Yijun; Rollins, Jeffrey A; Mou, Zhonglin

    2015-09-01

    Although Sclerotinia sclerotiorum is a devastating necrotrophic fungal plant pathogen in agriculture, the virulence mechanisms utilized by S. sclerotiorum and the host defense mechanisms against this pathogen have not been fully understood. Here, we report that the Arabidopsis (Arabidopsis thaliana) Mediator complex subunit MED16 is a key component of basal resistance against S. sclerotiorum. Mutants of MED16 are markedly more susceptible to S. sclerotiorum than mutants of 13 other Mediator subunits, and med16 has a much stronger effect on S. sclerotiorum-induced transcriptome changes compared with med8, a mutation not altering susceptibility to S. sclerotiorum. Interestingly, med16 is also more susceptible to S. sclerotiorum than coronatine-insensitive1-1 (coi1-1), which is the most susceptible mutant reported so far. Although the jasmonic acid (JA)/ethylene (ET) defense pathway marker gene PLANT DEFENSIN1.2 (PDF1.2) cannot be induced in either med16 or coi1-1, basal transcript levels of PDF1.2 in med16 are significantly lower than in coi1-1. Furthermore, ET-induced suppression of JA-activated wound responses is compromised in med16, suggesting a role for MED16 in JA-ET cross talk. Additionally, MED16 is required for the recruitment of RNA polymerase II to PDF1.2 and OCTADECANOID-RESPONSIVE ARABIDOPSIS ETHYLENE/ETHYLENE-RESPONSIVE FACTOR59 (ORA59), two target genes of both JA/ET-mediated and the transcription factor WRKY33-activated defense pathways. Finally, MED16 is physically associated with WRKY33 in yeast and in planta, and WRKY33-activated transcription of PDF1.2 and ORA59 as well as resistance to S. sclerotiorum depends on MED16. Taken together, these results indicate that MED16 regulates resistance to S. sclerotiorum by governing both JA/ET-mediated and WRKY33-activated defense signaling in Arabidopsis.

  14. B-GATA transcription factors - insights into their structure, regulation and role in plant development

    Directory of Open Access Journals (Sweden)

    Claus eSchwechheimer

    2015-02-01

    Full Text Available GATA transcription factors are evolutionarily conserved transcriptional regulators that recognize promoter elements with a G-A-T-A core sequence. In comparison to animal genomes, the GATA transcription factor family in plants is comparatively large with approximately 30 members. In spite of a long-standing interest of plant molecular biologists in GATA factors, only research conducted in the last years has led to reliable insights into their functions during plant development. Here, we review the current knowledge on B-GATAs, one of four GATA factor subfamilies from Arabidopsis thaliana. We show that B-GATAs can be subdivided based on structural features and their biological function into family members with a C-terminal LLM- (leucine-leucine-methionine domain or an N-terminal HAN- (HANABA TARANU domain. The paralogous GNC (GATA, NITRATE-INDUCIBLE, CARBON-METABOLISM INVOLVED and CGA1/GNL (CYTOKININ-INDUCED GATA1/GNC-LIKE are introduced as LLM-domain containing B-GATAs from Arabidopsis that control germination, greening, senescence and flowering time downstream from several growth regulatory signals including light and the hormones gibberellin, auxin, and cytokinin. Arabidopsis HAN and its monocot-specific paralogs from rice (NECK LEAF1, maize (TASSEL SHEATH1, and barley (THIRD OUTER GLUME are HAN-domain-containing B-GATAs with a predominant role in embryo development and floral development. We also review GATA23, a regulator of lateral root initiation from Arabidopsis, that is closely related to GNC and GNL but has a degenerate LLM-domain that is seemingly specific for the Brassicaceae family. The Brassicaceae-specific GATA23 together with the above-mentioned monocot-specific HAN-domain GATAs provide evidence that neofunctionalization of the B-GATAs was used during plant evolution to expand the functional repertoire of these transcription factors.

  15. Transcript profiling reveals expression differences in wild-type and glabrous soybean lines

    OpenAIRE

    Stromvik Martina; Kaur Navneet; Hunt Matt; Vodkin Lila

    2011-01-01

    Abstract Background Trichome hairs affect diverse agronomic characters such as seed weight and yield, prevent insect damage and reduce loss of water but their molecular control has not been extensively studied in soybean. Several detailed models for trichome development have been proposed for Arabidopsis thaliana, but their applicability to important crops such as cotton and soybean is not fully known. Results Two high throughput transcript sequencing methods, Digital Gene Expression (DGE) Ta...

  16. AtMYB12 regulates flavonoids accumulation and abiotic stress tolerance in transgenic Arabidopsis thaliana.

    Science.gov (United States)

    Wang, Feibing; Kong, Weili; Wong, Gary; Fu, Lifeng; Peng, Rihe; Li, Zhenjun; Yao, Quanhong

    2016-08-01

    In plants, transcriptional regulation is the most important tool for modulating flavonoid biosynthesis. The AtMYB12 gene from Arabidopsis thaliana has been shown to regulate the expression of key enzyme genes involved in flavonoid biosynthesis, leading to the increased accumulation of flavonoids. In this study, the codon-optimized AtMYB12 gene was chemically synthesized. Subcellular localization analysis in onion epidermal cells indicated that AtMYB12 was localized to the nucleus. Its overexpression significantly increased accumulation of flavonoids and enhanced salt and drought tolerance in transgenic Arabidopsis plants. Real-time quantitative PCR (qRT-PCR) analysis showed that overexpression of AtMYB12 resulted in the up-regulation of genes involved in flavonoid biosynthesis, abscisic acid (ABA) biosynthesis, proline biosynthesis, stress responses and ROS scavenging under salt and drought stresses. Further analyses under salt and drought stresses showed significant increases of ABA, proline content, superoxide dismutase (SOD) and peroxidase (POD) activities, as well as significant reduction of H2O2 and malonaldehyde (MDA) content. The results demonstrate the explicit role of AtMYB12 in conferring salt and drought tolerance by increasing the levels of flavonoids and ABA in transgenic Arabidopsis. The AtMYB12 gene has the potential to be used to enhance tolerance to abiotic stresses in plants. PMID:27033553

  17. Overexpression of Late Embryogenesis Abundant 14 enhances Arabidopsis salt stress tolerance.

    Science.gov (United States)

    Jia, Fengjuan; Qi, Shengdong; Li, Hui; Liu, Pu; Li, Pengcheng; Wu, Changai; Zheng, Chengchao; Huang, Jinguang

    2014-11-28

    Late embryogenesis abundant (LEA) proteins are implicated in various abiotic stresses in higher plants. In this study, we identified a LEA protein from Arabidopsis thaliana, AtLEA14, which was ubiquitously expressed in different tissues and remarkably induced with increased duration of salt treatment. Subcellular distribution analysis demonstrated that AtLEA14 was mainly localized in the cytoplasm. Transgenic Arabidopsis and yeast overexpressing AtLEA14 all exhibited enhanced tolerance to high salinity. The transcripts of salt stress-responsive marker genes (COR15a, KIN1, RD29B and ERD10) were overactivated in AtLEA14 overexpressing lines compared with those in wild type plants under normal or salt stress conditions. In vivo and in vitro analysis showed that AtLEA14 could effectively stabilize AtPP2-B11, an important E3 ligase. These results suggested that AtLEA14 had important protective functions under salt stress conditions in Arabidopsis. PMID:25450686

  18. Isolation and characterization of an Arabidopsis biotin carboxylase gene and its promoter.

    Science.gov (United States)

    Bao, X; Shorrosh, B S; Ohlrogge, J B

    1997-11-01

    In the plastids of most plants, acetyl-CoA carboxylase (ACCase; EC 6.4.1.2) is a multisubunit complex consisting of biotin carboxylase (BC), biotin-carboxyl carrier protien (BCCP), and carboxytransferase (alpha-CT, beta-CT) subunits. To better understand the regulation of this enzyme, we have isolated and sequenced a BC genomic clone from Arabidopsis and partially characterized its promoter. Fifteen introns were identified. The deduced amino acid sequence of the mature BC protein is highly conserved between Arabidopsis and tobacco (92.6% identity). BC expression was evaluated using northern blots and BC/GUS fusion constructs in transgenic Arabidopsis. GUS activity in the BC/GUS transgenics as well as transcript level of the native gene were both found to be higher in silique and flower than in root and leaf. Analysis of tobacco suspension cells transformed with truncated BC promoter/GUS gene fusions indicated the region from -140 to +147 contained necessary promoter elements which supported basal gene expression. A positive regulatory region was found to be located between -2100 and -140, whereas a negative element was possibly located in the first intron. In addition, several conserved regulatory elements were identified in the BC promoter. Surprisingly, although BC is a low-abundance protein, the expression of BC/GUS fusion constructs was similar to 35S/GUS constructs.

  19. 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.

  20. Prokaryotic expression of soluble Arabidopsis protein AtERF1 and preparation of its polyclonal antibodies

    Directory of Open Access Journals (Sweden)

    ZHANG Yu

    2013-08-01

    Full Text Available AtERF1 encodes a member of the ERF subfamily B-3 of ERF/AP2 transcription factor family.It has been demonstrated almost every member of the B3 subgroup of AP2/ERF genes is involved in defense responses in Arabidopsis.Codon usage within a gene is a critical determinant of achievable protein expression level in E.coli. Gene optimization,therefore,is an effective method for synthetic genes with the aim of enhancing soluble expression,particular in heterologous hosts.In this paper,the AtERF1 protein of Arabidopsis thaliana was expressed in Escherichia coli using its optimized DNA sequence for E.coli. and yielded high level of soluble AtERF-1 protein in recombinant E.coli. The AtERF1 protein was used as an antigen to immune rabbits and obtains high titer antibodies.The immunological specificity of the polyclonal antibodies to AtERF1 was confirmed by Western blot assay.The prepared antibody in this work would facilitate the further functional investigation of AtERF1 in biochemical levels in Arabidopsis anther development.

  1. Ectopic expression of a hyacinth AGL6 homolog caused earlier flowering and homeotic conversion in Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    MADS-box genes are involved in floral organ development. Here we report that an AGL6(Agamous-like 6)-like MADS-box gene, HoAGL6, was isolated from Hyacinthus orientalis L. Expression pattern analysis demonstrated that HoAGL6 transcript was detected in inflorescence buds, tepals, carpels and ovules, but not in stamina, leaves or scales. Transgenic Arabidopsis plants ectopically expressing HoAGL6 exhibited novel phenotypes of significantly reduced plant size, extremely early flowering, and losing inflorescence indeterminacy. In addition, wide homeotic conversion of sepals, petals, and leaves into carpel-like or ovary structures, and disappearance or number reduction of stamens in 35S::HoAGL6 Arabidopsis plants were also observed. RT-PCR analysis indicated that the expressions of flowering time gene SOC1 and flower meristem identity gene LFY were significantly up-regulated in 35S::HoAGL6 transgenic Arabidopsis plants, and the expression levels of floral organ identity genes AG and SEP1 in leaves were also elevated. These results indicated that HoAGL6 was involved in the regulation of flower transition and flower organ formation.

  2. Genomewide analysis of intronic microRNAs in rice and Arabidopsis

    Indian Academy of Sciences (India)

    G. D. Yang; K. Yan; B. J. Wu; Y. H. Wang; Y. X. Gao; C. C. Zheng

    2012-12-01

    MicroRNAs (miRNAs) are potent regulators of gene transcription and posttranscriptional processes. The majority of miRNAs are localized within intronic regions of protein-coding genes (host genes) and have diverse functions in regulating important cellular processes in animals. To date, few plant intronic miRNAs have been studied functionally. Here we report a comprehensive computational analysis to characterize intronic miRNAs in rice and Arabidopsis. RT-PCR analysis confirmed that the identified intronic miRNAs were derived from the real introns of host genes. Interestingly, 13 intronic miRNAs in rice and two in Arabidopsis were located within seven clusters, of which four polycistronic clusters contain miRNAs derived from different families, suggesting that these clustered intronic miRNAs might be involved in extremely complex regulation in rice. Length analysis of miRNA-carrying introns, promoter prediction and qRT-PCR analysis results indicated that intronic miRNAs are coexpressed with their host genes. Expression pattern analysis demonstrated that host genes had a very broad expression spectrum in different stages of development, suggesting the intronic miRNAs might play an important role in plant development. This comparative genomics analysis of intronic miRNAs in rice and Arabidopsis provides new insight into the functions and regulatory mechanisms of intronic miRNAs in monocots and dicots.

  3. Redox state of plastoquinone pool regulates expression of Arabidopsis thaliana genes in response to elevated irradiance.

    Science.gov (United States)

    Adamiec, Małgorzata; Drath, Maria; Jackowski, Grzegorz

    2008-01-01

    DNA microarray technology was applied to gain insight into the role of the redox state of PQ pool as a retrograde factor mediating differential expression of Arabidopsis nuclear genes during the acclimation to changing irradiance. DNA microarray chips containing probes corresponding to 24,000 Arabidopsis nuclear genes were screened with cRNA samples prepared from leaves of plants exposed for 5 h to low irradiance (control) vs. medium, high and excessive irradiances (MI, HI and EI, respectively). Six hundred and sixty three genes were differentially expressed as a result of an exposure to at least one elevated irradiance. Among 663 differentially expressed genes a total of 50 were reverted by DCMU--24 ones modulated at medium irradiance, 32 ones modulated at high irradiance and a single one modulated at excessive irradiance. We postulate that their expression is regulated by redox state of plastoquinone (PQ) pool. Thus the PQ-mediated redox regulation of expression of Arabidopsis nuclear genes is probably limited to the irradiance window representing non-stressing conditions. We found that the promoter regions of the PQ-regulated genes contained conserved elements, suggesting transcriptional control by a shared set of trans-acting factors which participate in signal transduction from the redox state of the PQ pool. PMID:18231654

  4. Arabidopsis microRNA expression regulation in a wide range of abiotic stress responses.

    Science.gov (United States)

    Barciszewska-Pacak, Maria; Milanowska, Kaja; Knop, Katarzyna; Bielewicz, Dawid; Nuc, Przemyslaw; Plewka, Patrycja; Pacak, Andrzej M; Vazquez, Franck; Karlowski, Wojciech; Jarmolowski, Artur; Szweykowska-Kulinska, Zofia

    2015-01-01

    Arabidopsis microRNA expression regulation was studied in a wide array of abiotic stresses such as drought, heat, salinity, copper excess/deficiency, cadmium excess, and sulfur deficiency. A home-built RT-qPCR mirEX platform for the amplification of 289 Arabidopsis microRNA transcripts was used to study their response to abiotic stresses. Small RNA sequencing, Northern hybridization, and TaqMan® microRNA assays were performed to study the abundance of mature microRNAs. A broad response on the level of primary miRNAs (pri-miRNAs) was observed. However, stress response at the level of mature microRNAs was rather confined. The data presented show that in most instances, the level of a particular mature miRNA could not be predicted based on the level of its pri-miRNA. This points to an essential role of posttranscriptional regulation of microRNA expression. New Arabidopsis microRNAs responsive to abiotic stresses were discovered. Four microRNAs: miR319a/b, miR319b.2, and miR400 have been found to be responsive to several abiotic stresses and thus can be regarded as general stress-responsive microRNA species.

  5. Hydrogen peroxide modulates abscisic acid signaling in root growth and development in Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    BAI Ling; ZHOU Yun; ZHANG XiaoRan; SONG ChunPeng; Gao MingQing

    2007-01-01

    Exogenous abscisic acid (ABA) can inhibit root growth and promote formation of more root hairs in the root tip of Arabidopsis. However, the molecular mechanisms that underlie root ABA signaling are largely unknown. We report here that hydrogen peroxide (H2O2) reduces the root growth of wild type,and the phenotype of H2O2 on the root growth is similar to ABA response. Meanwhile ABA-induced changes in the morphology of root system can be partly reversed by ascorbic acid in wild type and abolished in NADPH oxidase defective mutant atrbohF and atrbohC. Further, ABA can induce H2O2 accumulation in the root cells and enhance transcription level of OXI1, which is necessary for many more AOS-dependent processes such as root hair growth in Arabidopsis. Our results suggest that H2O2 as an important signal molecule is required for the ABA-regulated root growth and development in Arabidopsis.

  6. Recent Progress in Arabidopsis Research in China: A Preface

    Institute of Scientific and Technical Information of China (English)

    Zhi-Hong Xu

    2006-01-01

    @@ In 2002, a workshop on Arabidopsis research in China was held in Shanghai, when a small group of Chinese plant scientists was working on this model species. Since then, we have witnessed the rapid growth of Arabidopsis research in China. This special issue of Journal of Integrative Plant Biology is dedicated exclusively to the Fourth Workshop on Arabidopsis Research in China, scheduled on November 30, 2005, in Beijing. In addition to reports collected in this special issue, the Chinese Arabidopsis community has been able to make significant contributions to many research fields. Here, I briefly summarize recent advances in Arabidopsis research in China.

  7. The Synthetic Elicitor DPMP (2,4-dichloro-6-{(E)-[(3-methoxyphenyl)imino]methyl}phenol) Triggers Strong Immunity in Arabidopsis thaliana and Tomato

    Science.gov (United States)

    Bektas, Yasemin; Rodriguez-Salus, Melinda; Schroeder, Mercedes; Gomez, Adilene; Kaloshian, Isgouhi; Eulgem, Thomas

    2016-01-01

    Synthetic elicitors are drug-like compounds that are structurally distinct from natural defense elicitors. They can protect plants from diseases by activating host immune responses and can serve as tools for the dissection of the plant immune system as well as leads for the development of environmentally-safe pesticide alternatives. By high-throughput screening, we previously identified 114 synthetic elicitors that activate expression of the pathogen-responsive CaBP22−333::GUS reporter gene in Arabidopsis thaliana (Arabidopsis), 33 of which are [(phenylimino)methyl]phenol (PMP) derivatives or PMP-related compounds. Here we report on the characterization of one of these compounds, 2,4-dichloro-6-{(E)-[(3-methoxyphenyl)imino]methyl}phenol (DPMP). DPMP strongly triggers disease resistance of Arabidopsis against bacterial and oomycete pathogens. By mRNA-seq analysis we found transcriptional profiles triggered by DPMP to resemble typical defense-related responses. PMID:27412821

  8. Accumulation of eicosapolyenoic acids enhances sensitivity to abscisic acid and mitigates the effects of drought in transgenic Arabidopsis thaliana.

    Science.gov (United States)

    Yuan, Xiaowei; Li, Yaxiao; Liu, Shiyang; Xia, Fei; Li, Xinzheng; Qi, Baoxiu

    2014-04-01

    IgASE1, a C₁₈ Δ(9)-specific polyunsaturated fatty acid elongase from the marine microalga Isochrysis galbana, is able to convert linoleic acid and α-linolenic acid to eicosadienoic acid and eicosatrienoic acid in Arabidopsis. Eicosadienoic acid and eicosatrienoic acid are precursors of arachidonic acid, eicosapentaenoic acid, and docosahexaenoic acid, which are synthesized via the Δ(8) desaturation biosynthetic pathways. This study shows that the IgASE1-expressing transgenic Arabidopsis exhibited altered morphology (decreased leaf area and biomass) and enhanced drought resistance compared to wild-type plants. The transgenic Arabidopsis were hypersensitive to abscisic acid (ABA) during seed germination, post-germination growth, and seedling development. They had elevated leaf ABA levels under well-watered and dehydrated conditions and their stomata were more sensitive to ABA. Exogenous application of eicosadienoic acid and eicosatrienoic acid can mimic ABA and drought responses in the wild type plants, similar to that found in the transgenic ones. The transcript levels of genes involved in the biosynthesis of ABA (NCED3, ABA1, AAO3) as well as other stress-related genes were upregulated in this transgenic line upon osmotic stress (300 mM mannitol). Taken together, these results indicate that these two eicosapolyenoic acids or their derived metabolites can mitigate the effects of drought in transgenic Arabidopsis, at least in part, through the action of ABA.

  9. Accumulation of eicosapolyenoic acids enhances sensitivity to abscisic acid and mitigates the effects of drought in transgenic Arabidopsis thaliana.

    Science.gov (United States)

    Yuan, Xiaowei; Li, Yaxiao; Liu, Shiyang; Xia, Fei; Li, Xinzheng; Qi, Baoxiu

    2014-04-01

    IgASE1, a C₁₈ Δ(9)-specific polyunsaturated fatty acid elongase from the marine microalga Isochrysis galbana, is able to convert linoleic acid and α-linolenic acid to eicosadienoic acid and eicosatrienoic acid in Arabidopsis. Eicosadienoic acid and eicosatrienoic acid are precursors of arachidonic acid, eicosapentaenoic acid, and docosahexaenoic acid, which are synthesized via the Δ(8) desaturation biosynthetic pathways. This study shows that the IgASE1-expressing transgenic Arabidopsis exhibited altered morphology (decreased leaf area and biomass) and enhanced drought resistance compared to wild-type plants. The transgenic Arabidopsis were hypersensitive to abscisic acid (ABA) during seed germination, post-germination growth, and seedling development. They had elevated leaf ABA levels under well-watered and dehydrated conditions and their stomata were more sensitive to ABA. Exogenous application of eicosadienoic acid and eicosatrienoic acid can mimic ABA and drought responses in the wild type plants, similar to that found in the transgenic ones. The transcript levels of genes involved in the biosynthesis of ABA (NCED3, ABA1, AAO3) as well as other stress-related genes were upregulated in this transgenic line upon osmotic stress (300 mM mannitol). Taken together, these results indicate that these two eicosapolyenoic acids or their derived metabolites can mitigate the effects of drought in transgenic Arabidopsis, at least in part, through the action of ABA. PMID:24609499

  10. Gibberellins control fruit patterning in Arabidopsis thaliana.

    Science.gov (United States)

    Arnaud, Nicolas; Girin, Thomas; Sorefan, Karim; Fuentes, Sara; Wood, Thomas A; Lawrenson, Tom; Sablowski, Robert; Østergaard, Lars

    2010-10-01

    The Arabidopsis basic helix-loop-helix (bHLH) proteins INDEHISCENT (IND) and ALCATRAZ (ALC) specify tissues required for fruit opening that have major roles in seed dispersal and plant domestication. Here, we show that synthesis of the phytohormone gibberellin is a direct and necessary target of IND, and that ALC interacts directly with DELLA repressors, which antagonize ALC function but are destabilized by gibberellin. Thus, the gibberellin/DELLA pathway has a key role in patterning the Arabidopsis fruit, and the interaction between DELLA and bHLH proteins, previously shown to connect gibberellin and light responses, is a versatile regulatory module also used in tissue patterning. PMID:20889713

  11. Extensive Natural Variation in Arabidopsis Seed Mucilage Structure

    Directory of Open Access Journals (Sweden)

    Cătălin eVoiniciuc

    2016-06-01

    Full Text Available Hydrated Arabidopsis thaliana seeds are coated by a gelatinous layer called mucilage, which is mainly composed of cell wall polysaccharides. Since mucilage is rich in pectin, its architecture can be visualized with the ruthenium red (RR dye. We screened the seeds of around 280 Arabidopsis natural accessions for variation in mucilage structure, and identified a large number of novel variants that differed from the Col-0 wild-type. Most of the accessions released smaller RR-stained capsules compared to the Col-0 reference. By biochemically characterizing the phenotypes of 25 of these accessions in greater detail, we discovered that distinct changes in polysaccharide structure resulted in gelatinous coatings with a deceptively similar appearance. Monosaccharide composition analysis of total mucilage extracts revealed a remarkable variation (from 50% to 200% of Col-0 levels in the content of galactose and mannose, which are important subunits of heteromannan. In addition, most of the natural variants had altered Pontamine Fast Scarlet 4B staining of cellulose and significantly reduced birefringence of crystalline structures. This indicates that the production or organization of cellulose may be affected by the presence of different amounts of hemicellulose. Although the accessions described in this study were primarily collected from Western Europe, they form five different phenotypic classes based on the combined results of our experiments. This suggests that polymorphisms at multiple loci are likely responsible for the observed mucilage structure. The transcription of MUCILAGE-RELATED10 (MUCI10, which encodes a key enzyme for galactoglucomannan synthesis, was severely reduced in multiple variants that phenocopied the muci10-1 insertion mutant. Although we could not pinpoint any causal polymorphisms in this gene, constitutive expression of fluorescently-tagged MUCI10 proteins complemented the mucilage defects of a muci10-like accession. This leads

  12. Extensive Natural Variation in Arabidopsis Seed Mucilage Structure

    Science.gov (United States)

    Voiniciuc, Cătălin; Zimmermann, Eva; Schmidt, Maximilian Heinrich-Wilhelm; Günl, Markus; Fu, Lanbao; North, Helen M.; Usadel, Björn

    2016-01-01

    Hydrated Arabidopsis thaliana seeds are coated by a gelatinous layer called mucilage, which is mainly composed of cell wall polysaccharides. Since mucilage is rich in pectin, its architecture can be visualized with the ruthenium red (RR) dye. We screened the seeds of around 280 Arabidopsis natural accessions for variation in mucilage structure, and identified a large number of novel variants that differed from the Col-0 wild-type. Most of the accessions released smaller RR-stained capsules compared to the Col-0 reference. By biochemically characterizing the phenotypes of 25 of these accessions in greater detail, we discovered that distinct changes in polysaccharide structure resulted in gelatinous coatings with a deceptively similar appearance. Monosaccharide composition analysis of total mucilage extracts revealed a remarkable variation (from 50 to 200% of Col-0 levels) in the content of galactose and mannose, which are important subunits of heteromannan. In addition, most of the natural variants had altered Pontamine Fast Scarlet 4B staining of cellulose and significantly reduced birefringence of crystalline structures. This indicates that the production or organization of cellulose may be affected by the presence of different amounts of hemicellulose. Although, the accessions described in this study were primarily collected from Western Europe, they form five different phenotypic classes based on the combined results of our experiments. This suggests that polymorphisms at multiple loci are likely responsible for the observed mucilage structure. The transcription of MUCILAGE-RELATED10 (MUCI10), which encodes a key enzyme for galactoglucomannan synthesis, was severely reduced in multiple variants that phenocopied the muci10-1 insertion mutant. Although, we could not pinpoint any causal polymorphisms in this gene, constitutive expression of fluorescently-tagged MUCI10 proteins complemented the mucilage defects of a muci10-like accession. This leads us to

  13. Putative sugarcane FT/TFL1 genes delay flowering time and alter reproductive architecture in Arabidopsis

    Directory of Open Access Journals (Sweden)

    Carla P. Coelho

    2014-05-01

    Full Text Available Agriculturally important grasses such as rice, maize and sugarcane are evolutionarily distant from Arabidopsis, yet some components of the floral induction process are highly conserved. Flowering in sugarcane is an important factor that negatively affects cane yield and reduces sugar/ethanol production from this important perennial bioenergy crop. Comparative studies have facilitated the identification and characterization of putative orthologs of key flowering time genes in sugarcane, a complex polyploid plant whose genome has yet to be sequenced completely. Using this approach we identified phosphatidylethanolamine-binding protein (PEBP gene family members in sugarcane that are similar to the archetypical FT and TFL1 genes of Arabidopsis that play an essential role in controlling the transition from vegetative to reproductive growth. Expression analysis of ScTFL1, which falls into the TFL1-clade of floral repressors, showed transcripts in developing leaves surrounding the shoot apex but not at the apex itself. ScFT1 was detected in immature leaves and apical regions of vegetatively growing plants and, after the floral transition, expression also occurred in mature leaves. Ectopic over-expression of ScTFL1 in Arabidopsis caused delayed flowering in Arabidopsis, as might be expected for a gene related to TFL1. In addition, lines with the latest flowering phenotype exhibited aerial rosette formation. Unexpectedly, over-expression of ScFT1, which has greatest similarity to the florigen-encoding FT, also caused a delay in flowering. This preliminary analysis of divergent sugarcane FT and TFL1 gene family members from Saccharum spp. suggests that their expression patterns and roles in the floral transition has diverged from the predicted role of similar PEBP family members.

  14. Hydrogen Sulfide Regulates Ethylene-induced Stomatal Closure in Arabidopsis thaliana

    Institute of Scientific and Technical Information of China (English)

    Zhihui Hou; Lanxiang Wang; Jing Liu; Lixia Hou; Xin Liu

    2013-01-01

    Hydrogen sulfide (H2S) is a newly-discovered signaling molecule in plants and has caused increasing attention in recent years,but its function in stomatal movement is unclear.In plants,H2S is synthesized via cysteine degradation catalyzed by D-/L-cysteine desulfhydrase (D-/L-CDes).AtD-/L-CDes::GUS transgenic Arabidopsis thaliana (L.) Heynh.plants were generated and used to investigate gene expression patterns,and results showed that AtD-/L-CDes can be expressed in guard cells.We also determined the subcellular localization of AtD-/L-CDes using transgenic plants of AtD-/L-CDes::GFP,and the results showed that AtD-CDes and AtL-CDes are located in the chloroplast and in the cytoplasm,respectively.The transcript levels of AtD-CDes and AtL-CDes were affected by the chemicals that cause stomatal closure.Among these factors,ACC,a precursor of ethylene,has the most significant effect,which indicates that the H2S generated from D-/L-CDes may play an important role in ethylene-induced stomatal closure.Meanwhile,H2S synthetic inhibitors significantly inhibited ethylene-induced stomatal closure in Arabidopsis.Ethylene treatment caused an increase of H2S production and of AtD-/L-CDes activity in Arabidopsis leaves.AtD-/L-CDes over-expressing plants exhibited enhanced induction of stomatal closure compared to the wild-type after ethylene treatment; however,the effect was not observed in the Atd-cdes and Atl-cdes mutants.In conclusion,our results suggest that the D-/L-CDes-generated H2S is involved in the regulation of ethylene-induced stomatal closure in Arabidopsis thaliana.

  15. Putative sugarcane FT/TFL1 genes delay flowering time and alter reproductive architecture in Arabidopsis

    Science.gov (United States)

    Coelho, Carla P.; Minow, Mark A. A.; Chalfun-Júnior, Antonio; Colasanti, Joseph

    2014-01-01

    Agriculturally important grasses such as rice, maize, and sugarcane are evolutionarily distant from Arabidopsis, yet some components of the floral induction process are highly conserved. Flowering in sugarcane is an important factor that negatively affects cane yield and reduces sugar/ethanol production from this important perennial bioenergy crop. Comparative studies have facilitated the identification and characterization of putative orthologs of key flowering time genes in sugarcane, a complex polyploid plant whose genome has yet to be sequenced completely. Using this approach we identified phosphatidylethanolamine-binding protein (PEBP) gene family members in sugarcane that are similar to the archetypical FT and TFL1 genes of Arabidopsis that play an essential role in controlling the transition from vegetative to reproductive growth. Expression analysis of ScTFL1, which falls into the TFL1-clade of floral repressors, showed transcripts in developing leaves surrounding the shoot apex but not at the apex itself. ScFT1 was detected in immature leaves and apical regions of vegetatively growing plants and, after the floral transition, expression also occurred in mature leaves. Ectopic over-expression of ScTFL1 in Arabidopsis caused delayed flowering in Arabidopsis, as might be expected for a gene related to TFL1. In addition, lines with the latest flowering phenotype exhibited aerial rosette formation. Unexpectedly, over-expression of ScFT1, which has greatest similarity to the florigen-encoding FT, also caused a delay in flowering. This preliminary analysis of divergent sugarcane FT and TFL1 gene family members from Saccharum spp. suggests that their expression patterns and roles in the floral transition has diverged from the predicted role of similar PEBP family members. PMID:24904616

  16. MYB103 is required for FERULATE-5-HYDROXYLASE expression and syringyl lignin biosynthesis in Arabidopsis stems.

    Science.gov (United States)

    Öhman, David; Demedts, Brecht; Kumar, Manoj; Gerber, Lorenz; Gorzsás, András; Goeminne, Geert; Hedenström, Mattias; Ellis, Brian; Boerjan, Wout; Sundberg, Björn

    2013-01-01

    The transcription factor MYB103 was previously identified as a member of the transcriptional network regulating secondary wall biosynthesis in xylem tissues of Arabidopsis, and was proposed to act on cellulose biosynthesis. It is a direct transcriptional target of the transcription factor SECONDARY WALL ASSOCIATED NAC DOMAIN PROTEIN 1 (SND1), and 35S-driven dominant repression or over-expression of MYB103 modifies secondary wall thickness. We identified two myb103 T-DNA insertion mutants and chemically characterized their lignocellulose by pyrolysis/GC/MS, 2D NMR, FT-IR microspectroscopy and wet chemistry. The mutants developed normally but exhibited a 70-75% decrease in syringyl (S) lignin. The level of guaiacyl (G) lignin was co-ordinately increased, so that total Klason lignin was not affected. The transcript abundance of FERULATE-5-HYDROXYLASE (F5H), the key gene in biosynthesis of S lignin, was strongly decreased in the myb103 mutants, and the metabolomes of the myb103 mutant and an F5H null mutant were very similar. Other than modification of the lignin S to G ratio, there were only very minor changes in the composition of secondary cell-wall polymers in the inflorescence stem. In conclusion, we demonstrate that F5H expression and hence biosynthesis of S lignin are dependent on MYB103. PMID:22967312

  17. Identification of brassinosteroid responsive genes in Arabidopsis by cDNA array

    Institute of Scientific and Technical Information of China (English)

    胡玉欣; 汪政科; 王永红; 包方; 李凝; 彭镇华; 李家洋

    2001-01-01

    We have systematically monitored brassinosteroid (BR) responsive genes in a BR-deficient mutant det2 suspension culture of Arabidopsis by using a cDNA array approach. Among 13000 cDNA clones arrayed on filters, 53 BR responsive clones were identified and designated BRR1-BRR53. Sequence analysis of 43 clones showed that 19 clones are novel genes, 3 clones are genes involved in the control of cell division, 4 clones are genes related to plant stress responses, 4 clones are transcriptional factor or signal transduction component genes, and 3 clones are genes involved in RNA splicing or structure forming. In addition, we also found that BR regulated the transcription of genes related to many physiological processes, such as photoreaction, ion transportation and some metabolic processes. These findings present molecular evidence that BR plays an essential role in plant growth and development.

  18. Organelle RNA recognition motif-containing (ORRM) proteins are plastid and mitochondrial editing factors in Arabidopsis.

    Science.gov (United States)

    Shi, Xiaowen; Bentolila, Stephane; Hanson, Maureen R

    2016-05-01

    Post-transcriptional C-to-U RNA editing occurs at specific sites in plastid and plant mitochondrial transcripts. Members of the Arabidopsis pentatricopeptide repeat (PPR) motif-containing protein family and RNA-editing factor Interacting Protein (RIP, also known as MORF) family have been characterized as essential components of the RNA editing apparatus. Recent studies reveal that several organelle-targeted RNA recognition motif (RRM)-containing proteins are involved in either plastid or mitochondrial RNA editing. ORRM1 (Organelle RRM protein 1) is essential for plastid editing, whereas ORRM2, ORRM3 and ORRM4 are involved in mitochondrial RNA editing. The RRM domain of ORRM1, ORRM3 and ORRM4 is required for editing activity, whereas the auxiliary RIP and Glycine-Rich (GR) domains mediate the ORRM proteins' interactions with other editing factors. The identification of the ORRM proteins as RNA editing factors further expands our knowledge of the composition of the editosome. PMID:27082488

  19. 拟南芥韧皮部防卫反应转录调控与小麦抗蚜虫机制%Transcriptional regulation of Arabidopsis phloem-defenses as a paradigm to explore molecular mechinisam underlying wheat resistance to aphids

    Institute of Scientific and Technical Information of China (English)

    张春玲; 付茂强; 徐衡; 董汉松

    2012-01-01

    Phloem-feeding insects are highly specialized in their mode of feeding and present a unique stress on plant fitness. These insects use their slender stylets to feed from a single-cell type,the phloem sieve element. In response,plants defend themselves by using the phloem-based defense ( PBD). A suggested PBD component is the lectin-type phloem protein (PP) , which may form high molecular weight polymers to close the sieve pores. An additional PBD component is the [3-1,3-glucan callose produced by glucan synthase( originally designated as glucan synthase-like, GSL) and accumulated on sieve plates. PP plugging and callose closure of sieve pores, and callose coagulation on sieve plates as well, is hypothesized to serve as a physical barrier to prevent the insects from phloem feeding. In general, plant defenses to insects are mediated by phytohormones ethylene and jasmonate, but whether both hormones have crosstalk with PBD is unclear. Therefore, the purposed study is to elucidate the regulation of PBD in wheat under attacks by aphids, which represent a typical group of phloem-feeding insects. Up to date,73 ,22 and 50 wheat genes of full length sequences respectively coding for MYB transcription factors, GSL enzymes and lectins or their receptors have been identified up to date, but their roles in PBD are unclear. To address the quenstion, studies could first include a transcriptional screening to identify MYB, lectin ( especially PP) and GSL genes involved in wheat PBD against aphids. Selected genes may be subjected to the pharmacological analysis to characterize their functions in association with ethylene or jasmonate signaling regulatory genes. Then,the defensive functions of identified genes could be confirmed by investigating effects of gene silencing and overexpression on aphid feeding and wheat defense responses. For overexpression,MYB,PP and GSL are pertinent to be linked with genes encoding green, yellow and red fluorescence proteins ( GFP, YFP and RFP

  20. Overexpressing HRS1 Confers Hypersensitivity to Low Phosphate-Elicited Inhibition of Primary Root Growth in Arabidopsis thaliana

    Institute of Scientific and Technical Information of China (English)

    Hong Liu; Huixia Yang; Chongming Wu; Juanjuan Feng; Xin Liu; Huanju Qin; Daowen Wang

    2009-01-01

    Phosphate (Pi) deficiency causes dramatic root system architecture (RSA) changes in higher plants.Here we report that overexpression of HRS1 leads to enhanced sensitivity to low Pi-elicited inhibition of primary root growth in Arabidopsis thaliana seedlings.Bioinformatic investigations uncovered that HRS1 and its six homologs encode putative G2-1ike transcription factors in Arabidopsis.Analysis of promoter::GUS reporter lines revealed that HRS1 transcripts were present mainly in the root hair region and root hair cells under Pi-sufficient conditions.Pi deprivation Increased HRS1 expression level and expanded its expression domain.Although HRS1 knockout mutant did not differ from wild type (WT) control irrespective of Pi status,its overexpreesion lines were significantly more susceptible to low Pi-elicited primary root shortening.In both WT and HRS1 overexpression seedlings,low Pi-induced primary root shortening was accompanied by enhanced root hair cell differentiation,but this enhancement occurred to a greater extent in the latter genotype.Collectively,our data suggest that HRS1 may be involved in the modulation of primary root and root hair growth in Pi-deprived Arabidopsis seedlings,and provide useful clues for further research into the function of HRS1 and its homologs and the mechanisms behind RSA changes under Pi-deficient conditions.

  1. Genome structures and halophyte-specific gene expression of the extremophile thellungiella parvula in comparison with Thellungiella salsuginea (Thellungiella halophila) and arabidopsis

    KAUST Repository

    Oh, Dongha

    2010-09-10

    The genome of Thellungiella parvula, a halophytic relative of Arabidopsis (Arabidopsis thaliana), is being assembled using Roche-454 sequencing. Analyses of a 10-Mb scaffold revealed synteny with Arabidopsis, with recombination and inversion and an uneven distribution of repeat sequences. T. parvula genome structure and DNA sequences were compared with orthologous regions from Arabidopsis and publicly available bacterial artificial chromosome sequences from Thellungiella salsuginea (previously Thellungiella halophila). The three-way comparison of sequences, from one abiotic stress-sensitive species and two tolerant species, revealed extensive sequence conservation and microcolinearity, but grouping Thellungiella species separately from Arabidopsis. However, the T. parvula segments are distinguished from their T. salsuginea counterparts by a pronounced paucity of repeat sequences, resulting in a 30% shorter DNA segment with essentially the same gene content in T. parvula. Among the genes is SALT OVERLY SENSITIVE1 (SOS1), a sodium/proton antiporter, which represents an essential component of plant salinity stress tolerance. Although the SOS1 coding region is highly conserved among all three species, the promoter regions show conservation only between the two Thellungiella species. Comparative transcript analyses revealed higher levels of basal as well as salt-induced SOS1 expression in both Thellungiella species as compared with Arabidopsis. The Thellungiella species and other halophytes share conserved pyrimidine-rich 5\\' untranslated region proximal regions of SOS1 that are missing in Arabidopsis. Completion of the genome structure of T. parvula is expected to highlight distinctive genetic elements underlying the extremophile lifestyle of this species. © American Society of Plant Biologists.

  2. Phospholipase D affects translocation of NPR1 to the nucleus in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Martin eJanda

    2015-02-01

    Full Text Available Phytohormone salicylic acid (SA is a crucial component of plant induced defense against biotrophic pathogens. Although the key players of SA pathway are known, there are still gaps in our understanding of molecular mechanism and regulation of particular steps. In our previous research we showed in Arabidopsis suspension cells that n-butanol, which specifically modulates phospholipase D activity, significantly supresses transcription of pathogenesis related (PR1 gene generally accepted as SA pathway marker. In the presented study, we have investigated the site of n-butanol action in SA pathway. We were able to show in Arabidopsis plants treated with SA that n-butanol inhibits the transcription of defense genes (PR-1, WRKY38. Fluorescence microscopy of Arabidopsis thaliana mutants expressing 35S::NPR1-GFP (nonexpressor pathogenesis related 1 revealed significantly decreased nuclear localization of NPR1 in the presence of n-butanol. On the other hand, n-butanol did not affect nuclear localization of NPR1 in 35S::npr1C82A-GFP and 35S::npr1C216A-GFP mutants constitutively expressing NPR1 monomers. We also observed decreasing effect of n-butanol on ROS production, another important factor in plant response to pathogen attack.Mass spectrometric analysis of plant extracts showed that n-butanol significantly changes metabolic fingerprinting while t-butanol had no effect. We found groups of plant metabolites, influenced differently by SA and n-butanol treatment and we proposed several metabolites as markers for n-butanol action.

  3. Expression profiling and functional analysis reveals that TOR is a key player in regulating photosynthesis and phytohormone signaling pathways in Arabidopsis.

    Science.gov (United States)

    Dong, Pan; Xiong, Fangjie; Que, Yumei; Wang, Kai; Yu, Lihua; Li, Zhengguo; Ren, Maozhi

    2015-01-01

    Target of rapamycin (TOR) acts as a master regulator to control cell growth by integrating nutrient, energy, and growth factors in all eukaryotic species. TOR plays an evolutionarily conserved role in regulating the transcription of genes associated with anabolic and catabolic processes in Arabidopsis, but little is known about the functions of TOR in photosynthesis and phytohormone signaling, which are unique features of plants. In this study, AZD8055 (AZD) was screened as the strongest active-site TOR inhibitor (asTORi) in Arabidopsis compared with TORIN1 and KU63794 (KU). Gene expression profiles were evaluated using RNA-seq after treating Arabidopsis seedlings with AZD. More than three-fold differentially expressed genes (DEGs) were identified in AZD-treated plants relative to rapamycin-treated plants in previous studies. Most of the DEGs and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways involved in cell wall elongation, ribosome biogenesis, and cell autophagy were common to both AZD- and rapamycin-treated samples, but AZD displayed much broader and more efficient inhibition of TOR compared with rapamycin. Importantly, the suppression of TOR by AZD resulted in remodeling of the expression profile of the genes associated with photosynthesis and various phytohormones, indicating that TOR plays a crucial role in modulating photosynthesis and phytohormone signaling in Arabidopsis. These newly identified DEGs expand the understanding of TOR signaling in plants. This study elucidates the novel functions of TOR in photosynthesis and phytohormone signaling and provides a platform to study the downstream targets of TOR in Arabidopsis.

  4. Expression of a High Mobility Group Protein Isolated from Cucumis sativus Affects the Germination of Arabidopsis thaliana under Abiotic Stress Conditions

    Institute of Scientific and Technical Information of China (English)

    Ji Young Jang; Kyung Jin Kwak; Hunseung Kang

    2008-01-01

    Although high mobility group B (HMGB) proteins have been identified from a variety of plant species, their importance and functional roles in plant responses to changing environmental conditions are largely unknown. Here, we investigated the functional roles of a CsHMGB isolated from cucumber (Cucurnis sativus L.) in plant responses to environmental stimuli. Under normal growth conditions or when subjected to cold stress, no differences in plant growth were found between the wild.type and transgenic Arabidopsis thaliana overexpressing CsHMGB. By contrast, the transgenic Arabidopsis plants displayed retarded germination compared with the wild-type plants when grown under high salt or dehydration stress conditions. Germination of the transgenic plants was delayed by the addition of abscisic acid (ABA), implying that CsHMGB affects germination through an ABA-dependent way. The expression of CsHMGB had affected only the germination stage, and CsHMGB did not affect the seedling growth of the transgenic plants under the stress conditions. The transcript levels of several germination-responsive genes were modulated by the expression of CsHMGB in Arabidopsis. Taken together, these results suggest that ectopic expression of a CsHMGB in Arabidopsis modulates the expression of several germination-responsive genes, and thereby affects the germination of Arabidopsis plants under different stress conditions.

  5. Differential Gene Expression and Protein Phosphorylation as Factors Regulating the State of the Arabidopsis SNX1 Protein Complexes in Response to Environmental Stimuli

    Science.gov (United States)

    Brumbarova, Tzvetina; Ivanov, Rumen

    2016-01-01

    Endosomal recycling of plasma membrane proteins contributes significantly to the regulation of cellular transport and signaling processes. Members of the Arabidopsis (Arabidopsis thaliana) SORTING NEXIN (SNX) protein family were shown to mediate the endosomal retrieval of transporter proteins in response to external challenges. Our aim is to understand the possible ways through which external stimuli influence the activity of SNX1 in the root. Several proteins are known to contribute to the function of SNX1 through direct protein–protein interaction. We, therefore, compiled a list of all Arabidopsis proteins known to physically interact with SNX1 and employed available gene expression and proteomic data for a comprehensive analysis of the transcriptional and post-transcriptional regulation of this interactome. The genes encoding SNX1-interaction partners showed distinct expression patterns with some, like FAB1A, being uniformly expressed, while others, like MC9 and BLOS1, were expressed in specific root zones and cell types. Under stress conditions known to induce SNX1-dependent responses, two genes encoding SNX1-interacting proteins, MC9 and NHX6, showed major gene-expression variations. We could also observe zone-specific transcriptional changes of SNX1 under iron deficiency, which are consistent with the described role of the SNX1 protein. This suggests that the composition of potential SNX1-containing protein complexes in roots is cell-specific and may be readjusted in response to external stimuli. On the level of post-transcriptional modifications, we observed stress-dependent changes in the phosphorylation status of SNX1, FAB1A, and CLASP. Interestingly, the phosphorylation events affecting SNX1 interactors occur in a pattern which is largely complementary to transcriptional regulation. Our analysis shows that transcriptional and post-transcriptional regulation play distinct roles in SNX1-mediated endosomal recycling under external stress. PMID:27725825

  6. Novel biosensors based on flavonoid-responsive transcriptional regulators introduced into Escherichia coli

    DEFF Research Database (Denmark)

    Siedler, Solvej; Stahlhut, Steen Gustav; Malla, Sailesh;

    2014-01-01

    This study describes the construction of two flavonoid biosensors, which can be applied for metabolic engineering of Escherichia coli strains. The biosensors are based on transcriptional regulators combined with autofluorescent proteins. The transcriptional activator FdeR from Herbaspirillum sero....... coli cells containing a flavonol synthase from Arabidopsis thaliana (fls1). We expect the designed biosensors to be applied for isolation of genes involved in flavonoid biosynthetic pathways. © 2013 The Authors.......This study describes the construction of two flavonoid biosensors, which can be applied for metabolic engineering of Escherichia coli strains. The biosensors are based on transcriptional regulators combined with autofluorescent proteins. The transcriptional activator FdeR from Herbaspirillum...... seropedicae SmR1 responds to naringenin, while the repressor QdoR from Bacillus subtilis is inactivated by quercetin and kaempferol. Both biosensors showed over a 7-fold increase of the fluorescent signal after addition of their specific effectors, and a linear correlation between the fluorescence intensity...

  7. Transcriptomic profiling of Arabidopsis gene expression in response to varying micronutrient zinc supply

    Directory of Open Access Journals (Sweden)

    Herlânder Azevedo

    2016-03-01

    Full Text Available Deficiency of the micronutrient zinc is a widespread condition in agricultural soils, causing a negative impact on crop quality and yield. Nevertheless, there is an insufficient knowledge on the regulatory and molecular mechanisms underlying the plant response to inadequate zinc nutrition [1]. This information should contribute to the development of plant-based solutions with improved nutrient-use-efficiency traits in crops. Previously, the transcription factors bZIP19 and bZIP23 were identified as essential regulators of the response to zinc deficiency in Arabidopsis thaliana [2]. A microarray experiment comparing gene expression between roots of wild-type and the mutant bzip19 bzip23, exposed to zinc deficiency, led to the identification of differentially expressed genes related with zinc homeostasis, namely its transport and plant internal translocation [2]. Here, we provide the detailed methodology, bioinformatics analysis and quality controls related to the microarray gene expression profiling published by Assunção and co-workers [2]. Most significantly, the present dataset comprises new experimental variables, including analysis of shoot tissue, and zinc sufficiency and excess supply. Thus, it expands from 8 to 42 microarrays hybridizations, which have been deposited at the Gene Expression Omnibus (GEO under the accession number GSE77286. Overall, it provides a resource for research on the molecular basis and regulatory events of the plant response to zinc supply, emphasizing the importance of Arabidopsis bZIP19 and bZIP23 transcription factors.

  8. Arabidopsis VIRE2 INTERACTING PROTEIN2 is required for Agrobacterium T-DNA integration in plants.

    Science.gov (United States)

    Anand, Ajith; Krichevsky, Alexander; Schornack, Sebastian; Lahaye, Thomas; Tzfira, Tzvi; Tang, Yuhong; Citovsky, Vitaly; Mysore, Kirankumar S

    2007-05-01

    Agrobacterium tumefaciens-mediated genetic transformation is an efficient tool for genetic engineering of plants. VirE2 is a single-stranded DNA binding Agrobacterium protein that is transported into the plant cell and presumably protects the T-DNA from degradation. Using a yeast two-hybrid system, we identified Arabidopsis thaliana VIRE2-INTERACTING PROTEIN2 (VIP2) with a NOT domain that is conserved in both plants and animals. Furthermore, we provide evidence supporting VIP2 interaction with VIP1, a basic domain/leucine zipper motif-containing protein required for nuclear import and integration of T-DNA. Virus-induced gene silencing of VIP2 in Nicotiana benthamiana and characterization of the Arabidopsis vip2 mutant (At vip2) demonstrate that VIP2 is required for Agrobacterium-mediated stable transformation but not for transient transformation. Assays based upon a promoter-trap vector and quantification of T-DNA integration further confirmed VIP2 involvement in T-DNA integration. Interestingly, VIP2 transcripts were induced to a greater extent over prolonged periods after infection with a T-DNA transfer-competent Agrobacterium strain compared with the transfer-deficient Agrobacterium strain. Transcriptome analyses of At vip2 suggest that VIP2 is likely a transcriptional regulator, and the recalcitrancy to transformation in At vip2 is probably due to the combination of muted gene expression response upon Agrobacterium infection and repression of histone genes resulting in decreased T-DNA integration events. PMID:17496122

  9. 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.

  10. Potential role of salicylic acid in modulating diacylglycerol homeostasis in response to freezing temperatures in Arabidopsis.

    Science.gov (United States)

    Tan, Wei-Juan; Xiao, Shi; Chen, Qin-Fang

    2015-01-01

    In our recent article in Molecular Plant, we reported that 3 lipase-like defense regulators SENESCENCE-ASSOCIATED GENE101 (SAG101), ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1) and PHYTOALEXIN DEFICIENT4 (PAD4) are involved in the regulation of freezing tolerance in Arabidopsis. The transcripts of SAG101, EDS1 and PAD4 were inducible by cold stress and their knockout or knockdown mutants exhibited enhanced chilling and freezing tolerance in comparison to the wild type. The freezing tolerance phenotype showed in the sag101, eds1 and pad4 mutants was correlated with the transcriptional upregulation of C-REPEAT/DRE BINDING FACTORs (CBFs) and their regulons as well as increased levels of proline. Upon cold exposure, the sag101, eds1 and pad4 mutants showed ameliorated cell death and accumulation of hydrogen peroxide, which were highly induced by freezing stress in the wild-type leaves. Moreover, the contents of salicylic acid (SA) and diacylglycerol (DAG) were significantly decreased in the sag101, eds1 and pad4 mutants compared to the wild type. Taken together, our results suggest that the SAG101, EDS1 and PAD4 are negative regulators in the freezing response and function, at least in part, by modulating the homeostasis of SA and DAG in Arabidopsis.

  11. Efficient Silencing of Endogenous MicroRNAs Using Artificial MicroRNAs in Arabidopsis thaliana

    Institute of Scientific and Technical Information of China (English)

    Andrew L. Eamens; Claire Agius; Neil A. Smith; Peter M. Waterhouse; Ming-Bo Wang

    2011-01-01

    We report here that the expression of endogenous microRNAs (miRNAs) can be efficiently silenced in Arabidopsis thaliana (Arabidopsis) using artificial miRNA (amiRNA) technology. We demonstrate that an amiRNA designed to target a mature miRNA directs silencing against all miRNA family members, whereas an amiRNA designed to target the stem-loop region of a miRNA precursor transcript directs silencing against only the individual family member targeted.Furthermore, our results indicate that amiRNAs targeting both the mature miRNA and stem-loop sequence direct RNA silencing through cleavage of the miRNA precursor transcript, which presumably occurs in the nucleus of a plant cell during the initial stages of miRNA biogenesis. This suggests that small RNA (sRNA)-guided RNA cleavage in plants occurs not only in the cytoplasm, but also in the nucleus. Many plant miRNA gene families have been identified via sequencing and bioinformatic analysis, but, to date, only a small tranche of these have been functionally characterized due to a lack of effective forward or reverse genetic tools. Our findings therefore provide a new and powerful reverse-genetic tool for the analysis of miRNA function in plants.

  12. Arabidopsis MSI1 Is Required for Negative Regulation of the Response to Drought Stress

    Institute of Scientific and Technical Information of China (English)

    Cristina Alexandre; Yvonne M(o)ller-Steinbach; Nicole Sch(o)nrock; Wilhelm Gruissem; Lars Hennig

    2009-01-01

    Arabidopsis MSI1 has fundamental functions in plant development.MSI1 is a subunit of Polycomb group protein complexes and Chromatin assembly factor 1,and it interacts with the Retinoblastoma-related protein 1.Altered levels of MSI1 result in pleiotropic phenotypes,reflecting the complexity of MSI1 protein functions.In order to uncover additional functions of MSI1,we performed transcriptional profiling of wild-type and plants with highly reduced MSI1 levels (msil-cs).Surprisingly,the known functions of MSI1 could only account for a minor part of the transcriptional changes in msi1-cs plants.One of the most striking unexpected observations was the up-regulation of a subset of ABA-responsive genes eliciting the response to drought and salt stress.We report that MSI1 can bind to the chromatin of the drought-inducible downstream target RD20 and suggest a new role for MSI1 in the negative regulation of the Arabidopsis drought-stress response.

  13. Proteomics Analysis Reveals Post-Translational Mechanisms for Cold-Induced Metabolic Changes in Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    Tian Li; Alma L.Burlingame; Zhi-Ping Deng; Zhi Yong Wang; Shou-Ling Xu; Juan A.Oses-Prieto; Sunita Putil; Peng Xu; Rui-Ju Wang; Kathy H.Li; David A.Malty; Liz-He An

    2011-01-01

    Cold-induced changes of gene expression and metabolism are critical for plants to survive freezing. Largely by changing gene expression, exposure to a period of non-freezing low temperatures increases plant tolerance to freezing-a phenomenon known as cold acclimation. Cold also induces rapid metabolic changes, which provide instant protection before temperature drops below freezing point. The molecular mechanisms for such rapid metabolic responses to cold remain largely unknown. Here, we use two-dimensional difference gel electrophoresis (2-D DIGE) analysis of sub-cellular fractions of Arabidopsis thaliana proteome coupled with spot identification by tandem mass spectrometry to identify early cold-responsive proteins in Arabidopsis. These proteins include four enzymes involved in starch degradation, three HSP100 proteins, several proteins in the tricarboxylic acid cycle, and sucrose metabolism. Upon cold treatment, the Disproportionating Enzyme 2 (DPE2), a cytosolic transglucosidase metabolizing maltose to glucose, increased rapidly in the centrifugation pellet fraction and decreased in the soluble fraction. Consistent with cold-induced inactivation of DPE2 enzymatic activity, the dpe2 mutant showed increased freezing tolerance without affecting the C-repeat binding transcription factor (CBF) transcriptional pathway. These results support a model that cold-induced inactivation of DPE2 leads to rapid accumulation of maltose, which is a cold-induced compatible solute that protects cells from freezing damage. This study provides evidence for a key role of rapid post-translational regulation of carbohydrate metabolic enzymes in plant protection against sudden temperature drop.

  14. Nitric Oxide Mediated Transcriptome Profiling Reveals Activation of Multiple Regulatory Pathways in Arabidopsis thaliana.

    Science.gov (United States)

    Hussain, Adil; Mun, Bong-Gyu; Imran, Qari M; Lee, Sang-Uk; Adamu, Teferi A; Shahid, Muhammad; Kim, Kyung-Min; Yun, Byung-Wook

    2016-01-01

    Imbalance between the accumulation and removal of nitric oxide and its derivatives is a challenge faced by all plants at the cellular level, and is especially important under stress conditions. Exposure of plants to various biotic and abiotic stresses causes rapid changes in cellular redox tone potentiated by the rise in reactive nitrogen species that serve as signaling molecules in mediating defensive responses. To understand mechanisms mediated by these signaling molecules, we performed a large-scale analysis of the Arabidopsis transcriptome induced by nitrosative stress. We generated an average of 84 and 91 million reads from three replicates each of control and 1 mM S-nitrosocysteine (CysNO)-infiltrated Arabidopsis leaf samples, respectively. After alignment, more than 95% of all reads successfully mapped to the reference and 32,535 genes and 55,682 transcripts were obtained. CysNO infiltration caused differential expression of 6436 genes (3448 up-regulated and 2988 down-regulated) and 6214 transcripts (3335 up-regulated and 2879 down-regulated) 6 h post-infiltration. These differentially expressed genes were found to be involved in key physiological processes, including plant defense against various biotic and abiotic stresses, hormone signaling, and other developmental processes. After quantile normalization of the FPKM values followed by student's T-test (P level and would prove helpful in understanding and incorporating mechanisms associated with nitrosative stress responses in plants. PMID:27446194

  15. Plant growth in Arabidopsis is assisted by compost soil-derived microbial communities.

    Science.gov (United States)

    Carvalhais, Lilia C; Muzzi, Frederico; Tan, Chin-Hong; Hsien-Choo, Jin; Schenk, Peer M

    2013-01-01

    Plants in natural and agricultural environments are continuously exposed to a plethora of diverse microorganisms resulting in microbial colonization of roots and the rhizosphere. This process is believed to be accompanied by an intricate network of ongoing simultaneous interactions. In this study, we examined Arabidopsis thaliana roots and shoots in the presence or absence of whole microbial communities extracted from compost soil. The results show a clear growth promoting effect on Arabidopsis shoots in the presence of soil microbes compared to plants grown in microbe-free soil under otherwise identical conditions. Element analyses showed that iron uptake was facilitated by these mixed microbial communities which also led to transcriptional downregulation of genes required for iron transport. In addition, soil microbial communities suppressed the expression of marker genes involved in nitrogen uptake, oxidative stress/redox signaling, and salicylic acid (SA)-mediated plant defense while upregulating jasmonate (JA) signaling, cell wall organization/biosynthesis and photosynthesis. Multi-species analyses such as simultaneous transcriptional profiling of plants and their interacting microorganisms (metatranscriptomics) coupled to metagenomics may further increase our understanding of the intricate networks underlying plant-microbe interactions. PMID:23847639

  16. In vitro Reconstitution Assay of miRNA Biogenesis by Arabidopsis DCL1

    Science.gov (United States)

    Wang, Tian; Castillo-González, Claudia; You, Lan; Li, Rui; Wen, Liwei; Zhu, Hongliang; Zhang, Xiuren

    2016-01-01

    microRNAs (miRNAs) are small non-coding RNAs, regulating most if not all, biological processes in eukaryotic organisms. miRNAs are initially processed from primary transcripts (pri-miRNAs) to produce miRNA precursors (pre-miRNAs), that are further processed into miRNA and its complementary strands (miRNA/*). In Arabidopsis, and possibly other plants, the processing from pri-miRNAs to pre-miRNAs and from pre-miRNAs to miRNA/* are both implemented through Dicer-like 1 (DCL1) complexes. Recently, we demonstrated isolation of DCL1 complexes of unprecedented quality from in planta. We further successfully reconstituted DCL1 cleavage assays in vitro that were able to fully recapitulate in vivo miRNA biogenesis. Here we provide a detailed protocol of DCL1 reconstitution assays. The protocol comprises three major parts (Figure 1): 1) Preparation of pri- and pre-miRNA transcripts (Procedures A-C); 2) Purification of the recombinant Arabidopsis DCL1 machinery from Nicotiana benthamiana (N. benthamiana) through immunoprecipitation (IP) (Procedures D and E); and 3) in vitro processing of radioisotope-labeled pri- or pre-miRNAs using the isolated DCL1 complexes (Procedure F). It is our desire that the protocol be a powerful tool for the RNAi community to study mechanistic issues or to develop RNA silencing technologies.

  17. Isolation and RNA gel blot analysis of genes that could serve as potential molecular markers for leaf senescence in Arabidopsis thaliana.

    Science.gov (United States)

    Yoshida, S; Ito, M; Nishida, I; Watanabe, A

    2001-02-01

    Nine cDNAs, representing genes in which the transcripts accumulated in senescent leaves of Arabidopsis thaliana, were isolated by differential display reverse transcription polymerase chain reaction (DDRT-PCR) and the genes were designated yellow-leaf-specific gene 1 to 9 (YLS1-YLS9). Sequence analysis revealed that none of the YLS genes, except YLS6, had been reported as senescence-up-regulated genes. RNA gel blot analysis revealed that the transcripts of YLS3 accumulated at the highest level at an early senescence stage, whereas the transcripts from the other YLS genes reached their maximum levels in late senescence stages. Transcripts of YLS genes showed various accumulation patterns under natural senescence, and under artificial senescence induced by darkness, ethylene or ABA. These expression characteristics of YLS genes will be useful as potential molecular markers, which will enhance our understanding of natural and artificial senescence processes.

  18. The involvement of ethylene in regulation of Arabidopsis gravitropism

    Science.gov (United States)

    Li, Ning; Zhu, Lin

    green 1, Chen et al 2005; Guo et al 2008). To address the molecular mechanism by which ethylene regulates gravitropism, a cutting-edge phosphopro-teomics approach has been adopted to discover new components involved in ethylene signaling pathways (Li et al 2009). Two putative ethylene response transcription factors: EIL1 and ERF110, have been identified to contain ethylene-regulated phosphorylation sites, the phos-phorylation status of which are ethylene treatment-dependent but EIN2-independent, strongly suggestive of the existence of novel signaling components mediating an alternative ethylene signal pathway. Combination of the time-dependent ethylene treatments with the systematic profiling of protein phosphorylation using functional phosphoproteomics among Arabidopsis ethylene response mutants is able to provide more valuable information about the molecular mechanisms underlying ethylene and gravity signaling pathways. (This work is supported by grants: RPC07/08.SC16, 661408, 661207, N HKUST627/06, DAG04/05.SC08, HKUST6105/01M, and HKUST6413/06M)

  19. Arabidopsis CDS blastp result: AK073532 [KOME

    Lifescience Database Archive (English)

    Full Text Available ical to ARL2 G-protein (Halimasch; HAL; TITAN5) GI:20514265 from [Arabidopsis thaliana]; identical to cDNA A...AK073532 J033046D12 At2g18390.1 ADP-ribosylation factor-like protein 2 (ARL2) ident

  20. Arabidopsis CDS blastp result: AK061294 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK061294 006-301-D01 At3g08900.1 reversibly glycosylated polypeptide-3 (RGP3) nearl...y identical to reversibly glycosylated polypeptide-3 [Arabidopsis thaliana] GI:11863238; contains non-consensus GA-donor splice site at intron 2 0.0 ...