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Sample records for annulatus bm86 ortholog

  1. Expression of recombinant Rhipicephalus (Boophilus) microplus, R. annulatus and R. decoloratus Bm86 orthologs as secreted proteins in Pichia pastoris.

    OpenAIRE

    Jongejan Frans; Hope Michelle; Nijhof Ard M; Naranjo Victoria; de la Lastra José; Canales Mario; de la Fuente José

    2009-01-01

    Abstract Background Rhipicephalus (Boophilus) spp. ticks economically impact on cattle production in Africa and other tropical and subtropical regions of the world. Tick vaccines constitute a cost-effective and environmentally friendly alternative to tick control. The R. microplus Bm86 protective antigen has been produced by recombinant DNA technology and shown to protect cattle against tick infestations. Results In this study, the genes for Bm86 (R. microplus), Ba86 (R. annulatus) and Bd86 (...

  2. Vaccination against Bm86 Homologues in Rabbits Does Not Impair Ixodes ricinus Feeding or Oviposition.

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    Jeroen Coumou

    Full Text Available Human tick-borne diseases that are transmitted by Ixodes ricinus, such as Lyme borreliosis and tick borne encephalitis, are on the rise in Europe. Diminishing I. ricinus populations in nature can reduce tick exposure to humans, and one way to do so is by developing an anti-vector vaccine against tick antigens. Currently, there is only one anti-vector vaccine available against ticks, which is a veterinary vaccine based on the tick antigen Bm86 in the gut of Rhipicephalus microplus. Bm86 vaccine formulations cause a reduction in the number of Rhipicephalus microplus ticks that successfully feed, i.e. lower engorgement weights and a decrease in the number of oviposited eggs. Furthermore, Bm86 vaccines reduce transmission of bovine Babesia spp. Previously two conserved Bm86 homologues in I. ricinus ticks, designated as Ir86-1 and Ir86-2, were described. Here we investigated the effect of a vaccine against recombinant Ir86-1, Ir86-2 or a combination of both on Ixodes ricinus feeding. Recombinant Ixodes ricinus Bm86 homologues were expressed in a Drosophila expression system and rabbits were immunized with rIr86-1, rIr86-2, a combination of both or ovalbumin as a control. Each animal was infested with 50 female adults and 50 male adults Ixodes ricinus and tick mortality, engorgement weights and egg mass were analyzed. Although serum IgG titers against rIr86 proteins were elicited, no effect was found on tick feeding between the rIr86 vaccinated animals and ovalbumin vaccinated animals. We conclude that vaccination against Bm86 homologues in Ixodes ricinus is not an effective approach to control Ixodes ricinus populations, despite the clear effects of Bm86 vaccination against Rhipicephalus microplus.

  3. Immunisation with recombinant proteins subolesin and Bm86 for the control of Dermanyssus gallinae in poultry.

    Science.gov (United States)

    Harrington, David; Canales, Mario; de la Fuente, José; de Luna, Carlos; Robinson, Karen; Guy, Jonathan; Sparagano, Olivier

    2009-06-19

    Dermanyssus gallinae has a worldwide distribution and is considered to be the most serious and economically significant ectoparasite affecting egg-laying poultry in Europe. Recombinant Bm86 and subolesin proteins derived from Boophilus microplus ticks and Aedes albopictus mosquitoes were used to immunise poultry in an attempt to control D. gallinaein vitro. Immunisation with subolesin and Bm86 stimulated different profiles of IgY response, whilst Bm86 but not subolesin was recognized by IgY on western blots. Orthologues for Bm86 were not found in D. gallinae by PCR, but a 150 bp fragment aligned with mammalian akirin 1 and a 300 bp fragment aligned with Amblyomma hebraeum were amplified by subolesin PCR. D. gallinae mortality after feeding was 35.1% higher (P=0.009) in the Subolesin group and 23% higher (not significant) in the Bm86 compared to the Control group. Thus it can be concluded that immunisation with recombinant subolesin can stimulate a protective response in laying hens against D. gallinae.

  4. Rhipicephalus (Boophilus microplus: expression and characterization of Bm86-CG in Pichia pastoris Rhipicephalus (Boophilus microplus: expressão e caracterização da Bm86-CG em Pichia pastoris

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    Rodrigo Casquero Cunha

    2011-06-01

    Full Text Available The cattle tick Rhipicephalus (Boophilus microplus is responsible for great economic losses. It is mainly controlled chemically, with limitations regarding development of resistance to the chemicals. Vaccines may help control this parasite, thereby reducing tick pesticide use. In this light, we performed subcloning of the gene of the protein Bm86-GC, the homologue protein that currently forms the basis of vaccines (GavacTM and TickGardPLUS that have been developed against cattle ticks. The subcloning was done in the pPIC9 expression vector, for transformation in the yeast Pichia pastoris. This protein was characterized by expression of the recombinant Mut+ strain, which expressed greater quantities of protein. The expressed protein (rBm86-CG was recognized in the Western-blot assay using anti-Gavac, anti-TickGard, anti-larval extract and anti-rBm86-CG polyclonal sera. The serum produced in cattle vaccinated with the antigen CG rBm86 presented high antibody titers and recognized the native protein. The rBm86-GC has potential relevance as an immunogen for vaccine formulation against cattle ticks.O carrapato-do-boi Rhipicephalus (Boophilus microplus é responsável por grandes perdas econômicas. Seu controle é principalmente químico e apresenta limitações quanto ao desenvolvimento de resistência aos princípios ativos. As vacinas podem auxiliar no controle deste parasita diminuindo as aplicações de carrapaticidas. Considerando isso, foi realizada a subclonagem do gene da proteína Bm86-CG, proteína homologa a que atualmente é a base das vacinas desenvolvidas (GavacTM e TickGardPLUS contra o carrapato-do-boi, no vetor de expressão pPIC9, para ser transformado em levedura, Pichia pastoris. Esta proteína foi caracterizada pela expressão da cepa recombinante Mut+ que expressou maior quantidade de proteína. A proteína expressa, rBm86-CG, foi reconhecida no ensaio de Western-blot pelos soros policlonais anti-Gavac, anti-TickGard, anti

  5. Bovine immunoprotection against Rhipicephalus (Boophilus microplus with recombinant Bm86-Campo Grande antigen Imunoproteção de bovinos contra Rhipicephalus (Boophilus microplus com antígeno recombinante Bm86-Campo Grande

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    Rodrigo Casquero Cunha

    2012-09-01

    Full Text Available The southern cattle fever tick, Rhipicephalus (Boophilus microplus, is no doubt the most economically important ectoparasite of cattle globally. The inappropriate use of chemical acaricides has driven the evolution of resistance in populations of R. (B. microplus. Anti-tick vaccines represent a technology that can be combined with acaricides in integrated control programs to mitigate the impact of R. (B. microplus. The recombinant form of Bm86 antigen from the Campo Grande (rBm86-CG strain of R. (B. microplus was produced using the Pichiapastoris expression system to test its ability to immunoprotect cattle against tick infestation. Secretion of rBm86-CG by P. pastoris through the bioprocess reported here simplified purification of the antigen. A specific humoral immune response was detected by ELISA in vaccinated cattle. Immunoblot results revealed that polyclonal antibodies from vaccinated cattle recognized a protein in larval extracts with a molecular weight corresponding to Bm86. The rBm86-CG antigen showed 31% efficacy against the Campo Grande strain of R. (B. microplus infesting vaccinated cattle. The rBm86-CG is an antigen that could be used in a polyvalent vaccine as part of an integrated program for the control of R. (B. microplus in the region that includes Mato Grosso do Sul.O carrapato Rhipicephalus (Boophilus microplus é, sem dúvidas, o ectoparasito economicamente mais importante para o gado a nível mundial. A utilização inadequada de acaricidas tem impulsionado a evolução da resistência em populações de R. (B. microplus. Vacinas contra o carrapato representam uma tecnologia que pode ser combinada com acaricidas em programas de controle integrado para diminuir o impacto de R. (B. microplus. A forma recombinante da Bm86 da cepa Campo Grande (rBm86-CG de R. (B. microplus foi produzido utilizando o sistema de expressão em Pichia pastoris para testar sua capacidade de imunoproteção ao gado contra a infestação de

  6. On Paradoxurus annulatus, Wagner

    NARCIS (Netherlands)

    Jentink, F.A.

    1886-01-01

    In »die Säugethiere Schreber’s, Supplementband II” we find on p. 353 the following description of a new Paradoxurus by J. E. Wagner: P. annulatus Wagn. Der geringelte Roller. P. supra. e nigro fulvoque mixtus, subtus e ferrugineo lutescens, cauda nigro-annulata, auriculis dense pilosis.

  7. The Rhipicephalus (Boophilus microplus Bm86 gene plays a critical role in the fitness of ticks fed on cattle during acute Babesia bovis infection

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    Knowles Donald P

    2010-11-01

    Full Text Available Abstract Background Rhipicephalus (Boophilus microplus is an economically important tick of cattle involved in the transmission of Babesia bovis, the etiological agent of bovine babesiosis. Commercial anti-tick vaccines based on the R. microplus Bm86 glycoprotein have shown some effect in controlling tick infestation; however their efficacy as a stand-alone solution for tick control has been questioned. Understanding the role of the Bm86 gene product in tick biology is critical to identifying additional methods to utilize Bm86 to reduce R. microplus infestation and babesia transmission. Additionally, the role played by Bm86 in R. microplus fitness during B. bovis infection is unknown. Results Here we describe in two independent experiments that RNA interference-mediated silencing of Bm86 decreased the fitness of R. microplus females fed on cattle during acute B. bovis infection. Notably, Bm86 silencing decreased the number and survival of engorged females, and decreased the weight of egg masses. However, gene silencing had no significant effect on the efficiency of transovarial transmission of B. bovis from surviving female ticks to their larval offspring. The results also show that Bm86 is expressed, in addition to gut cells, in larvae, nymphs, adult males and ovaries of partially engorged adult R. microplus females, and its expression was significantly down-regulated in ovaries of ticks fed on B. bovis-infected cattle. Conclusion The R. microplus Bm86 gene plays a critical role during tick feeding and after repletion during blood digestion in ticks fed on cattle during acute B. bovis infection. Therefore, the data indirectly support the rationale for using Bm86-based vaccines, perhaps in combination with acaricides, to control tick infestation particularly in B. bovis endemic areas.

  8. Labidiasteroside A, a Novel Saponin from the Antartic Starfish Labidiaster Annulatus

    OpenAIRE

    M. E. Díaz de Vivar; M. S. Maier; A. M. Seldes

    2000-01-01

    Purification of the ethanolic extract of the starfish L. annulatus led to the isolation of two sulfated glycosides and a pentahydroxylated steroid. One of the saponins contains a novel pentasaccharide chain attached to C-6 of the steroidal aglycone.

  9. Acaricidal effect of Cassia fistula Linn. leaf ethanolic extract against Rhipicephlaus (Boophilus) annulatus.

    Science.gov (United States)

    Sunil, A R; Amithamol, K K; Juliet, S; Nair, S N; Ajithkumar, K G; Soorya, V C; Divya, T M; Jyothymol, G; Ghosh, S; Ravindran, R

    2013-06-01

    The present study evaluates the acaricidal properties of crude ethanolic extract of Cassia fistula leaves for controlling Rhipicephalus (Boophilus) annulatus based on adult immersion test (AIT). The percentage of adult mortality, inhibition of fecundity and hatching of ova laid were studied at different concentrations of the extract ranging from 50 to 100 mg / ml. The results were compared using one-way ANOVA. The extract produced complete inhibition of hatching of eggs at concentrations above 80 mg / ml of the extract. Mortality of adult engorged female ticks and inhibition of fecundity were concentration dependent. The LC50 value of extract against R. (B.) annulatus was 97.1 mg / ml.

  10. Labidiasteroside A, a Novel Saponin from the Antartic Starfish Labidiaster Annulatus

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    M. E. Díaz de Vivar

    2000-03-01

    Full Text Available Purification of the ethanolic extract of the starfish L. annulatus led to the isolation of two sulfated glycosides and a pentahydroxylated steroid. One of the saponins contains a novel pentasaccharide chain attached to C-6 of the steroidal aglycone.

  11. First report of pyrethroid resistance in Rhipicephalus (Boophilus) annulatus larvae (Say, 1821) from Iran.

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    Ziapour, Seyyed Payman; Kheiri, Sadegh; Asgarian, Fatemeh; Fazeli-Dinan, Mahmoud; Yazdi, Fariborz; Mohammadpour, Reza Ali; Aarabi, Mohsen; Enayati, Ahmadali

    2016-04-01

    Rhipicephalus (Boophilus) annulatus is one of the most important hard ticks parasitizing cattle in northern Iran. The aim of this study was to evaluate pyrethroid resistance levels of this species from Nur County, northern Iran. The hard ticks were collected through a multistage cluster randomized sampling method from the study area and fully engorged female R. (B.) annulatus were reared in a controlled insectary until they produced larvae for bioassay. Seventeen populations of the hard ticks were bioassayed with cypermethrin and 12 populations with lambda-cyhalothrin using a modified larval packet test (LPT). Biochemical assays to measure the contents/activity of different enzyme groups including mixed function oxidases (MFOs), glutathione S-transferases (GSTs) and general esterases were performed. Population 75 showed a resistance ratio of 4.05 with cypermethrin when compared with the most susceptible field population 66 at the LC50 level. With lambda-cyhalothrin the resistance ratio based on LC50 was 3.67 when compared with the susceptible population. The results of biochemical assays demonstrated significantly elevated levels of GSTs and esterases in populations tested compared with the heterozygous susceptible filed population and a correlation coefficient of these enzymes was found in association to lambda-cyhalothrin resistance. Based on the results, pyrethroid acaricides may operationally fail to control R. (B.) annulatus in North of Iran. This study is the first document of pyrethroid resistance in R. (B.) annulatus populations from Iran.

  12. Molecular cloning and expression of a larval immunogenic protein from the cattle tick Boophilus annulatus.

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    Shahein, Yasser Ezzat

    2008-02-15

    A full-length cDNA of an immunogenic protein was cloned from a cDNA library of the local Egyptian cattle tick Boophilus annulatus. Antibodies raised against B. annulatus larval proteins were used to screen a cDNA expression library. A 936bp cloned fragment was sequenced and showed an open reading frame of 516bp encoding a protein of 171 amino acids. Comparison of the deduced amino acid sequence with protein data bank revealed that the sequence is related to a sequence isolated from the hard tick Haemaphysalis qinghaiensis (Hq05). Southern blot analysis of B. annulatus genomic DNA showed that the cloned cDNA hybridized to double bands per restriction digest, suggesting that the cloned cDNA is a double copy gene. Amino acid analysis of the cloned gene revealed the presence of two casein kinase II phosphorylation sites in the N-terminal domain suggesting that this molecule may be involved in the signal transduction or gene expression pathways. RT-PCR and northern blotting revealed the presence of two isoforms of the Ba05 gene in salivary glands and in the 3-day-old eggs. The cloned gene without the signal peptide, was expressed in Escherichia coli under T7 promotor of pET-30b vector, and purified under denaturation conditions. The purified protein appeared as a single band on 12% SDS-PAGE with a molecular weight around 22.8kDa including the histidine tag of the vector. Antibodies raised against the purified molecule were used to detect the B. annulatus homologue to the Hq05 gene in whole tick, larvae and gut protein extracts. Immunoblotting revealed the presence of this molecule Ba05 only in whole tick and larval protein extracts and not in the gut protein extract. Using the same antibodies, homologues to the Ba05 gene were detected in other tick species as Hyalomma dromedarii and Rhipicephalus sp. but not in Ornithodoros moubata.

  13. Laboratory evaluation of Mesocyclops annulatus (Wierzejski, 1892 (Copepoda: Cyclopidea as a predator of container-breeding mosquitoes in Argentina

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    María V Micieli

    2002-09-01

    Full Text Available In laboratory bioassays we tested the predatory capacity of the copepod Mesocyclops annulatus on Aedes aegypti and Culex pipiens larvae. A single adult female of M. annulatus caused 51.6% and 52.3% mortality of 50 first instar larvae of Ae. aegypti and Cx. pipiens respectively, in a 72 h test period. When alternative food was added to the containers, mortality rates declined to 16% and 10.3% for Ae. aegypti and Cx. pipiens respectively. When 50 first instar larvae of each of the two mosquito species tested were placed together with a single adult female of M. annulatus, mortality rates were 75.5% for Ae. aegypti larvae and 23.5% for Cx. pipiens larvae in a three day test period. Different density of adult females of M. annulatus ranged from 5 to 25 females produced mortality rates of Ae. aegypti first instar larvae from 50% to 100% respectively. When a single adult female of M. annulatus was exposed to an increasing number of first-instar Ae. aegypti larvae ranging from 10 to 100, 100% mortality was recorded from 1 to 25 larvae, then mortality declined to 30% with 100 larvae. The average larvae killed per 24 h period by a single copepod were 29.

  14. Detection of Humoral Immune Response of Calves to Boophilus annulatus by ELISA

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    N Alidadi

    2008-04-01

    Full Text Available Background: Ticks are blood feeder acarians that feed on variety of animals and introduce a wide variety of molecules to their host immune system and some of them may stimulate host immune system to produce antibodies. This study was carried out to detect humoral immune responses following Boophilus annulatus infestation.Methods: Seven cattle were each experimentally infested with 10000 B. annulatus larvae and their humoral immune re­sponse to salivary gland; ovary and larval extracts were determined by ELISA. Measurements of serum antibodies level were recorded weekly, in a period of nine weeks post infestation. Results: An increase of the antibody level was observed in all animals at one week post infestation and reached in a peak at week ninth, then decreased in week 9.Conclusion: Sera of infected animals showed approximately similar reactions to all of tissue extracts that might be due to the presence of common proteins in tick tissues and could be a candidate for immunization.

  15. Histology of the kidney and urinary bladder of Siphonops annulatus (Amphibia-Gymnophiona).

    Science.gov (United States)

    Carvalho, E T; Junqueira, L C

    1999-03-01

    The histology of the kidney and urinary bladder of Siphonops annulatus was studied by light microscopy in semithin sections of tissue embedded in hydrophilic resin. The kidney's nephron comprises the renal corpuscle, neck segment, proximal tubule, intermediate segment, distal tubule and collecting tubule. Nephrostomes are present. This structure, the neck segment, and intermediate tubules present long cilia, and probably play important roles in the propulsion of the peritoneal fluid and glomerular filtrate. The proximal tubule cells possess loosely packed microvilli and contain abundant polymorphic granules and vesicles that assume the aspect of lysosomes in different stages of intracellular digestion. The distal tubules are characterized by large, vertically disposed mitochondria assuming the aspect of ions transporting cells. The urinary bladder is lined with a transitional epithelium, whose aspect varies according to the quantity of urine.

  16. Histology of the trachea and lung of Siphonops annulatus (Amphibia, Gymnophiona).

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    Kuehne, B; Junqueira, L C

    2000-02-01

    The structure of the trachea and lung of Siphonops annulatus was studied in ten specimens of routinely fed animals. The trachea is constituted mainly by incomplete cartilage rings lined by a respiratory epithelium (ciliated and mucous cells) with variable morphology according to the region observed. A rich vascularization of this organ suggests its participation in blood-air gas exchange. The right lung in this species is developed and the left one is atrophied. This organ is constituted mainly by longitudinal septa formed by connective tissue, smooth muscle cells and blood capillaries. These structures are covered by pneumocytes of one type only, which present cytoplasmic particles that have been related with surfactant activity described in the lung of Gymnophiona.

  17. Molecular cloning, expression and characterization of a functional GSTmu class from the cattle tick Boophilus annulatus.

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    Shahein, Yasser Ezzat; El Sayed El-Hakim, Amr; Abouelella, Amira Mohamed Kamal; Hamed, Ragaa Reda; Allam, Shaimaa Abdul-Moez; Farid, Nevin Mahmoud

    2008-03-25

    A full-length cDNA of a glutathione S-transferase (GST) was cloned from a cDNA library of the local Egyptian cattle tick Boophilus annulatus. The 672 bp cloned fragment was sequenced and showed an open reading frame encoding a protein of 223 amino acids. Comparison of the deduced amino acid sequence with GSTs from other species revealed that the sequence is closely related to the mammalian mu-class GST. The cloned gene was expressed in E. coli under T7 promotor of pET-30b vector, and purified under native conditions. The purified enzyme appeared as a single band on 12% SDS-PAGE and has a molecular weight of 30.8 kDa including the histidine tag of the vector. The purified enzyme was assayed upon the chromogenic substrate 1-chloro-2,4-dinitrobenzene (CDNB) and the recombinant enzyme showed high level of activity even in the presence of the beta-galactosidase region on its 5' end and showed maximum activity at pH 7.5. The Km values for CDNB and GSH were 0.57 and 0.79 mM, respectively. The over expressed rBaGST showed high activity toward CDNB (121 units/mg protein) and less toward DCNB (29.3 units/mg protein). rBaGST exhibited peroxidatic activity on cumene hydroperoxide sharing this property with GSTs belonging to the GST alpha class. I50 values for cibacron blue and bromosulfophthalein were 0.22 and 8.45 microM, respectively, sharing this property with the mammalian GSTmu class. Immunoblotting revealed the presence of the GST molecule in B. annulatus protein extracts; whole tick, larvae, gut, salivary gland and ovary. Homologues to the GSTmu were also detected in other tick species as Hyalomma dromedarii and Rhipicephalus sp. while in Ornithodoros moubata, GSTmu homologue could not be detected.

  18. Acaricidal effect of Pelargonium roseum and Eucalyptus globulus essential oils against adult stage of Rhipicephalus (Boophilus) annulatus in vitro.

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    Pirali-Kheirabadi, Khodadad; Razzaghi-Abyaneh, Mehdi; Halajian, Ali

    2009-06-10

    In a laboratory trial, in west-central Iran, the acaricidal effects of the essential oils (EOs) prepared from two medicinal plants, i.e. Pelargonium roseum and Eucalyptus globulus on the adult stage of Rhipicephalus (Boophilus) annulatus were evaluated. For this purpose, the engorged females of R. (B) annulatus were exposed to two-fold serial dilutions of oils (0.31-5.0%) using a "dipping method" in vitro. The engorged ticks were immersed in different plant dilutions (eight per dilution) for 1min then each replicate was incubated in separate petri dishes at 26 degrees C and 80% relative humidity. The mortality rate for adult ticks exposed to different dilutions of P. roseum and E. globulus EO's showed a dose-dependent decrease. It was however significant only for the 2.5% and 5.0% dilutions of P. roseum EO, when compared to the non-treated control (P<0.05). The mass of produced eggs in adult female ticks exposed to both P. roseum and E. globulus EOs had decreased dose-dependently. It was significant for only 2.5% and 5.0% dilutions of P. roseum EO, comparing the non-treated control (P<0.05). The highest decrease in egg laying was reported for ticks treated with 5% dilutions of P. roseum (87.5%) and E. globosus (25%) (P<0.05). This is the first report that details the acaricidal activity of EO's obtained from P. roseum and E. globosus against R. (B) annulatus. The results show that both plants, particularly P. Roseum can be considered as potential candidates for biocontrol of R. (B) annulatus in the field.

  19. Capillariid nematodes in Brazilian turkeys, Meleagris gallopavo (Galliformes, Phasianidae: pathology induced by Baruscapillaria obsignata and Eucoleus annulatus (Trichinelloidea, Capillariidae

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    Roberto Magalhães Pinto

    2008-05-01

    Full Text Available The pathology induced in turkeys (Meleagris gallopavo by two capillariid nematodes, Baruscapillaria obsignata and Eucoleus annulatus is described together with data on prevalences, mean infection and range of worm burdens. B. obsignata occurred with a prevalence of 72.5% in the 40 examined hosts in a range of 2-461 nematodes and a mean intensity of 68.6, whereas E. annulatus was present in 2.5% of the animals, with a total amount of five recovered parasites. Gross lesions were not observed in the parasitized birds. Lesions due to B. obsignata mainly consisted of the thickening of intestinal villi with a mild mixed inflammatory infiltrate with the presence of mononuclear cells and heterophils. The lesions induced by E. annulatus were represented by foci of inflammatory infiltrate with heterophils in the crop epithelium and esophagus of a single infected female. These are the first pathological findings related to the presence of capillariid worms in turkeys to be reported in Brazil so far. Capillaria anatis, although present, was not pathogenic to the investigated turkeys.

  20. Capillariid nematodes in Brazilian turkeys, Meleagris gallopavo (Galliformes, Phasianidae): pathology induced by Baruscapillaria obsignata and Eucoleus annulatus (Trichinelloidea, Capillariidae).

    Science.gov (United States)

    Pinto, Roberto Magalhães; Brener, Beatriz; Tortelly, Rogério; Menezes, Rodrigo Caldas; Muniz-Pereira, Luís Cláudio

    2008-05-01

    The pathology induced in turkeys (Meleagris gallopavo) by two capillariid nematodes, Baruscapillaria obsignata and Eucoleus annulatus is described together with data on prevalences, mean infection and range of worm burdens. B. obsignata occurred with a prevalence of 72.5% in the 40 examined hosts in a range of 2-461 nematodes and a mean intensity of 68.6, whereas E. annulatus was present in 2.5% of the animals, with a total amount of five recovered parasites. Gross lesions were not observed in the parasitized birds. Lesions due to B. obsignata mainly consisted of the thickening of intestinal villi with a mild mixed inflammatory infiltrate with the presence of mononuclear cells and heterophils. The lesions induced by E. annulatus were represented by foci of inflammatory infiltrate with heterophils in the crop epithelium and esophagus of a single infected female. These are the first pathological findings related to the presence of capillariid worms in turkeys to be reported in Brazil so far. Capillaria anatis, although present, was not pathogenic to the investigated turkeys.

  1. Identification of Tropomyosin and Its Immunological Properties from Larvae of Cattle Tick, Boophilus Annulatus

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    S Nabian

    2013-06-01

    Full Text Available Background: Boophilus annulatus is an obligate blood feeder tick that can cause great losses in animals due to anemia and its ability to injure its host skin directly. The aim of this study was identification of cattle humoral immune response to some tick proteins during experimental infestation.Methods: Immune sera against tick were collected from experimentally infested cattle with ticks. One and two-dimensional electrophoresis and Western blotting methods were used for the detection of immunogenic proteins in larval tick extract and eight of these proteins were identified by MALDI-TOF and MALDI-TOF-TOF mass spectrometry.Results: In non-reducing one-dimensional SDS- PAGE, some bounds between 12 to more than 250-kDa appeared. In two-dimensional SDS-PAGE, numerous spot appeared and the identified immuno­genic proteins by parallel immunoblotting weighted between 14 and 97 kDa. Amino acid sequences of protein spot with 37-kDa molecular weight had identity to tropomyosin based on Mas­cot search in NCBI.Conclusion: Anti tropomyosin antibodies can be induced in experimentally infested hosts with ticks and it seems that tropomyosin can be useful for the development of anti tick vaccines.

  2. Efficacy of deltamethrin, diazinon, and ivermectin on Boophilus annulatus ticks (in vitro and in vivo study).

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    El-Bahy, Nasr M; Bazh, Eman K; Shaheen, Hazem M

    2015-01-01

    Tick infection is considered a cause of major concern as it is a vector for some disease transmission. The use of chemicals to control tick infection is increasing in farm systems. The efficacy of three chemicals was studied on the tick Boophilus annulatus. In vitro and in vivo studies were done. The active ticks were collected from naturally infected cattle for in vitro study. They were incubated with the three chemicals which are commercially used. An in vitro study recorded that the highest effect of the three chemicals was 100% at 3 h postexposure (p.e.) time for deltamethrin and 6 h for diazinon and ivermectin on the adult ticks. Egg batches were less affected. In vivo results showed more plain efficacy. The efficacy of deltamethrin was increased gradually until complete cessation of ticks showed within 3rd day posttreatment (d.p.t.), 100% efficacy. But the tick population begins to reappear gradually within 7 d.p.t., while diazinon showed 100% efficacy at 7 d.p.t. and the ticks reappear again within 14 d.p.t. The most preferred results were obtained with ivermectin which showed 100% efficacy at 7 d.p.t., and the cattle was still free from infection until 21 d.p.t. only. Ticks begin to reappear within 28 d.p.t. in slight few numbers. This concluded that the powerful and safe chemical which is commercially used was ivermectin. Even so, it is used also as an anthelmintic drug.

  3. Rhipicephalus annulatus (Acari: Ixodidae Control by Nigella sativa, Thyme and Spinosad Preparations

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    Shawky Mohamed Aboelhadid

    2016-01-01

    Full Text Available Background: Several compounds obtained from plants have potential insecticidal, growth deterrent or repellent characteristics. The control of hard ticks by non-chemical substances was targeted in this study.Methods: The effect of 36 materials on in-vitro ticks was studied, including 2 absolute controls (water only or ab­solute ethyl alcohol only, 6 conventionally used spinosad preparations (aqueous solutions, 12 Nigella sativa (N. sativa preparations (aqueous and alcoholic solutions, and 12 Thyme preparations (aqueous and alcoholic solutions. The engorged ticks were tested in-vitro for mortality and oviposition ability using the studied materials.Results: The final mortality after 48 hours of application in N. sativa aqueous preparations began from 10.0% con­centration, 1.0% to 100% by concentration preparations ≥10%. In addition, N. sativa alcoholic preparations began from 50.0% concentration, 2 % to 100% by concentration ≥5%. Meanwhile, Thyme aqueous and alcoholic prepa­rations began from 70.0% concentration, 5% to 90% by concentration 10–20%. Additionally, spinosad aqueous preparations and both of control preparations (Water and Alcohol resulted in no mortality. All differences were sta­tistically significant. The oviposition was stopped in N. sativa (aqueous ≥10% and alcoholic ≥5% and in spinosad (aqueous≥25%. The aqoues dilution of the used matters killed B. annulatus larvae beginning from the concentration 5%.Conclusion: Nigella sativa alcohol 20% was the best of studied preparations being the lowest concentration (20% that could achieve the highest lethal (100% effect in shortest time (12 hours. Moreover, Thyme oil and spinosad could not kill 100% of adult but did on larvae.

  4. Seasonality of parasitic copepods on bullseye puffer, Sphoeroides annulatus (Pisces: Tetraodontidae), from the northwestern coast of Mexico.

    Science.gov (United States)

    Morales-Serna, Francisco Neptalí; Rubio-Godoy, Miguel; Gómez, Samuel

    2011-08-01

    Seasonal occurrence of parasitic copepods in wild bullseye puffer, Sphoeroides annulatus (Pisces: Tetraodontidae), was analyzed in conjunction with variation of biotic and abiotic factors. Eleven samples were taken between February 2007 and February 2008 in Santa María La Reforma lagoon (northwestern coast of México). In total, 337 fish was examined; 5 parasitic copepod species were observed, including Acantholochus zairae , Caligus serratus , Lepeophtheirus simplex , Pseudochondracanthus diceraus , and Parabrachiella sp. The most common species were L. simplex , P. diceraus, and C. serratus (overall prevalence, 59, 53, and 35%, respectively), which significantly varied in prevalence and mean intensity between sampling months. A seasonal pattern was only observed for L. simplex, with higher infection levels in the warmest month than in the coldest month. Statistical analyses indicated that the intensity of L. simplex was positively correlated with water temperature. There were no significant differences in prevalence and intensity of infection among female and male hosts. At the component community level, species richness ranged between 4 and 5 during most of the study period, and no seasonality was observed in the number of individuals, Shannon diversity index, evenness index, or the Berger-Parker dominance index. At the infracommunity level, 4 descriptors used (mean species richness, mean number of individuals, mean Brillouin's diversity index, and mean Berger-Parker index) varied significantly between sampling months, but no seasonality was observed, except for a slight increase in the number of individuals during the warmest month. A significant positive association was detected between number of individuals and water temperature and between host size and both species richness and number of individuals. This is the first account of the ecology of these 5 parasitic copepods. Although no significant association was detected between fish condition factor and the

  5. Effect of surfactants on Ra-sHSPI - A small heat shock protein from the cattle tick Rhipicephalus annulatus

    Science.gov (United States)

    Siddiqi, Mohammad Khursheed; Shahein, Yasser E.; Hussein, Nahla; Khan, Rizwan H.

    2016-09-01

    Electrostatic interaction plays an important role in protein aggregation phenomenon. In this study, we have checked the effect of anionic - Sodium Dodecyl Sulfate (SDS) and cationic-Cetyltrimethyl Ammonium Bromide (CTAB) surfactant on aggregation behavior of Ra-sHSPI, a small heat shock protein purified from Rhipicephalus annulatus tick. To monitor the effect of these surfactants, we have employed several spectroscopic methods such as Rayleigh light scattering measurements, ANS (8-Anilinonaphthalene-1-sulfonic acid) fluorescence measurements, ThT (Thioflavin T) binding assays, Far-UV CD (Circular Dichroism) and dynamic light scattering measurements. In the presence of anionic surfactant-SDS, Ra-sHSPI forms amyloid fibrils, in contrast, no amyloid formation was observed in presence of cationic surfactant at low pH. Enhancement of ANS fluorescence intensity confirms the exposition of more hydrophobic patches during aggregation. ThT binding assay confirms the amyloid fibrillar nature of the SDS induced Ra-sHSPI aggregates and supported by PASTA 2.0 (prediction of amyloid structural aggregation) software. This study demonstrates the crucial role of charge during amyloid fibril formation at low pH in Ra-sHSPI.

  6. Effect of UV radiation on the genetic inactivation of sperm of the bullseye puffer Sphoeroides annulatus (Jenyns, 1842); Efecto de la radiacion UV en la inactivacion genetica del esperma de botete diana Sphoeroides annulatus (Jenyns, 1842)

    Energy Technology Data Exchange (ETDEWEB)

    Arias-Rodriguez, Lenin; Rodriguez-Ibarra, Luz Estela; Del Valle-Pignataro, Gabriela [Laboratorio de Genetica, Centro de Investigacion en Alimentacion y Desarrollo, A. C., Sinaloa (Mexico)

    2004-09-15

    Genetic (DNA) inactivation of fish sperm with ultraviolet irradiation is generally accompanied by a paradoxical effect on survival rates (Hertwig effect). In the present study, sperm samples from ten males bullseye puffer fish (Sphoeroides annulatus) were diluted 1:50 using Cortland's extender solution and used to test the effect of nine ultraviolet doses (0.2-1.0 J cm{sup -}2 ) on motility time in seconds, motility index, and embryo survival rate after fertilizing eggs from five bullseye puffer females. Motility time of sperm irradiated with 0.2-0.9 J cm{sup -}2 were not statistically different from the controls, but sperm irradiated with a dosage of 1.0 J cm{sup -}2 dosage had significant lower motility time. Motility indices (MI) allowed for the statistical differentiation of four groups in relation to their response to different radiation doses: the first had high MI, and included the controls and 0.2-0.3 J cm{sup -}2 treatments; the second had lower MI and included the 0.4-0.7 J cm{sup -}2 treatments; the third showed recovery of MI and included the 0.8-0.9 J cm{sup -}2 treatments; and the fourth showed the lowest MI with the 1.0 J cm{sup -}2 treatment. Embryo survival was highest for the controls and 0.2 J cm{sup -}2 treatment, decreasing in the 0.3-0.4 J cm{sup -}2 treatments, increasing again in the 0.5-0.8 J cm{sup -}2 treatments, until reaching lowest survival in the 0.9-1.0 J cm{sup -}2 treatments. These results indicate that the best ultraviolet dosage to achieve genetic inactivation of sperm of this species is close to 0.7 J cm{sup -}2, a dosage in which fish fry showed typical haploid syndrome characteristics. [Spanish] La inactivacion genetica (ADN) del esperma de peces se realiza mediante luz ultravioleta que, en irradiaciones crecientes, genera efectos paradojicos (efecto Hertwig) en los porcentajes de supervivencia. En este trabajo se diluyeron muestras de semen provenientes de diez machos de botete diana (Sphoeroides annulatus) en solucion

  7. Standardized benchmarking in the quest for orthologs

    DEFF Research Database (Denmark)

    Altenhoff, Adrian M; Boeckmann, Brigitte; Capella-Gutierrez, Salvador;

    2016-01-01

    -recall trade-offs. As a result, it is difficult to assess the performance of orthology inference methods. Here, we present a community effort to establish standards and an automated web-based service to facilitate orthology benchmarking. Using this service, we characterize 15 well-established inference methods...... and resources on a battery of 20 different benchmarks. Standardized benchmarking provides a way for users to identify the most effective methods for the problem at hand, sets a minimum requirement for new tools and resources, and guides the development of more accurate orthology inference methods....

  8. Assessment of orthologous splicing isoforms in human and mouse orthologous genes

    Directory of Open Access Journals (Sweden)

    Horner David S

    2010-10-01

    Full Text Available Abstract Background Recent discoveries have highlighted the fact that alternative splicing and alternative transcripts are the rule, rather than the exception, in metazoan genes. Since multiple transcript and protein variants expressed by the same gene are, by definition, structurally distinct and need not to be functionally equivalent, the concept of gene orthology should be extended to the transcript level in order to describe evolutionary relationships between structurally similar transcript variants. In other words, the identification of true orthology relationships between gene products now should progress beyond primary sequence and "splicing orthology", consisting in ancestrally shared exon-intron structures, is required to define orthologous isoforms at transcript level. Results As a starting step in this direction, in this work we performed a large scale human- mouse gene comparison with a twofold goal: first, to assess if and to which extent traditional gene annotations such as RefSeq capture genuine splicing orthology; second, to provide a more detailed annotation and quantification of true human-mouse orthologous transcripts defined as transcripts of orthologous genes exhibiting the same splicing patterns. Conclusions We observed an identical exon/intron structure for 32% of human and mouse orthologous genes. This figure increases to 87% using less stringent criteria for gene structure similarity, thus implying that for about 13% of the human RefSeq annotated genes (and about 25% of the corresponding transcripts we could not identify any mouse transcript showing sufficient similarity to be confidently assigned as a splicing ortholog. Our data suggest that current gene and transcript data may still be rather incomplete - with several splicing variants still unknown. The observation that alternative splicing produces large numbers of alternative transcripts and proteins, some of them conserved across species and others truly species

  9. Identifying single copy orthologs in Metazoa.

    Directory of Open Access Journals (Sweden)

    Christopher J Creevey

    2011-12-01

    Full Text Available The identification of single copy (1-to-1 orthologs in any group of organisms is important for functional classification and phylogenetic studies. The Metazoa are no exception, but only recently has there been a wide-enough distribution of taxa with sufficiently high quality sequenced genomes to gain confidence in the wide-spread single copy status of a gene.Here, we present a phylogenetic approach for identifying overlooked single copy orthologs from multigene families and apply it to the Metazoa. Using 18 sequenced metazoan genomes of high quality we identified a robust set of 1,126 orthologous groups that have been retained in single copy since the last common ancestor of Metazoa. We found that the use of the phylogenetic procedure increased the number of single copy orthologs found by over a third more than standard taxon-count approaches. The orthologs represented a wide range of functional categories, expression profiles and levels of divergence.To demonstrate the value of our set of single copy orthologs, we used them to assess the completeness of 24 currently published metazoan genomes and 62 EST datasets. We found that the annotated genes in published genomes vary in coverage from 79% (Ciona intestinalis to 99.8% (human with an average of 92%, suggesting a value for the underlying error rate in genome annotation, and a strategy for identifying single copy orthologs in larger datasets. In contrast, the vast majority of EST datasets with no corresponding genome sequence available are largely under-sampled and probably do not accurately represent the actual genomic complement of the organisms from which they are derived.

  10. Assisted transcriptome reconstruction and splicing orthology

    Directory of Open Access Journals (Sweden)

    Samuel Blanquart

    2016-11-01

    Full Text Available Abstract Background Transcriptome reconstruction, defined as the identification of all protein isoforms that may be expressed by a gene, is a notably difficult computational task. With real data, the best methods based on RNA-seq data identify barely 21 % of the expressed transcripts. While waiting for algorithms and sequencing techniques to improve — as has been strongly suggested in the literature — it is important to evaluate assisted transcriptome prediction; this is the question of how alternative transcription in one species performs as a predictor of protein isoforms in another relatively close species. Most evidence-based gene predictors use transcripts from other species to annotate a genome, but the predictive power of procedures that use exclusively transcripts from external species has never been quantified. The cornerstone of such an evaluation is the correct identification of pairs of transcripts with the same splicing patterns, called splicing orthologs. Results We propose a rigorous procedural definition of splicing orthologs, based on the identification of all ortholog pairs of splicing sites in the nucleotide sequences, and alignments at the protein level. Using our definition, we compared 24 382 human transcripts and 17 909 mouse transcripts from the highly curated CCDS database, and identified 11 122 splicing orthologs. In prediction mode, we show that human transcripts can be used to infer over 62 % of mouse protein isoforms. When restricting the predictions to transcripts known eight years ago, the percentage grows to 74 %. Using CCDS timestamped releases, we also analyze the evolution of the number of splicing orthologs over the last decade. Conclusions Alternative splicing is now recognized to play a major role in the protein diversity of eukaryotic organisms, but definitions of spliced isoform orthologs are still approximate. Here we propose a definition adapted to the subtle variations of conserved alternative

  11. Population structure and reproductive aspects of puffer fish Sphoeroides annulatus (Jenyns, 1842 (Osteichthyes: Tetraodontidae, landed in Teacapán, Sinaloa, Mexico

    Directory of Open Access Journals (Sweden)

    María Candelaria Valdez-Pineda

    2014-03-01

    Full Text Available The puffer fish Sphoeroides annulatus is an important target species for the artisanal fishing fleets of NW Mexico. To obtain information on population structure of the local stock, we determined the total length and total weight (TL and TW ranges, sex ratio and reproductive stages of 745 specimens of this species, landed from May 2010 to April 2011 in Teacapán, Sinaloa, NW Mexico. TL ranged from 15 to 40 cm and TW from 100 to 1600 g. There were no differences between mean TL (27.41 ± 4.14 cm and TW (534.5 ± 226.0 g of males and females respectively. Sex ratio was not significantly different (χ2 = 0.03, P > 0.05 from 1F:1M. The length-weight relationship for both sexes was TW = 0.044TL2.815, R² = 0.895. The value of the slope b was significantly lower than 3 (P < 0.05, and indicated negative allometric growth. The distribution of maturity stages indicated one main reproductive period from June to September and one less intense, from November to December for females, and in December for males. Size at first maturity (L50% of females was 26.52 cm and that of males was 27.41 cm.

  12. HieranoiDB: a database of orthologs inferred by Hieranoid

    Science.gov (United States)

    Kaduk, Mateusz; Riegler, Christian; Lemp, Oliver; Sonnhammer, Erik L. L.

    2017-01-01

    HieranoiDB (http://hieranoiDB.sbc.su.se) is a freely available on-line database for hierarchical groups of orthologs inferred by the Hieranoid algorithm. It infers orthologs at each node in a species guide tree with the InParanoid algorithm as it progresses from the leaves to the root. Here we present a database HieranoiDB with a web interface that makes it easy to search and visualize the output of Hieranoid, and to download it in various formats. Searching can be performed using protein description, identifier or sequence. In this first version, orthologs are available for the 66 Quest for Orthologs reference proteomes. The ortholog trees are shown graphically and interactively with marked speciation and duplication nodes that show the inferred evolutionary scenario, and allow for correct extraction of predicted orthologs from the Hieranoid trees. PMID:27742821

  13. Effects of season, sex and body size on the feeding ecology of turtle-headed sea snakes ( Emydocephalus annulatus) on IndoPacific inshore coral reefs

    Science.gov (United States)

    Goiran, C.; Dubey, S.; Shine, R.

    2013-06-01

    In terrestrial snakes, many cases of intraspecific shifts in dietary habits as a function of predator sex and body size are driven by gape limitation and hence are most common in species that feed on relatively large prey and exhibit a wide body-size range. Our data on sea snakes reveal an alternative mechanism for intraspecific niche partitioning, based on sex-specific seasonal anorexia induced by reproductive activities. Turtle-headed sea snakes ( Emydocephalus annulatus) on coral reefs in the New Caledonian Lagoon feed entirely on the eggs of demersal-spawning fishes. DNA sequence data (cytochrome b gene) on eggs that we palpated from stomachs of 37 snakes showed that despite this ontogenetic stage specialization, the prey comes from a taxonomically diverse array of species including damselfish (41 % of samples, at least 5 species), blennies (41 %, 4 species) and gobies (19 %, 5 species). The composition of snake diets shifted seasonally (with damselfish dominating in winter but not summer), presumably reflecting seasonality of fish reproduction. That seasonal shift affects male and female snakes differently, because reproduction is incompatible with foraging. Adult female sea snakes ceased feeding when they became heavily distended with developing embryos in late summer, and males ceased feeding while they were mate searching in winter. The sex divergence in foraging habits may be amplified by sexual size dimorphism; females grow larger than males, and larger snakes (of both sexes) feed more on damselfish (which often lay their eggs in exposed sites) than on blennies and gobies (whose eggs are hidden within narrow crevices). Specific features of reproductive biology of coral reef fish (seasonality and nest type) have generated intraspecific niche partitioning in these sea snakes, by mechanisms different from those that apply to terrestrial snakes.

  14. Genetic polymorphism of Babesia bovis merozoite surface antigens-2 (MSA-2) isolates from bovine blood and Rhipicephalus annulatus ticks in Israel.

    Science.gov (United States)

    Molad, T; Fleiderovitz, L; Leibovich, B; Wolkomirsky, R; Erster, O; Roth, A; Mazuz, M L; Markovics, A; Shkap, V

    2014-09-15

    This study demonstrated the genetic diversity among MSA-2c, MSA-2a1 and MSA-2b proteins of Babesia bovis isolates obtained from bovine blood and Rhipicephalus annulatus tick samples. The least identities that were observed among the deduced amino acid sequences of MSA-2c, MSA-2a1 and MSA-2b were 55, 63, and 71%, respectively. During the study four B. bovis calves, aged about 1 month, were found to be infected with virulent field strains and developed babesiosis. Probably, the calves had received insufficient antibodies, or the antibodies raised against the vaccine strain did not cross-protect against virulent field isolates. The complete msa-2 locus from the Israeli B. bovis vaccine strain and two field isolates were characterized. Similarly to the Australian strains and isolates, the msa-2 loci of the examined Israeli strain and isolates had only two msa-2 genes - msa-2c and msa-2a/b - located between msa-2c and orfB. Several of the examined samples, contained different MSA-2 genotypes concurrently. No obvious geographical relationships among isolates from various regions of Israel were established. Moreover, in the phylogenetic analyses, the Israeli deduced MSA-2 amino acid sequences of the three examined genes were clustered together with sequences derived from other countries, proving that the msa-2 gene sequences of B. bovis shared the same genetic characters worldwide. The present study clearly showed that the MSA-2 proteins of B. bovis isolates from Israel were genetically distinct from the vaccine strains. Thus, further research will be needed in order to understand the genetic diversity mechanisms of B. bovis, and the immunological responses of the infected animals.

  15. Multiple nuclear ortholog next generation sequencing phylogeny of Daucus

    Science.gov (United States)

    Next generation sequencing is helping to solve the data insufficiency problem hindering well-resolved dominant gene phylogenies. We used Roche 454 technology to obtain DNA sequences from 93 nuclear orthologs, dispersed throughout all linkage groups of Daucus. Of these 93 orthologs, ten were designed...

  16. Benchmarking ortholog identification methods using functional genomics data.

    NARCIS (Netherlands)

    Hulsen, T.; Huynen, M.A.; Vlieg, J. de; Groenen, P.M.

    2006-01-01

    BACKGROUND: The transfer of functional annotations from model organism proteins to human proteins is one of the main applications of comparative genomics. Various methods are used to analyze cross-species orthologous relationships according to an operational definition of orthology. Often the defini

  17. WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning.

    Science.gov (United States)

    Sutphin, George L; Mahoney, J Matthew; Sheppard, Keith; Walton, David O; Korstanje, Ron

    2016-11-01

    The rapid advancement of technology in genomics and targeted genetic manipulation has made comparative biology an increasingly prominent strategy to model human disease processes. Predicting orthology relationships between species is a vital component of comparative biology. Dozens of strategies for predicting orthologs have been developed using combinations of gene and protein sequence, phylogenetic history, and functional interaction with progressively increasing accuracy. A relatively new class of orthology prediction strategies combines aspects of multiple methods into meta-tools, resulting in improved prediction performance. Here we present WORMHOLE, a novel ortholog prediction meta-tool that applies machine learning to integrate 17 distinct ortholog prediction algorithms to identify novel least diverged orthologs (LDOs) between 6 eukaryotic species-humans, mice, zebrafish, fruit flies, nematodes, and budding yeast. Machine learning allows WORMHOLE to intelligently incorporate predictions from a wide-spectrum of strategies in order to form aggregate predictions of LDOs with high confidence. In this study we demonstrate the performance of WORMHOLE across each combination of query and target species. We show that WORMHOLE is particularly adept at improving LDO prediction performance between distantly related species, expanding the pool of LDOs while maintaining low evolutionary distance and a high level of functional relatedness between genes in LDO pairs. We present extensive validation, including cross-validated prediction of PANTHER LDOs and evaluation of evolutionary divergence and functional similarity, and discuss future applications of machine learning in ortholog prediction. A WORMHOLE web tool has been developed and is available at http://wormhole.jax.org/.

  18. Defining orthologs and pangenome size metrics.

    Science.gov (United States)

    Bosi, Emanuele; Fani, Renato; Fondi, Marco

    2015-01-01

    Since the advent of ultra-massive sequencing techniques, the consequent drop-off in both price and time required made feasible the sequencing of increasingly more genomes from microbes belonging to the same taxonomic unit. Eventually, this led to the concept of pangenome, that is, the entire set of genes present in a group of representatives of the same genus/species, which, in turn, can be divided into core genome, defined as the set of those genes present in all the genomes under study, and a dispensable genome, the set of genes possessed only by one or a subset of organism. When analyzing a pangenome, an interesting point is to measure its size, thus estimating the gene repertoire of a given taxonomic group. This is usually performed counting the novel genes added to the overall pangenome when new genomes are sequenced and annotated. A pangenome can be also classified as open or close: in an open pangenome its size increases indefinitely when adding new genomes; thus sequencing additional strains will likely yield novel genes. Conversely, in a close pangenome, adding new genomes will not lead to the discovery of new coding capabilities. A central point in pangenomics is the definition of homology relationships between genes belonging to different genomes. This may turn into the search of those genes with similar sequences between different organisms (and including both paralogous and orthologous genes). In this chapter, methods for finding groups of orthologs between genomes and for estimating the pangenome size are discussed. Also, working codes to address these tasks are provided.

  19. Berkeley PHOG: PhyloFacts orthology group prediction web server.

    Science.gov (United States)

    Datta, Ruchira S; Meacham, Christopher; Samad, Bushra; Neyer, Christoph; Sjölander, Kimmen

    2009-07-01

    Ortholog detection is essential in functional annotation of genomes, with applications to phylogenetic tree construction, prediction of protein-protein interaction and other bioinformatics tasks. We present here the PHOG web server employing a novel algorithm to identify orthologs based on phylogenetic analysis. Results on a benchmark dataset from the TreeFam-A manually curated orthology database show that PHOG provides a combination of high recall and precision competitive with both InParanoid and OrthoMCL, and allows users to target different taxonomic distances and precision levels through the use of tree-distance thresholds. For instance, OrthoMCL-DB achieved 76% recall and 66% precision on this dataset; at a slightly higher precision (68%) PHOG achieves 10% higher recall (86%). InParanoid achieved 87% recall at 24% precision on this dataset, while a PHOG variant designed for high recall achieves 88% recall at 61% precision, increasing precision by 37% over InParanoid. PHOG is based on pre-computed trees in the PhyloFacts resource, and contains over 366 K orthology groups with a minimum of three species. Predicted orthologs are linked to GO annotations, pathway information and biological literature. The PHOG web server is available at http://phylofacts.berkeley.edu/orthologs/.

  20. OMA 2011: orthology inference among 1000 complete genomes.

    Science.gov (United States)

    Altenhoff, Adrian M; Schneider, Adrian; Gonnet, Gaston H; Dessimoz, Christophe

    2011-01-01

    OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genomes. Initiated in 2004, the project is at its 11th release. It now includes 1000 genomes, making it one of the largest resources of its kind. Here, we describe recent developments in terms of species covered; the algorithmic pipeline--in particular regarding the treatment of alternative splicing, and new features of the web (OMA Browser) and programming interface (SOAP API). In the second part, we review the various representations provided by OMA and their typical applications. The database is publicly accessible at http://omabrowser.org.

  1. Ortholog identification in genera of high genetic diversity and evolution

    DEFF Research Database (Denmark)

    Rasmussen, Jane Lind Nybo; Vesth, Tammi Camilla; Frisvad, Jens Christian;

    In the era of high-throughput sequencing, comparative genomics is vastly used in the discovery of genetic diversity between species, but also in defining the core and pan genome of single species to whole genera. Current comparative approaches are implementing ortholog identification to establish...... genome annotations, gene or protein evolutions or defining functional features in individual species and groups....

  2. Toward community standards in the quest for orthologs.

    NARCIS (Netherlands)

    Dessimoz, C.; Gabaldon, T.; Roos, D.S.; Sonnhammer, E.L.; Herrero, J.; Szklarczyk, R.J.

    2012-01-01

    The identification of orthologs-genes pairs descended from a common ancestor through speciation, rather than duplication-has emerged as an essential component of many bioinformatics applications, ranging from the annotation of new genomes to experimental target prioritization. Yet, the development a

  3. Factors affecting the concordance between orthologous gene trees and species tree in bacteria

    Directory of Open Access Journals (Sweden)

    González Víctor

    2008-10-01

    Full Text Available Abstract Background As originally defined, orthologous genes implied a reflection of the history of the species. In recent years, many studies have examined the concordance between orthologous gene trees and species trees in bacteria. These studies have produced contradictory results that may have been influenced by orthologous gene misidentification and artefactual phylogenetic reconstructions. Here, using a method that allows the detection and exclusion of false positives during identification of orthologous genes, we address the question of whether putative orthologous genes within bacteria really reflect the history of the species. Results We identified a set of 370 orthologous genes from the bacterial order Rhizobiales. Although manifesting strong vertical signal, almost every orthologous gene had a distinct phylogeny, and the most common topology among the orthologous gene trees did not correspond with the best estimate of the species tree. However, each orthologous gene tree shared an average of 70% of its bipartitions with the best estimate of the species tree. Stochastic error related to gene size affected the concordance between the best estimated of the species tree and the orthologous gene trees, although this effect was weak and distributed unevenly among the functional categories. The nodes showing the greatest discordance were those defined by the shortest internal branches in the best estimated of the species tree. Moreover, a clear bias was evident with respect to the function of the orthologous genes, and the degree of divergence among the orthologous genes appeared to be related to their functional classification. Conclusion Orthologous genes do not reflect the history of the species when taken as individual markers, but they do when taken as a whole. Stochastic error affected the concordance of orthologous genes with the species tree, albeit weakly. We conclude that two important biological causes of discordance among

  4. Retrotranspositions in orthologous regions of closely related grass species

    Directory of Open Access Journals (Sweden)

    Swigoňová Zuzana

    2006-08-01

    Full Text Available Abstract Background Retrotransposons are commonly occurring eukaryotic transposable elements (TEs. Among these, long terminal repeat (LTR retrotransposons are the most abundant TEs and can comprise 50–90% of the genome in higher plants. By comparing the orthologous chromosomal regions of closely related species, the effects of TEs on the evolution of plant genomes can be studied in detail. Results Here, we compared the composition and organization of TEs within five orthologous chromosomal regions among three grass species: maize, sorghum, and rice. We identified a total of 132 full or fragmented LTR retrotransposons in these regions. As a percentage of the total cumulative sequence in each species, LTR retrotransposons occupy 45.1% of the maize, 21.1% of the rice, and 3.7% of the sorghum regions. The most common elements in the maize retrotransposon-rich regions are the copia-like retrotransposons with 39% and the gypsy-like retrotransposons with 37%. Using the contiguous sequence of the orthologous regions, we detected 108 retrotransposons with intact target duplication sites and both LTR termini. Here, we show that 74% of these elements inserted into their host genome less than 1 million years ago and that many retroelements expanded in size by the insertion of other sequences. These inserts were predominantly other retroelements, however, several of them were also fragmented genes. Unforeseen was the finding of intact genes embedded within LTR retrotransposons. Conclusion Although the abundance of retroelements between maize and rice is consistent with their different genome sizes of 2,364 and 389 Mb respectively, the content of retrotransposons in sorghum (790 Mb is surprisingly low. In all three species, retrotransposition is a very recent activity relative to their speciation. While it was known that genes re-insert into non-orthologous positions of plant genomes, they appear to re-insert also within retrotransposons, potentially

  5. SirA Orthologs Affect both Motility and Virulence

    OpenAIRE

    Goodier, Robert I.; Ahmer, Brian M. M.

    2001-01-01

    The sirA gene of Salmonella enterica serovar Typhimurium encodes a two-component response regulator of the FixJ family that has a positive regulatory influence on the expression of type III secretion genes involved with epithelial cell invasion and the elicitation of bovine gastroenteritis. SirA orthologs in Pseudomonas, Vibrio, and Erwinia control the expression of distinct virulence genes in these genera, but an evolutionarily conserved target of SirA regulation has never been identified. I...

  6. KIF27 is one of orthologs for Drosophila Costal-2.

    Science.gov (United States)

    Katoh, Yuriko; Katoh, Masaru

    2004-12-01

    Signals of Hedgehog family proteins (SHH, IHH and DHH) are transduced through Patched family receptors (PTCH1 and PTCH2) and Smoothened (SMO) to GLI family transcription factors (GLI1, GLI2 and GLI3). SHH plays a key role in development and progression of pancreatic cancer, gastric cancer, basal cell carcinoma, and brain tumors. Drosophila Costal-2 (Cos2) is implicated in the Hedgehog pathway through the interaction with Smoothened (Smo), Cubitus interruptus (Ci), Fused (Fu), and microtubule; however, mammalian ortholog of Drosophila Cos2 remained to be identified. Here we identified and characterized human ortholog of Drosophila Cos2 by using bioinformatics. Full-length Drosophila Cos2 was most homologous to human KIF27, followed by mouse Kif7, and other KIF family members. KIF27 gene at human chromosome 9q22.1 and KIF7 gene at human chromosome 15q26.1 were paralogs within the human genome. Phylogenetic analysis revealed that KIF27, Kif7, KIF4A, KIF4B and KIF21A constitute the KIF27 subfamily among mammalian Kinesin family. Drosophila Cos2 protein consists of Kinesin motor (KISc) domain, Ci-binding domain, and Smo-binding domain. KIF27 itself shared the common domain structure with Drosophila Cos2, while other members of KIF27 subfamily shared partial domain structure with Drosophila Cos2. These facts indicate that KIF27 is one of mammalian orthologs for Drosophila Cos2.

  7. Update History of This Database - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PGDBj - Ortholog DB Up...date History of This Database Date Update contents 2014/05/12 PGDBj Ortholog DB Englis...a SEF URLs by Artio About This Database Database Description Download License Upd...ate History of This Database Site Policy | Contact Us Update History of This Database - PGDBj - Ortholog DB | LSDB Archive ...

  8. Protein (Cyanobacteria) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

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    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PGD... The IDs of clusters that the amino acid sequences belong to in each taxon are indicated. Data file File name: pgd...bj_ortholog_db_cyanobacteria_protein.zip File URL: ftp://ftp.biosciencedbc.jp/archive/pgdbj-ortholog-db/LATEST/pgd...ch URL http://togodb.biosciencedbc.jp/togodb/view/pgdbj_ortholog_db_cyanobacteria_protein#en Data acquisitio...ase Database Description Download License Update History of This Database Site Policy | Contact Us Protein (Cyanobacteria) - PGDBj - Ortholog DB | LSDB Archive ...

  9. SirA orthologs affect both motility and virulence.

    Science.gov (United States)

    Goodier, R I; Ahmer, B M

    2001-04-01

    The sirA gene of Salmonella enterica serovar Typhimurium encodes a two-component response regulator of the FixJ family that has a positive regulatory influence on the expression of type III secretion genes involved with epithelial cell invasion and the elicitation of bovine gastroenteritis. SirA orthologs in Pseudomonas, Vibrio, and Erwinia control the expression of distinct virulence genes in these genera, but an evolutionarily conserved target of SirA regulation has never been identified. In this study we tested the hypothesis that sirA may be an ancient member of the flagellar regulon. We examined the effect of a sirA mutation on transcriptional fusions to flagellar promoters (flhD, fliE, fliF, flgA, flgB, fliC, fliD, motA, and fliA) while using fusions to the virulence gene sopB as a positive control. SirA had only small regulatory effects on all fusions in liquid medium (less than fivefold). However, in various types of motility agar plates, sirA was able to activate a sopB fusion by up to 63-fold while repressing flagellar fusions by values exceeding 100-fold. Mutations in the sirA orthologs of Escherichia coli, Vibrio cholerae, Pseudomonas fluorescens, and Pseudomonas aeruginosa result in defects in either motility or motility gene regulation, suggesting that control of flagellar regulons may be an evolutionarily conserved function of sirA orthologs. The implications for our understanding of virulence gene regulation in the gamma Proteobacteria are discussed.

  10. Expression analysis of kenaf cinnamate 4-hydroxylase (C4H) ortholog during developmental and stress responses

    Science.gov (United States)

    This study was conducted to clone and analyze the expression pattern of a C4H gene encoding cinnamate 4-hydroxylase from kenaf (Hibiscus cannabinus L.). A full-length C4H ortholog was cloned using degenerate primers and the RACE (rapid amplification of cDNA ends) method. The full-length C4H ortholog...

  11. Human and mouse mitochondrial orthologs of bacterial ClpX

    DEFF Research Database (Denmark)

    Corydon, T J; Wilsbech, M; Jespersgaard, C;

    2000-01-01

    We have determined the cDNA sequence and exon/intron structure of the human CLPX gene encoding a human ortholog of the E. coli ClpX chaperone and protease subunit. The CLPX gene comprises 14 exons and encodes a 633-amino acid-long precursor polypeptide. The polypeptide contains an N-terminal puta......We have determined the cDNA sequence and exon/intron structure of the human CLPX gene encoding a human ortholog of the E. coli ClpX chaperone and protease subunit. The CLPX gene comprises 14 exons and encodes a 633-amino acid-long precursor polypeptide. The polypeptide contains an N......-terminal putative mitochondrial transit peptide, and expression of a full-length ClpX cDNA tagged at its C-terminus (Myc-His) shows that the polypeptide is transported into mitochondria. FISH analysis localized the CLPX gene to human Chromosome (Chr) 15q22.1-22.32. This localization was refined by radiation hybrid...... variability between mouse ClpX cDNAs from different strains. Alignment of the human and mouse ClpX amino acid sequences with ClpX sequences from other organisms shows that they display the typical modular organization of domains with one AAA(+) domain common to a large group of ATPases and several other...

  12. An integrative approach to ortholog prediction for disease-focused and other functional studies

    Directory of Open Access Journals (Sweden)

    Perrimon Norbert

    2011-08-01

    Full Text Available Abstract Background Mapping of orthologous genes among species serves an important role in functional genomics by allowing researchers to develop hypotheses about gene function in one species based on what is known about the functions of orthologs in other species. Several tools for predicting orthologous gene relationships are available. However, these tools can give different results and identification of predicted orthologs is not always straightforward. Results We report a simple but effective tool, the Drosophila RNAi Screening Center Integrative Ortholog Prediction Tool (DIOPT; http://www.flyrnai.org/diopt, for rapid identification of orthologs. DIOPT integrates existing approaches, facilitating rapid identification of orthologs among human, mouse, zebrafish, C. elegans, Drosophila, and S. cerevisiae. As compared to individual tools, DIOPT shows increased sensitivity with only a modest decrease in specificity. Moreover, the flexibility built into the DIOPT graphical user interface allows researchers with different goals to appropriately 'cast a wide net' or limit results to highest confidence predictions. DIOPT also displays protein and domain alignments, including percent amino acid identity, for predicted ortholog pairs. This helps users identify the most appropriate matches among multiple possible orthologs. To facilitate using model organisms for functional analysis of human disease-associated genes, we used DIOPT to predict high-confidence orthologs of disease genes in Online Mendelian Inheritance in Man (OMIM and genes in genome-wide association study (GWAS data sets. The results are accessible through the DIOPT diseases and traits query tool (DIOPT-DIST; http://www.flyrnai.org/diopt-dist. Conclusions DIOPT and DIOPT-DIST are useful resources for researchers working with model organisms, especially those who are interested in exploiting model organisms such as Drosophila to study the functions of human disease genes.

  13. Ortholog prediction of the Aspergillus genus applicable for synthetic biology

    DEFF Research Database (Denmark)

    Rasmussen, Jane Lind Nybo; Vesth, Tammi Camilla; Theobald, Sebastian

    The Aspergillus genus contains leading industrial microorganisms, excelling in producing bioactive compounds and enzymes. Using synthetic biology and bioinformatics, we aim to re-engineer these organisms for applications within human health, pharmaceuticals, environmental engineering, and food...... production. In this project, we compare the genomes of +300 species from the Aspergillus genus to generate a high-resolution pan-genomic map, representing genetic diversity spanning ~200 million years. We are identifying genes specific to species and clades to allow for guilt-by-association-based mapping......-directional hits. The result is orthologous protein families describing the genomic and functional features of individual species, clades and the core/pan genome of Aspergillus; and applicable to genotype-to-phenotype analyses in other microbial genera....

  14. Analysis of septins across kingdoms reveals orthology and new motifs

    Directory of Open Access Journals (Sweden)

    Malmberg Russell L

    2007-07-01

    Full Text Available Abstract Background Septins are cytoskeletal GTPase proteins first discovered in the fungus Saccharomyces cerevisiae where they organize the septum and link nuclear division with cell division. More recently septins have been found in animals where they are important in processes ranging from actin and microtubule organization to embryonic patterning and where defects in septins have been implicated in human disease. Previous studies suggested that many animal septins fell into independent evolutionary groups, confounding cross-kingdom comparison. Results In the current work, we identified 162 septins from fungi, microsporidia and animals and analyzed their phylogenetic relationships. There was support for five groups of septins with orthology between kingdoms. Group 1 (which includes S. cerevisiae Cdc10p and human Sept9 and Group 2 (which includes S. cerevisiae Cdc3p and human Sept7 contain sequences from fungi and animals. Group 3 (which includes S. cerevisiae Cdc11p and Group 4 (which includes S. cerevisiae Cdc12p contain sequences from fungi and microsporidia. Group 5 (which includes Aspergillus nidulans AspE contains sequences from filamentous fungi. We suggest a modified nomenclature based on these phylogenetic relationships. Comparative sequence alignments revealed septin derivatives of already known G1, G3 and G4 GTPase motifs, four new motifs from two to twelve amino acids long and six conserved single amino acid positions. One of these new motifs is septin-specific and several are group specific. Conclusion Our studies provide an evolutionary history for this important family of proteins and a framework and consistent nomenclature for comparison of septin orthologs across kingdoms.

  15. Protein (Viridiplantae) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PGD... IDs of clusters that the amino acid sequences belong to in each taxon are indicated. Data file File name: pgd...bj_ortholog_db_viridiplantae_protein.zip File URL: ftp://ftp.biosciencedbc.jp/archive/pgdbj-ortholog-db/LATEST/pgd...RL http://togodb.biosciencedbc.jp/togodb/view/pgdbj_ortholog_db_viridiplantae_protein#en Data acquisition me...BI GI number of Amino Acid sequence RefSeq ID NCBI Reference Sequence ID Cluster (Kingdom) Cluster ID (rank: Kingd

  16. Download - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available criptions are about the downloadable data in this page. They might not correspond to the contents of the ori... name File Simple search and download 1 README README_e.html - 2 Protein (Viridiplantae) pgdbj_ortholog_db_v...iridiplantae_protein.zip (85 MB) Simple search and download 3 Cluster (Viridiplantae) pgdbj_ortholog_db_viri...diplantae_cluster.zip (15.6 MB) Simple search and download 4 Taxon (Viridiplantae...) pgdbj_ortholog_db_viridiplantae_taxon.zip (2.3 KB) Simple search and download 5 Protein (Cyanobacteria) pg

  17. Cluster (Viridiplantae) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

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    Full Text Available tions of each amino acid sequence in the ortholog cluster. Frequency of the words.... Then, a most suitable annotation, which contains high-frequency words most, was selected as the explanator

  18. Cluster (Cyanobacteria) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available ations of each amino acid sequence in the ortholog cluster. Frequency of the words...d. Then, a most suitable annotation, which contains high-frequency words most, was selected as the explanato

  19. SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes

    Science.gov (United States)

    Curtis, Darren S.; Phillips, Aaron R.; Callister, Stephen J.; Conlan, Sean; McCue, Lee Ann

    2013-01-01

    Summary: At the rate that prokaryotic genomes can now be generated, comparative genomics studies require a flexible method for quickly and accurately predicting orthologs among the rapidly changing set of genomes available. SPOCS implements a graph-based ortholog prediction method to generate a simple tab-delimited table of orthologs and in addition, html files that provide a visualization of the predicted ortholog/paralog relationships to which gene/protein expression metadata may be overlaid. Availability and Implementation: A SPOCS web application is freely available at http://cbb.pnnl.gov/portal/tools/spocs.html. Source code for Linux systems is also freely available under an open source license at http://cbb.pnnl.gov/portal/software/spocs.html; the Boost C++ libraries and BLAST are required. Contact: leeann.mccue@pnnl.gov PMID:23956303

  20. SPOCS: Software for Predicting and Visualizing Orthology/Paralogy Relationships Among Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Curtis, Darren S.; Phillips, Aaron R.; Callister, Stephen J.; Conlan, Sean; McCue, Lee Ann

    2013-10-15

    At the rate that prokaryotic genomes can now be generated, comparative genomics studies require a flexible method for quickly and accurately predicting orthologs among the rapidly changing set of genomes available. SPOCS implements a graph-based ortholog prediction method to generate a simple tab-delimited table of orthologs and in addition, html files that provide a visualization of the predicted ortholog/paralog relationships to which gene/protein expression metadata may be overlaid. AVAILABILITY AND IMPLEMENTATION: A SPOCS web application is freely available at http://cbb.pnnl.gov/portal/tools/spocs.html. Source code for Linux systems is also freely available under an open source license at http://cbb.pnnl.gov/portal/software/spocs.html; the Boost C++ libraries and BLAST are required.

  1. Taxon (Cyanobacteria) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...Artio About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Taxon (Cyanobacteria) - PGDBj - Ortholog DB | LSDB Archive ...

  2. Taxon (Viridiplantae) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...Artio About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Taxon (Viridiplantae) - PGDBj - Ortholog DB | LSDB Archive ...

  3. Database Description - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available data in the databases. By submitting queries to the PGDBj Ortholog DB with keywords or amino acid sequences, users...ding both model plants and crop plants. Following the links obtained, users can retrieve the actual entries

  4. The Importance of Being Cis: Evolution of Orthologous Fish and Mammalian Enhancer Activity

    OpenAIRE

    Ritter, Deborah I.; Li, Qiang; Kostka, Dennis; Pollard, Katherine S.; Guo, Su; Chuang, Jeffrey H.

    2010-01-01

    Conserved noncoding elements (CNEs) in vertebrate genomes often act as developmental enhancers, but a critical issue is how well orthologous CNE sequences retain the same activity in their respective species, a characteristic important for generalization of model organism studies. To quantify how well CNE enhancer activity has been preserved, we compared the anatomy-specific activities of 41 zebra fish CNEs in zebra fish embryos with the activities of orthologous human CNEs in mouse embryos. ...

  5. Comment on "Tequila, a neurotrypsin ortholog, regulates long-term memory formation in Drosophila".

    Science.gov (United States)

    Sonderegger, Peter; Patthy, Laszlo

    2007-06-22

    Didelot et al. (Reports, 11 August 2006, p. 851) claimed that Drosophila Tequila (Teq) and human neurotrypsin are orthologs and concluded that deficient long-term memory after Teq inactivation indicates that neurotrypsin plays its essential role for human cognitive functions through a similar mechanism. Our analyses suggest that Teq and neurotrypsin are not orthologous, leading us to question their equivalent roles in higher brain function.

  6. A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation.

    Directory of Open Access Journals (Sweden)

    Kalliopi Trachana

    Full Text Available Accurate orthology prediction is crucial for many applications in the post-genomic era. The lack of broadly accepted benchmark tests precludes a comprehensive analysis of orthology inference. So far, functional annotation between orthologs serves as a performance proxy. However, this violates the fundamental principle of orthology as an evolutionary definition, while it is often not applicable due to limited experimental evidence for most species. Therefore, we constructed high quality "gold standard" orthologous groups that can serve as a benchmark set for orthology inference in bacterial species. Herein, we used this dataset to demonstrate 1 why a manually curated, phylogeny-based dataset is more appropriate for benchmarking orthology than other popular practices and 2 how it guides database design and parameterization through careful error quantification. More specifically, we illustrate how function-based tests often fail to identify false assignments, misjudging the true performance of orthology inference methods. We also examined how our dataset can instruct the selection of a "core" species repertoire to improve detection accuracy. We conclude that including more genomes at the proper evolutionary distances can influence the overall quality of orthology detection. The curated gene families, called Reference Orthologous Groups, are publicly available at http://eggnog.embl.de/orthobench2.

  7. A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation.

    Science.gov (United States)

    Trachana, Kalliopi; Forslund, Kristoffer; Larsson, Tomas; Powell, Sean; Doerks, Tobias; von Mering, Christian; Bork, Peer

    2014-01-01

    Accurate orthology prediction is crucial for many applications in the post-genomic era. The lack of broadly accepted benchmark tests precludes a comprehensive analysis of orthology inference. So far, functional annotation between orthologs serves as a performance proxy. However, this violates the fundamental principle of orthology as an evolutionary definition, while it is often not applicable due to limited experimental evidence for most species. Therefore, we constructed high quality "gold standard" orthologous groups that can serve as a benchmark set for orthology inference in bacterial species. Herein, we used this dataset to demonstrate 1) why a manually curated, phylogeny-based dataset is more appropriate for benchmarking orthology than other popular practices and 2) how it guides database design and parameterization through careful error quantification. More specifically, we illustrate how function-based tests often fail to identify false assignments, misjudging the true performance of orthology inference methods. We also examined how our dataset can instruct the selection of a "core" species repertoire to improve detection accuracy. We conclude that including more genomes at the proper evolutionary distances can influence the overall quality of orthology detection. The curated gene families, called Reference Orthologous Groups, are publicly available at http://eggnog.embl.de/orthobench2.

  8. Orthologous transcription factors in bacteria have different functions and regulate different genes.

    Directory of Open Access Journals (Sweden)

    Morgan N Price

    2007-09-01

    Full Text Available Transcription factors (TFs form large paralogous gene families and have complex evolutionary histories. Here, we ask whether putative orthologs of TFs, from bidirectional best BLAST hits (BBHs, are evolutionary orthologs with conserved functions. We show that BBHs of TFs from distantly related bacteria are usually not evolutionary orthologs. Furthermore, the false orthologs usually respond to different signals and regulate distinct pathways, while the few BBHs that are evolutionary orthologs do have conserved functions. To test the conservation of regulatory interactions, we analyze expression patterns. We find that regulatory relationships between TFs and their regulated genes are usually not conserved for BBHs in Escherichia coli K12 and Bacillus subtilis. Even in the much more closely related bacteria Vibrio cholerae and Shewanella oneidensis MR-1, predicting regulation from E. coli BBHs has high error rates. Using gene-regulon correlations, we identify genes whose expression pattern differs between E. coli and S. oneidensis. Using literature searches and sequence analysis, we show that these changes in expression patterns reflect changes in gene regulation, even for evolutionary orthologs. We conclude that the evolution of bacterial regulation should be analyzed with phylogenetic trees, rather than BBHs, and that bacterial regulatory networks evolve more rapidly than previously thought.

  9. Comparing the Statistical Fate of Paralogous and Orthologous Sequences.

    Science.gov (United States)

    Massip, Florian; Sheinman, Michael; Schbath, Sophie; Arndt, Peter F

    2016-10-01

    For several decades, sequence alignment has been a widely used tool in bioinformatics. For instance, finding homologous sequences with a known function in large databases is used to get insight into the function of nonannotated genomic regions. Very efficient tools like BLAST have been developed to identify and rank possible homologous sequences. To estimate the significance of the homology, the ranking of alignment scores takes a background model for random sequences into account. Using this model we can estimate the probability to find two exactly matching subsequences by chance in two unrelated sequences. For two homologous sequences, the corresponding probability is much higher, which allows us to identify them. Here we focus on the distribution of lengths of exact sequence matches between protein-coding regions of pairs of evolutionarily distant genomes. We show that this distribution exhibits a power-law tail with an exponent [Formula: see text] Developing a simple model of sequence evolution by substitutions and segmental duplications, we show analytically and computationally that paralogous and orthologous gene pairs contribute differently to this distribution. Our model explains the differences observed in the comparison of coding and noncoding parts of genomes, thus providing a better understanding of statistical properties of genomic sequences and their evolution.

  10. MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement

    Directory of Open Access Journals (Sweden)

    Zhang Liqing

    2010-01-01

    Full Text Available Abstract Background Ortholog assignment is a critical and fundamental problem in comparative genomics, since orthologs are considered to be functional counterparts in different species and can be used to infer molecular functions of one species from those of other species. MSOAR is a recently developed high-throughput system for assigning one-to-one orthologs between closely related species on a genome scale. It attempts to reconstruct the evolutionary history of input genomes in terms of genome rearrangement and gene duplication events. It assumes that a gene duplication event inserts a duplicated gene into the genome of interest at a random location (i.e., the random duplication model. However, in practice, biologists believe that genes are often duplicated by tandem duplications, where a duplicated gene is located next to the original copy (i.e., the tandem duplication model. Results In this paper, we develop MSOAR 2.0, an improved system for one-to-one ortholog assignment. For a pair of input genomes, the system first focuses on the tandemly duplicated genes of each genome and tries to identify among them those that were duplicated after the speciation (i.e., the so-called inparalogs, using a simple phylogenetic tree reconciliation method. For each such set of tandemly duplicated inparalogs, all but one gene will be deleted from the concerned genome (because they cannot possibly appear in any one-to-one ortholog pairs, and MSOAR is invoked. Using both simulated and real data experiments, we show that MSOAR 2.0 is able to achieve a better sensitivity and specificity than MSOAR. In comparison with the well-known genome-scale ortholog assignment tool InParanoid, Ensembl ortholog database, and the orthology information extracted from the well-known whole-genome multiple alignment program MultiZ, MSOAR 2.0 shows the highest sensitivity. Although the specificity of MSOAR 2.0 is slightly worse than that of InParanoid in the real data experiments

  11. An Effective Big Data Supervised Imbalanced Classification Approach for Ortholog Detection in Related Yeast Species

    Directory of Open Access Journals (Sweden)

    Deborah Galpert

    2015-01-01

    Full Text Available Orthology detection requires more effective scaling algorithms. In this paper, a set of gene pair features based on similarity measures (alignment scores, sequence length, gene membership to conserved regions, and physicochemical profiles are combined in a supervised pairwise ortholog detection approach to improve effectiveness considering low ortholog ratios in relation to the possible pairwise comparison between two genomes. In this scenario, big data supervised classifiers managing imbalance between ortholog and nonortholog pair classes allow for an effective scaling solution built from two genomes and extended to other genome pairs. The supervised approach was compared with RBH, RSD, and OMA algorithms by using the following yeast genome pairs: Saccharomyces cerevisiae-Kluyveromyces lactis, Saccharomyces cerevisiae-Candida glabrata, and Saccharomyces cerevisiae-Schizosaccharomyces pombe as benchmark datasets. Because of the large amount of imbalanced data, the building and testing of the supervised model were only possible by using big data supervised classifiers managing imbalance. Evaluation metrics taking low ortholog ratios into account were applied. From the effectiveness perspective, MapReduce Random Oversampling combined with Spark SVM outperformed RBH, RSD, and OMA, probably because of the consideration of gene pair features beyond alignment similarities combined with the advances in big data supervised classification.

  12. Testing the ortholog conjecture with comparative functional genomic data from mammals.

    Directory of Open Access Journals (Sweden)

    Nathan L Nehrt

    2011-06-01

    Full Text Available A common assumption in comparative genomics is that orthologous genes share greater functional similarity than do paralogous genes (the "ortholog conjecture". Many methods used to computationally predict protein function are based on this assumption, even though it is largely untested. Here we present the first large-scale test of the ortholog conjecture using comparative functional genomic data from human and mouse. We use the experimentally derived functions of more than 8,900 genes, as well as an independent microarray dataset, to directly assess our ability to predict function using both orthologs and paralogs. Both datasets show that paralogs are often a much better predictor of function than are orthologs, even at lower sequence identities. Among paralogs, those found within the same species are consistently more functionally similar than those found in a different species. We also find that paralogous pairs residing on the same chromosome are more functionally similar than those on different chromosomes, perhaps due to higher levels of interlocus gene conversion between these pairs. In addition to offering implications for the computational prediction of protein function, our results shed light on the relationship between sequence divergence and functional divergence. We conclude that the most important factor in the evolution of function is not amino acid sequence, but rather the cellular context in which proteins act.

  13. Patterns of nucleotides that flank substitutions in human orthologous genes

    Directory of Open Access Journals (Sweden)

    Huang Zhuoran

    2010-07-01

    Full Text Available Abstract Background Sequence context is an important aspect of base mutagenesis, and three-base periodicity is an intrinsic property of coding sequences. However, how three-base periodicity is influenced in the vicinity of substitutions is still unclear. The effect of context on mutagenesis should be revealed in the usage of nucleotides that flank substitutions. Relative entropy (also known as Kullback-Leibler divergence is useful for finding unusual patterns in biological sequences. Results Using relative entropy, we visualized the periodic patterns in the context of substitutions in human orthologous genes. Neighbouring patterns differed both among substitution categories and within a category that occurred at three codon positions. Transition tended to occur in periodic sequences relative to transversion. Periodic signals were stronger in a set of flanking sequences of substitutions that occurred at the third-codon positions than in those that occurred at the first- or second-codon positions. To determine how the three-base periodicity was affected near the substitution sites, we fitted a sine model to the values of the relative entropy. A sine of period equal to 3 is a good approximation for the three-base periodicity at sites not in close vicinity to some substitutions. These periods were interrupted near the substitution site and then reappeared away from substitutions. A comparative analysis between the native and codon-shuffled datasets suggested that the codon usage frequency was not the sole origin of the three-base periodicity, implying that the native order of codons also played an important role in this periodicity. Synonymous codon shuffling revealed that synonymous codon usage bias was one of the factors responsible for the observed three-base periodicity. Conclusions Our results offer an efficient way to illustrate unusual periodic patterns in the context of substitutions and provide further insight into the origin of three

  14. Gene family level comparative analysis of gene expression in mammals validates the ortholog conjecture.

    Science.gov (United States)

    Rogozin, Igor B; Managadze, David; Shabalina, Svetlana A; Koonin, Eugene V

    2014-04-01

    The ortholog conjecture (OC), which is central to functional annotation of genomes, posits that orthologous genes are functionally more similar than paralogous genes at the same level of sequence divergence. However, a recent study challenged the OC by reporting a greater functional similarity, in terms of Gene Ontology (GO) annotations and expression profiles, among within-species paralogs compared with orthologs. These findings were taken to indicate that functional similarity of homologous genes is primarily determined by the cellular context of the genes, rather than evolutionary history. However, several subsequent studies suggest that GO annotations and microarray data could artificially inflate functional similarity between paralogs from the same organism. We sought to test the OC using approaches distinct from those used in previous studies. Analysis of a large RNAseq data set from multiple human and mouse tissues shows that expression similarity (correlations coefficients, rank's, or Z-scores) between orthologs is substantially greater than that for between-species paralogs with the same sequence divergence, in agreement with the OC and the results of recent detailed analyses. These findings are further corroborated by a fine-grain analysis in which expression profiles of orthologs and paralogs were compared separately for individual gene families. Expression profiles of within-species paralogs are more strongly correlated than profiles of orthologs but it is shown that this is caused by high background noise, that is, correlation between profiles of unrelated genes in the same organism. Z-scores and rank scores show a nonmonotonic dependence of expression profile similarity on sequence divergence. This complexity of gene expression evolution after duplication might be at least partially caused by selection for protein dosage rebalancing following gene duplication.

  15. eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges.

    Science.gov (United States)

    Powell, Sean; Szklarczyk, Damian; Trachana, Kalliopi; Roth, Alexander; Kuhn, Michael; Muller, Jean; Arnold, Roland; Rattei, Thomas; Letunic, Ivica; Doerks, Tobias; Jensen, Lars J; von Mering, Christian; Bork, Peer

    2012-01-01

    Orthologous relationships form the basis of most comparative genomic and metagenomic studies and are essential for proper phylogenetic and functional analyses. The third version of the eggNOG database (http://eggnog.embl.de) contains non-supervised orthologous groups constructed from 1133 organisms, doubling the number of genes with orthology assignment compared to eggNOG v2. The new release is the result of a number of improvements and expansions: (i) the underlying homology searches are now based on the SIMAP database; (ii) the orthologous groups have been extended to 41 levels of selected taxonomic ranges enabling much more fine-grained orthology assignments; and (iii) the newly designed web page is considerably faster with more functionality. In total, eggNOG v3 contains 721,801 orthologous groups, encompassing a total of 4,396,591 genes. Additionally, we updated 4873 and 4850 original COGs and KOGs, respectively, to include all 1133 organisms. At the universal level, covering all three domains of life, 101,208 orthologous groups are available, while the others are applicable at 40 more limited taxonomic ranges. Each group is amended by multiple sequence alignments and maximum-likelihood trees and broad functional descriptions are provided for 450,904 orthologous groups (62.5%).

  16. ORCAN-a web-based meta-server for real-time detection and functional annotation of orthologs.

    Science.gov (United States)

    Zielezinski, Andrzej; Dziubek, Michal; Sliski, Jan; Karlowski, Wojciech M

    2017-01-05

    ORCAN (ORtholog sCANner) is a web-based meta-server for one-click evolutionary and functional annotation of protein sequences. The server combines information from the most popular orthology-prediction resources, including four tools and four online databases. Functional annotation utilizes five additional comparisons between the query and identified homologs, including: sequence similarity, protein domain architectures, functional motifs, Gene Ontology term assignments and a list of associated articles. Furthermore, the server uses a plurality-based rating system to evaluate the orthology relationships and to rank the reference proteins by their evolutionary and functional relevance to the query. Using a dataset of ∼1 million true yeast orthologs as a sample reference set, we show that combining multiple orthology-prediction tools in ORCAN increases the sensitivity and precision by 1-2 percent points.

  17. OrthoSelect: a web server for selecting orthologous gene alignments from EST sequences.

    Science.gov (United States)

    Schreiber, Fabian; Wörheide, Gert; Morgenstern, Burkhard

    2009-07-01

    In the absence of whole genome sequences for many organisms, the use of expressed sequence tags (EST) offers an affordable approach for researchers conducting phylogenetic analyses to gain insight about the evolutionary history of organisms. Reliable alignments for phylogenomic analyses are based on orthologous gene sequences from different taxa. So far, researchers have not sufficiently tackled the problem of the completely automated construction of such datasets. Existing software tools are either semi-automated, covering only part of the necessary data processing, or implemented as a pipeline, requiring the installation and configuration of a cascade of external tools, which may be time-consuming and hard to manage. To simplify data set construction for phylogenomic studies, we set up a web server that uses our recently developed OrthoSelect approach. To the best of our knowledge, our web server is the first web-based EST analysis pipeline that allows the detection of orthologous gene sequences in EST libraries and outputs orthologous gene alignments. Additionally, OrthoSelect provides the user with an extensive results section that lists and visualizes all important results, such as annotations, data matrices for each gene/taxon and orthologous gene alignments. The web server is available at http://orthoselect.gobics.de.

  18. Systematic Comparisons of Orthologous Selenocysteine Methyltransferase and Homocysteine Methyltransferase Genes from Seven Monocots Species

    Directory of Open Access Journals (Sweden)

    De-yong ZHAO

    2015-06-01

    Full Text Available Identifying and manipulating genes underlying selenium metabolism could be helpful for increasing selenium content in crop grain, which is an important way to overcome diseases resulted from selenium deficiency. A reciprocal smallest distance algorithm (RSD approach was applied using two experimentally confirmed Homocysteine S-Methyltransferases genes (HMT1 and HMT2 and a putative Selenocysteine Methyltransferase (SMT from dicots plant Arabidopsis thaliana, to explore their orthologs in seven sequenced diploid monocot species: Oryza sativa, Zea mays, Sorghum bicolor, Brachypodium distachyon, Hordeum vulgare, Aegilops tauschii (the D-genome donor of common wheat and Triticum urartu (the A-genome donor of common wheat. HMT1 was apparently diverged from HMT2 and most of SMT orthologs were the same with that of HMT2 in this study, leading to the hypothesis that SMT and HMT originate from one common ancestor gene. Identifying orthologs provide candidates for further experimental confirmation; also it could be helpful in designing primers to clone SMT or HMT orthologs in other crops.

  19. Assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data

    Directory of Open Access Journals (Sweden)

    Lespinet Olivier

    2007-11-01

    Full Text Available Abstract Background Comparison of completely sequenced microbial genomes has revealed how fluid these genomes are. Detecting synteny blocks requires reliable methods to determining the orthologs among the whole set of homologs detected by exhaustive comparisons between each pair of completely sequenced genomes. This is a complex and difficult problem in the field of comparative genomics but will help to better understand the way prokaryotic genomes are evolving. Results We have developed a suite of programs that automate three essential steps to study conservation of gene order, and validated them with a set of 107 bacteria and archaea that cover the majority of the prokaryotic taxonomic space. We identified the whole set of shared homologs between two or more species and computed the evolutionary distance separating each pair of homologs. We applied two strategies to extract from the set of homologs a collection of valid orthologs shared by at least two genomes. The first computes the Reciprocal Smallest Distance (RSD using the PAM distances separating pairs of homologs. The second method groups homologs in families and reconstructs each family's evolutionary tree, distinguishing bona fide orthologs as well as paralogs created after the last speciation event. Although the phylogenetic tree method often succeeds where RSD fails, the reverse could occasionally be true. Accordingly, we used the data obtained with either methods or their intersection to number the orthologs that are adjacent in for each pair of genomes, the Positional Orthologous Genes (POGs, and to further study their properties. Once all these synteny blocks have been detected, we showed that POGs are subject to more evolutionary constraints than orthologs outside synteny groups, whichever the taxonomic distance separating the compared organisms. Conclusion The suite of programs described in this paper allows a reliable detection of orthologs and is useful for evaluating gene

  20. Multicopper oxidase-1 orthologs from diverse insect species have ascorbate oxidase activity.

    Science.gov (United States)

    Peng, Zeyu; Dittmer, Neal T; Lang, Minglin; Brummett, Lisa M; Braun, Caroline L; Davis, Lawrence C; Kanost, Michael R; Gorman, Maureen J

    2015-04-01

    Members of the multicopper oxidase (MCO) family of enzymes can be classified by their substrate specificity; for example, ferroxidases oxidize ferrous iron, ascorbate oxidases oxidize ascorbate, and laccases oxidize aromatic substrates such as diphenols. Our previous work on an insect multicopper oxidase, MCO1, suggested that it may function as a ferroxidase. This hypothesis was based on three lines of evidence: RNAi-mediated knock down of Drosophila melanogaster MCO1 (DmMCO1) affects iron homeostasis, DmMCO1 has ferroxidase activity, and DmMCO1 has predicted iron binding residues. In our current study, we expanded our focus to include MCO1 from Anopheles gambiae, Tribolium castaneum, and Manduca sexta. We verified that MCO1 orthologs have similar expression profiles, and that the MCO1 protein is located on the basal surface of cells where it is positioned to oxidize substrates in the hemolymph. In addition, we determined that RNAi-mediated knock down of MCO1 in A. gambiae affects iron homeostasis. To further characterize the enzymatic activity of MCO1 orthologs, we purified recombinant MCO1 from all four insect species and performed kinetic analyses using ferrous iron, ascorbate and two diphenols as substrates. We found that all of the MCO1 orthologs are much better at oxidizing ascorbate than they are at oxidizing ferrous iron or diphenols. This result is surprising because ascorbate oxidases are thought to be specific to plants and fungi. An analysis of three predicted iron binding residues in DmMCO1 revealed that they are not required for ferroxidase or laccase activity, but two of the residues (His374 and Asp380) influence oxidation of ascorbate. These two residues are conserved in MCO1 orthologs from insects and crustaceans; therefore, they are likely to be important for MCO1 function. The results of this study suggest that MCO1 orthologs function as ascorbate oxidases and influence iron homeostasis through an unknown mechanism.

  1. 9 CFR 72.1 - Ticks [Boophilus annulatus (Margaropus annulatus), Boophilus microplus, or Rhipicephalus evertsi...

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Ticks ; interstate movement of... POULTRY) AND ANIMAL PRODUCTS TEXAS (SPLENETIC) FEVER IN CATTLE § 72.1 Ticks ; interstate movement of infested or exposed animals prohibited. No animals infested with ticks or exposed to tick infestation...

  2. Conserved repertoire of orthologous vomeronasal type 1 receptor genes in ruminant species

    Directory of Open Access Journals (Sweden)

    Okamura Hiroaki

    2009-09-01

    Full Text Available Abstract Background In mammals, pheromones play an important role in social and innate reproductive behavior within species. In rodents, vomeronasal receptor type 1 (V1R, which is specifically expressed in the vomeronasal organ, is thought to detect pheromones. The V1R gene repertoire differs dramatically between mammalian species, and the presence of species-specific V1R subfamilies in mouse and rat suggests that V1R plays a profound role in species-specific recognition of pheromones. In ruminants, however, the molecular mechanism(s for pheromone perception is not well understood. Interestingly, goat male pheromone, which can induce out-of-season ovulation in anestrous females, causes the same pheromone response in sheep, and vice versa, suggesting that there may be mechanisms for detecting "inter-species" pheromones among ruminant species. Results We isolated 23 goat and 21 sheep intact V1R genes based on sequence similarity with 32 cow V1R genes in the cow genome database. We found that all of the goat and sheep V1R genes have orthologs in their cross-species counterparts among these three ruminant species and that the sequence identity of V1R orthologous pairs among these ruminants is much higher than that of mouse-rat V1R orthologous pairs. Furthermore, all goat V1Rs examined thus far are expressed not only in the vomeronasal organ but also in the main olfactory epithelium. Conclusion Our results suggest that, compared with rodents, the repertoire of orthologous V1R genes is remarkably conserved among the ruminants cow, sheep and goat. We predict that these orthologous V1Rs can detect the same or closely related chemical compound(s within each orthologous set/pair. Furthermore, all identified goat V1Rs are expressed in the vomeronasal organ and the main olfactory epithelium, suggesting that V1R-mediated ligand information can be detected and processed by both the main and accessory olfactory systems. The fact that ruminant and rodent V1Rs

  3. Sequence variability of Rhizobiales orthologs and relationship with physico-chemical characteristics of proteins

    Directory of Open Access Journals (Sweden)

    Mora Jaime

    2011-10-01

    Full Text Available Abstract Background Chromosomal orthologs can reveal the shared ancestral gene set and their evolutionary trends. Additionally, physico-chemical properties of encoded proteins could provide information about functional adaptation and ecological niche requirements. Results We analyzed 7080 genes (five groups of 1416 orthologs each from Rhizobiales species (S. meliloti, R. etli, and M. loti, plant symbionts; A. tumefaciens, a plant pathogen; and B. melitensis, an animal pathogen. We evaluated their phylogenetic relationships and observed three main topologies. The first, with closer association of R. etli to A. tumefaciens; the second with R. etli closer to S. meliloti; and the third with A. tumefaciens and S. meliloti as the closest pair. This was not unusual, given the close relatedness of these three species. We calculated the synonymous (dS and nonsynonymous (dN substitution rates of these orthologs, and found that informational and metabolic functions showed relatively low dN rates; in contrast, genes from hypothetical functions and cellular processes showed high dN rates. An alternative measure of sequence variability, percentage of changes by species, was used to evaluate the most specific proportion of amino acid residues from alignments. When dN was compared with that measure a high correlation was obtained, revealing that much of evolutive information was extracted with the percentage of changes by species at the amino acid level. By analyzing the sequence variability of orthologs with a set of five properties (polarity, electrostatic charge, formation of secondary structures, molecular volume, and amino acid composition, we found that physico-chemical characteristics of proteins correlated with specific functional roles, and association of species did not follow their typical phylogeny, probably reflecting more adaptation to their life styles and niche preferences. In addition, orthologs with low dN rates had residues with more positive

  4. Investigation of tissue-specific human orthologous alternative splice events in pig

    DEFF Research Database (Denmark)

    Hillig, Ann-Britt Nygaard; Jørgensen, Claus Bøttcher; Salicio, Susanna Cirera;

    2010-01-01

    Alternative splicing of pre-mRNA can contribute to differences between tissues or cells either by regulating gene expression or creating proteins with various functions encoded by one gene. The number of investigated alternative splice events in pig has so far been limited. In this study we have...... investigated alternative splice events detected in humans, in orthologous pig genes. A total of 17 genes with predicted exon skipping events were selected for further studies. The splice events for the selected genes were experimentally verified using real-time quantitative PCR analysis (qPCR) with splice......-specific primers in 19 different tissues. The same splice variants as reported in humans were detected in 15 orthologous pig genes, however, the expression pattern predicted in the in silico analyses was only experimentally verified in a few cases. The results support the findings that splice events resulting...

  5. The importance of being cis: evolution of orthologous fish and mammalian enhancer activity.

    Science.gov (United States)

    Ritter, Deborah I; Li, Qiang; Kostka, Dennis; Pollard, Katherine S; Guo, Su; Chuang, Jeffrey H

    2010-10-01

    Conserved noncoding elements (CNEs) in vertebrate genomes often act as developmental enhancers, but a critical issue is how well orthologous CNE sequences retain the same activity in their respective species, a characteristic important for generalization of model organism studies. To quantify how well CNE enhancer activity has been preserved, we compared the anatomy-specific activities of 41 zebra fish CNEs in zebra fish embryos with the activities of orthologous human CNEs in mouse embryos. We found that 13/41 (∼30%) of the orthologous CNE pairs exhibit conserved positive activity in zebra fish and mouse. Conserved positive activity is only weakly associated with either sequence conservation or the absence of bases undergoing accelerated evolution. A stronger effect is that disparate activity is associated with transcription factor binding site divergence. To distinguish the contributions of cis- versus trans-regulatory changes, we analyzed 13 CNEs in a three-way experimental comparison: human CNE tested in zebra fish, human CNE tested in mouse, and orthologous zebra fish CNE tested in zebra fish. Both cis- and trans-changes affect a significant fraction of CNEs, although human and zebra fish sequences exhibit disparate activity in zebra fish (indicating cis regulatory changes) twice as often as human sequences show disparate activity when tested in mouse and zebra fish (indicating trans regulatory changes). In all four cases where the zebra fish and human CNE display a similar expression pattern in zebra fish, the human CNE also displays a similar expression pattern in mouse. This suggests that the endogenous enhancer activity of ∼30% of human CNEs can be determined from experiments in zebra fish alone, and to identify these CNEs, both the zebra fish and the human sequences should be tested.

  6. Characterization of the Drosophila ortholog of the human Usher Syndrome type 1G protein sans.

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    Fabio Demontis

    Full Text Available BACKGROUND: The Usher syndrome (USH is the most frequent deaf-blindness hereditary disease in humans. Deafness is attributed to the disorganization of stereocilia in the inner ear. USH1, the most severe subtype, is associated with mutations in genes encoding myosin VIIa, harmonin, cadherin 23, protocadherin 15, and sans. Myosin VIIa, harmonin, cadherin 23, and protocadherin 15 physically interact in vitro and localize to stereocilia tips in vivo, indicating that they form functional complexes. Sans, in contrast, localizes to vesicle-like structures beneath the apical membrane of stereocilia-displaying hair cells. How mutations in sans result in deafness and blindness is not well understood. Orthologs of myosin VIIa and protocadherin 15 have been identified in Drosophila melanogaster and their genetic analysis has identified essential roles in auditory perception and microvilli morphogenesis, respectively. PRINCIPAL FINDINGS: Here, we have identified and characterized the Drosophila ortholog of human sans. Drosophila Sans is expressed in tubular organs of the embryo, in lens-secreting cone cells of the adult eye, and in microvilli-displaying follicle cells during oogenesis. Sans mutants are viable, fertile, and mutant follicle cells appear to form microvilli, indicating that Sans is dispensable for fly development and microvilli morphogenesis in the follicle epithelium. In follicle cells, Sans protein localizes, similar to its vertebrate ortholog, to intracellular punctate structures, which we have identified as early endosomes associated with the syntaxin Avalanche. CONCLUSIONS: Our work is consistent with an evolutionary conserved function of Sans in vesicle trafficking. Furthermore it provides a significant basis for further understanding of the role of this Usher syndrome ortholog in development and disease.

  7. OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software.

    Science.gov (United States)

    Kriventseva, Evgenia V; Tegenfeldt, Fredrik; Petty, Tom J; Waterhouse, Robert M; Simão, Felipe A; Pozdnyakov, Igor A; Ioannidis, Panagiotis; Zdobnov, Evgeny M

    2015-01-01

    Orthology, refining the concept of homology, is the cornerstone of evolutionary comparative studies. With the ever-increasing availability of genomic data, inference of orthology has become instrumental for generating hypotheses about gene functions crucial to many studies. This update of the OrthoDB hierarchical catalog of orthologs (http://www.orthodb.org) covers 3027 complete genomes, including the most comprehensive set of 87 arthropods, 61 vertebrates, 227 fungi and 2627 bacteria (sampling the most complete and representative genomes from over 11,000 available). In addition to the most extensive integration of functional annotations from UniProt, InterPro, GO, OMIM, model organism phenotypes and COG functional categories, OrthoDB uniquely provides evolutionary annotations including rates of ortholog sequence divergence, copy-number profiles, sibling groups and gene architectures. We re-designed the entirety of the OrthoDB website from the underlying technology to the user interface, enabling the user to specify species of interest and to select the relevant orthology level by the NCBI taxonomy. The text searches allow use of complex logic with various identifiers of genes, proteins, domains, ontologies or annotation keywords and phrases. Gene copy-number profiles can also be queried. This release comes with the freely available underlying ortholog clustering pipeline (http://www.orthodb.org/software).

  8. Genomic analysis of NAC transcription factors in banana (Musa acuminata) and definition of NAC orthologous groups for monocots and dicots.

    Science.gov (United States)

    Cenci, Albero; Guignon, Valentin; Roux, Nicolas; Rouard, Mathieu

    2014-05-01

    Identifying the molecular mechanisms underlying tolerance to abiotic stresses is important in crop breeding. A comprehensive understanding of the gene families associated with drought tolerance is therefore highly relevant. NAC transcription factors form a large plant-specific gene family involved in the regulation of tissue development and responses to biotic and abiotic stresses. The main goal of this study was to set up a framework of orthologous groups determined by an expert sequence comparison of NAC genes from both monocots and dicots. In order to clarify the orthologous relationships among NAC genes of different species, we performed an in-depth comparative study of four divergent taxa, in dicots and monocots, whose genomes have already been completely sequenced: Arabidopsis thaliana, Vitis vinifera, Musa acuminata and Oryza sativa. Due to independent evolution, NAC copy number is highly variable in these plant genomes. Based on an expert NAC sequence comparison, we propose forty orthologous groups of NAC sequences that were probably derived from an ancestor gene present in the most recent common ancestor of dicots and monocots. These orthologous groups provide a curated resource for large-scale protein sequence annotation of NAC transcription factors. The established orthology relationships also provide a useful reference for NAC function studies in newly sequenced genomes such as M. acuminata and other plant species.

  9. The impact of gene duplication, insertion, deletion, lateral gene transfer and sequencing error on orthology inference: a simulation study.

    Science.gov (United States)

    Dalquen, Daniel A; Altenhoff, Adrian M; Gonnet, Gaston H; Dessimoz, Christophe

    2013-01-01

    The identification of orthologous genes, a prerequisite for numerous analyses in comparative and functional genomics, is commonly performed computationally from protein sequences. Several previous studies have compared the accuracy of orthology inference methods, but simulated data has not typically been considered in cross-method assessment studies. Yet, while dependent on model assumptions, simulation-based benchmarking offers unique advantages: contrary to empirical data, all aspects of simulated data are known with certainty. Furthermore, the flexibility of simulation makes it possible to investigate performance factors in isolation of one another.Here, we use simulated data to dissect the performance of six methods for orthology inference available as standalone software packages (Inparanoid, OMA, OrthoInspector, OrthoMCL, QuartetS, SPIMAP) as well as two generic approaches (bidirectional best hit and reciprocal smallest distance). We investigate the impact of various evolutionary forces (gene duplication, insertion, deletion, and lateral gene transfer) and technological artefacts (ambiguous sequences) on orthology inference. We show that while gene duplication/loss and insertion/deletion are well handled by most methods (albeit for different trade-offs of precision and recall), lateral gene transfer disrupts all methods. As for ambiguous sequences, which might result from poor sequencing, assembly, or genome annotation, we show that they affect alignment score-based orthology methods more strongly than their distance-based counterparts.

  10. Comparative sequence analysis of the Ghd7 orthologous regions revealed movement of Ghd7 in the grass genomes.

    Directory of Open Access Journals (Sweden)

    Lu Yang

    Full Text Available Ghd7 is an important rice gene that has a major effect on several agronomic traits, including yield. To reveal the origin of Ghd7 and sequence evolution of this locus, we performed a comparative sequence analysis of the Ghd7 orthologous regions from ten diploid Oryza species, Brachypodium distachyon, sorghum and maize. Sequence analysis demonstrated high gene collinearity across the genus Oryza and a disruption of collinearity among non-Oryza species. In particular, Ghd7 was not present in orthologous positions except in Oryza species. The Ghd7 regions were found to have low gene densities and high contents of repetitive elements, and that the sizes of orthologous regions varied tremendously. The large transposable element contents resulted in a high frequency of pseudogenization and gene movement events surrounding the Ghd7 loci. Annotation information and cytological experiments have indicated that Ghd7 is a heterochromatic gene. Ghd7 orthologs were identified in B. distachyon, sorghum and maize by phylogenetic analysis; however, the positions of orthologous genes differed dramatically as a consequence of gene movements in grasses. Rather, we identified sequence remnants of gene movement of Ghd7 mediated by illegitimate recombination in the B. distachyon genome.

  11. The impact of gene duplication, insertion, deletion, lateral gene transfer and sequencing error on orthology inference: a simulation study.

    Directory of Open Access Journals (Sweden)

    Daniel A Dalquen

    Full Text Available The identification of orthologous genes, a prerequisite for numerous analyses in comparative and functional genomics, is commonly performed computationally from protein sequences. Several previous studies have compared the accuracy of orthology inference methods, but simulated data has not typically been considered in cross-method assessment studies. Yet, while dependent on model assumptions, simulation-based benchmarking offers unique advantages: contrary to empirical data, all aspects of simulated data are known with certainty. Furthermore, the flexibility of simulation makes it possible to investigate performance factors in isolation of one another.Here, we use simulated data to dissect the performance of six methods for orthology inference available as standalone software packages (Inparanoid, OMA, OrthoInspector, OrthoMCL, QuartetS, SPIMAP as well as two generic approaches (bidirectional best hit and reciprocal smallest distance. We investigate the impact of various evolutionary forces (gene duplication, insertion, deletion, and lateral gene transfer and technological artefacts (ambiguous sequences on orthology inference. We show that while gene duplication/loss and insertion/deletion are well handled by most methods (albeit for different trade-offs of precision and recall, lateral gene transfer disrupts all methods. As for ambiguous sequences, which might result from poor sequencing, assembly, or genome annotation, we show that they affect alignment score-based orthology methods more strongly than their distance-based counterparts.

  12. Systematic discovery of unannotated genes in 11 yeast species using a database of orthologous genomic segments

    LENUS (Irish Health Repository)

    OhEigeartaigh, Sean S

    2011-07-26

    Abstract Background In standard BLAST searches, no information other than the sequences of the query and the database entries is considered. However, in situations where two genes from different species have only borderline similarity in a BLAST search, the discovery that the genes are located within a region of conserved gene order (synteny) can provide additional evidence that they are orthologs. Thus, for interpreting borderline search results, it would be useful to know whether the syntenic context of a database hit is similar to that of the query. This principle has often been used in investigations of particular genes or genomic regions, but to our knowledge it has never been implemented systematically. Results We made use of the synteny information contained in the Yeast Gene Order Browser database for 11 yeast species to carry out a systematic search for protein-coding genes that were overlooked in the original annotations of one or more yeast genomes but which are syntenic with their orthologs. Such genes tend to have been overlooked because they are short, highly divergent, or contain introns. The key features of our software - called SearchDOGS - are that the database entries are classified into sets of genomic segments that are already known to be orthologous, and that very weak BLAST hits are retained for further analysis if their genomic location is similar to that of the query. Using SearchDOGS we identified 595 additional protein-coding genes among the 11 yeast species, including two new genes in Saccharomyces cerevisiae. We found additional genes for the mating pheromone a-factor in six species including Kluyveromyces lactis. Conclusions SearchDOGS has proven highly successful for identifying overlooked genes in the yeast genomes. We anticipate that our approach can be adapted for study of further groups of species, such as bacterial genomes. More generally, the concept of doing sequence similarity searches against databases to which external

  13. Dynamic evolution of bz orthologous regions in the Andropogoneae and other grasses.

    Science.gov (United States)

    Wang, Qinghua; Dooner, Hugo K

    2012-10-01

    Genome structure exhibits remarkable plasticity within Zea mays. To examine how haplotype structure has evolved within the Andropogoneae tribe, we have analyzed the bz gene-rich region of maize (Zea mays), the Zea teosintes mays ssp. mexicana, luxurians and diploperennis, Tripsacum dactyloides, Coix lacryma-jobi and Sorghum propinquum. We sequenced and annotated BAC clones from these species and re-annotated the orthologous Sorghum bicolor region. Gene colinearity in the region is well conserved within the genus Zea. However, the orthologous regions of Coix and Sorghum exhibited several micro-rearrangements relative to Zea, including addition, truncation and deletion of genes. The stc1 gene, involved in the production of a terpenoid insect defense signal, is evolving particularly fast, and its progressive disappearance from some species is occurring by microhomology-mediated recombination. LTR retrotransposons are the main contributors to the dynamic evolution of the bz region. Common transposon insertion sites occur among haplotypes from different Zea mays sub-species, but not outside the species. As in Zea, different patterns of interspersion between genes and retrotransposons are observed in Sorghum. We estimate that the mean divergence times between maize and Tripsacum, Coix and Sorghum are 8.5, 12.1 and 12.4 million years ago, respectively, and that between Coix and Sorghum is 9.3 million years ago. A comparison of the bz orthologous regions of Zea, Sorghum and Coix with those of Brachypodium, Setaria and Oryza allows us to infer how the region has evolved by addition and deletion of genes in the approximately 50 million years since these genera diverged from a common progenitor.

  14. Characterization of AtSTOP1 orthologous genes in tobacco and other plant species.

    Science.gov (United States)

    Ohyama, Yoshinao; Ito, Hiroki; Kobayashi, Yuriko; Ikka, Takashi; Morita, Akio; Kobayashi, Masatomo; Imaizumi, Ryujiro; Aoki, Toshio; Komatsu, Kenji; Sakata, Yoichi; Iuchi, Satoshi; Koyama, Hiroyuki

    2013-08-01

    Aluminum (Al) and proton (H⁺) tolerances are essential traits for plants to adapt to acid soil environments. In Arabidopsis (Arabidopsis thaliana), these tolerances are mediated by a zinc-finger transcription factor, SENSITIVE TO PROTON RHIZOTOXICITY1 (AtSTOP1), which regulates the transcription of multiple genes critical for tolerance to both stressors. Here, the functions of orthologous proteins (STOP1-like proteins) in other plant species were characterized by reverse genetics analyses and in planta complementation assays. RNA interference of a gene for NtSTOP1 repressed Al and H⁺ tolerances of tobacco (Nicotiana tabacum) roots. Tobacco roots released citrate in response to Al, concomitant with the up-regulated transcription of an ortholog of an Al tolerance gene encoding a citrate-transporting multidrug and toxic compound extrusion protein. The RNA interference repression of NtSTOP1 blocked this process and also repressed the transcription of another orthologous gene for Al tolerance, ALUMINUM SENSITIVE3, which encodes a prokaryote-type transporter. These results demonstrated that NtSTOP1 regulates Al tolerance in tobacco through the transcriptional regulation of these genes. The in planta complementation assays revealed that other plant species, including woody plants, a legume, and a moss (Physcomitrella patens), possess functional STOP1-like proteins that can activate several H⁺ and Al-tolerance genes in Arabidopsis. Knocking out the gene encoding the STOP1-like protein decreased the Al tolerance of P. patens. Together, our results strongly suggest that transcriptional regulation by STOP1-like proteins is evolutionarily conserved among land plants and that it confers the ability to survive in acid soils through the transcriptional regulation of Al- and H⁺-tolerance genes.

  15. License - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available is database, under the license, as long as you comply with the following conditions: You must attribute this...PGDBj - Ortholog DB License License to Use This Database Last updated : 2014/04/04 You may use this database...se terms regarding the use of this database and the requirements you must follow ...in using this database. The license for this database is specified in the Creative Commons Attribution-Share Alike 2.1 Japan . If you...re . With regard to this database, you are licensed to: freely access part or whole of this database, and ac

  16. New Insights on Eggplant/Tomato/Pepper Synteny and Identification of Eggplant and Pepper Orthologous QTL

    Directory of Open Access Journals (Sweden)

    Riccardo Rinaldi

    2016-07-01

    Full Text Available Eggplant, pepper and tomato are the most exploited berry-producing vegetables within the Solanaceae family. Their genomes differ in size, but each has 12 chromosomes which have undergone rearrangements causing a redistribution of loci. The genome sequences of all three species are available but differ in coverage, assembly quality and percentage of anchorage.Determining their syntenic relationship and QTL orthology will contribute to exploit genomic resources and genetic data for key agronomic traits.The syntenic analysis between tomato and pepper based on the alignment of 34,727 tomato CDS to the pepper genome sequence, identified 19,734 unique hits. The resulting synteny map confirmed the 14 inversions and 10 translocations previously documented, but also highlighted 3 new translocations and 4 major new inversions. Furthermore, each of the 12 chromosomes exhibited a number of rearrangements involving small regions of 0.5-0.7 Mbp.Due to high fragmentation of the publicly available eggplant genome sequence, physical localization of most eggplant QTL was not possible, thus, we compared the organization of the eggplant genetic map with the genome sequence of both tomato and pepper. The eggplant/tomato syntenic map confirmed all the 10 translocations but only 9 of the 14 known inversions; on the other hand, a newly detected inversion was recognized while another one was not confirmed. The eggplant/pepper syntenic map confirmed 10 translocations and 8 inversions already detected and suggested a putative new translocation.In order to perform the assessment of eggplant and pepper QTL orthology, the eggplant and pepper sequence-based markers located in their respective genetic map were aligned onto the pepper genome. GBrowse in pepper was used as reference platform for QTL positioning. A set of 151 pepper QTL were located as well as 212 eggplant QTL, including 76 major QTL (PVE ≥ 10% affecting key agronomic traits. Most were confirmed to cluster in

  17. Orthologous endogenous retroviruses exhibit directional selection since the chimp-human split

    OpenAIRE

    Gemmell, Patrick; Hein, Jotun; Katzourakis, Aris

    2015-01-01

    Background Endogenous retroviruses (ERVs) are often viewed as selfish DNA that do not contribute to host phenotype. Yet ERVs have also been co-opted to play important roles in the maintenance of stem cell identity and placentation, amongst other things. This has led to debate over whether the typical ERV confers a cost or benefit upon the host. We studied the divergence of orthologous ERVs since the chimp-human split with the aim of assessing whether ERVs exert detectable fitness effects. Res...

  18. Transcriptome Profiling of the C. elegans Rb Ortholog Reveals Diverse Developmental Roles

    OpenAIRE

    Kirienko, Natalia V; Fay, David S.

    2007-01-01

    LIN-35 is the single C. elegans ortholog of the mammalian pocket protein family members, pRb, p107, and p130. To gain insight into the roles of pocket proteins during development, a microarray analysis was performed with lin-35 mutants. Stage-specific regulation patterns were revealed, indicating that LIN-35 plays diverse roles at distinct developmental stages. LIN-35 was found to repress the expression of many genes involved in cell proliferation in larvae, an activity that is carried out in...

  19. Tequila, a neurotrypsin ortholog, regulates long-term memory formation in Drosophila.

    Science.gov (United States)

    Didelot, Gérard; Molinari, Florence; Tchénio, Paul; Comas, Daniel; Milhiet, Elodie; Munnich, Arnold; Colleaux, Laurence; Preat, Thomas

    2006-08-11

    Mutations in the human neurotrypsin gene are associated with autosomal recessive mental retardation. To further understand the pathophysiological consequences of the lack of this serine protease, we studied Tequila (Teq), the Drosophila neurotrypsin ortholog, using associative memory as a behavioral readout. We found that teq inactivation resulted in a long-term memory (LTM)-specific defect. After LTM conditioning of wild-type flies, teq expression transiently increased in the mushroom bodies. Moreover, specific inhibition of teq expression in adult mushroom bodies resulted in a reversible LTM defect. Hence, the Teq pathway is essential for information processing in Drosophila.

  20. Versatile roles of CspA orthologs in complement inactivation of serum-resistant Lyme disease spirochetes.

    Science.gov (United States)

    Hammerschmidt, Claudia; Koenigs, Arno; Siegel, Corinna; Hallström, Teresia; Skerka, Christine; Wallich, Reinhard; Zipfel, Peter F; Kraiczy, Peter

    2014-01-01

    CspA of the Lyme disease spirochete Borrelia burgdorferi represents a key molecule in immune evasion, protecting borrelial cells from complement-mediated killing. As previous studies focused almost exclusively on CspA of B. burgdorferi, here we investigate the different binding capacities of CspA orthologs of Borrelia burgdorferi, B. afzelii, and B. spielmanii for complement regulator factor H and plasminogen and their ability to inhibit complement activation by either binding these host-derived plasma proteins or independently by direct interaction with components involved in formation of the lethal, pore-like terminal complement complex. To further examine their function in serum resistance in vivo, a serum-sensitive B. garinii strain was used to generate spirochetes, ectopically producing functional CspA orthologs. Irrespective of their species origin, all three CspA orthologs impart resistance to complement-mediated killing when produced in a serum-sensitive B. garinii surrogate strain. To analyze the inhibitory effect on complement activation and to assess the potential to inactivate C3b by binding of factor H and plasminogen, recombinant CspA orthologs were also investigated. All three CspA orthologs simultaneously bound factor H and plasminogen but differed in regard to their capacity to inactivate C3b via bound plasmin(ogen) and inhibit formation of the terminal complement complex. CspA of B. afzelii binds plasmin(ogen) and inhibits the terminal complement complex more efficiently than CspA of B. burgdorferi and B. spielmanii. Taken together, CspA orthologs of serum-resistant Lyme disease spirochetes act as multifunctional evasion molecules that inhibit complement on two central activation levels, C3b generation and assembly of the terminal complement complex.

  1. eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations

    DEFF Research Database (Denmark)

    Muller, J; Szklarczyk, D; Julien, P;

    2010-01-01

    The identification of orthologous relationships forms the basis for most comparative genomics studies. Here, we present the second version of the eggNOG database, which contains orthologous groups (OGs) constructed through identification of reciprocal best BLAST matches and triangular linkage clu...

  2. The Pea Photoperiod Response Gene STERILE NODES Is an Ortholog of LUX ARRHYTHMO.

    Science.gov (United States)

    Liew, Lim Chee; Hecht, Valérie; Sussmilch, Frances C; Weller, James L

    2014-06-01

    The STERILE NODES (SN) locus in pea (Pisum sativum) was one of the first photoperiod response genes to be described and provided early evidence for the genetic control of long-distance signaling in flowering-time regulation. Lines homozygous for recessive sn mutations are early flowering and photoperiod insensitive, with an increased ability to promote flowering across a graft union in short-day conditions. Here, we show that SN controls developmental regulation of genes in the FT family and rhythmic regulation of genes related to circadian clock function. Using a positional and functional candidate approach, we identify SN as the pea ortholog of LUX ARRHYTHMO, a GARP transcription factor from Arabidopsis (Arabidopsis thaliana) with an important role in circadian clock function. In addition to induced mutants, sequence analysis demonstrates the presence of at least three other independent, naturally occurring loss-of-function mutations among known sn cultivars. Examination of genetic and regulatory interactions between SN and two other circadian clock genes, HIGH RESPONSE TO PHOTOPERIOD (HR) and DIE NEUTRALIS (DNE), suggests a complex relationship in which HR regulates expression of SN and the role of DNE and HR in control of flowering is dependent on SN. These results extend previous work to show that pea orthologs of all three Arabidopsis evening complex genes regulate clock function and photoperiod-responsive flowering and suggest that the function of these genes may be widely conserved.

  3. The Cyclin-Dependent Kinase Ortholog pUL97 of Human Cytomegalovirus Interacts with Cyclins

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    Laura Graf

    2013-12-01

    Full Text Available The human cytomegalovirus (HCMV-encoded protein kinase, pUL97, is considered a cyclin-dependent kinase (CDK ortholog, due to shared structural and functional characteristics. The primary mechanism of CDK activation is binding to corresponding cyclins, including cyclin T1, which is the usual regulatory cofactor of CDK9. This study provides evidence of direct interaction between pUL97 and cyclin T1 using yeast two-hybrid and co-immunoprecipitation analyses. Confocal immunofluorescence revealed partial colocalization of pUL97 with cyclin T1 in subnuclear compartments, most pronounced in viral replication centres. The distribution patterns of pUL97 and cyclin T1 were independent of HCMV strain and host cell type. The sequence domain of pUL97 responsible for the interaction with cyclin T1 was between amino acids 231–280. Additional co-immunoprecipitation analyses showed cyclin B1 and cyclin A as further pUL97 interaction partners. Investigation of the pUL97-cyclin T1 interaction in an ATP consumption assay strongly suggested phosphorylation of pUL97 by the CDK9/cyclin T1 complex in a substrate concentration-dependent manner. This is the first demonstration of interaction between a herpesviral CDK ortholog and cellular cyclins.

  4. orthodenticle/otx ortholog expression in the anterior brain and eyes of Sepia officinalis (Mollusca, Cephalopoda).

    Science.gov (United States)

    Buresi, Auxane; Baratte, Sébastien; Da Silva, Corinne; Bonnaud, Laure

    2012-01-01

    The origin of cerebral structures is a major issue in both developmental and evolutionary biology. Among Lophotrochozoans, cephalopods present both a derived nervous system and an original body plan, therefore they constitute a key model to study the evolution of nervous system and molecular processes that control the neural organization. We characterized a partial sequence of an ortholog of otx2 in Sepia officinalis embryos, a gene specific to the anterior nervous system and eye development. By in situ hybridization, we assessed the expression pattern of otx2 during S. officinalis organogenesis and we showed that otx is expressed (1) in the eyes, from early to late developmental stages as observed in other species (2) in the nervous system during late developmental stages. The otx ortholog does not appear to be required for the precocious emergence of the nervous ganglia in cephalopods and is later expressed only in the most anterior ganglia of the future brain. Finally, otx expression becomes restricted to localized part of the brain, where it could be involved in the functional specification of the central nervous system of S. officinalis. These results suggest a conserved involvement of otx in eye maturation and development of the anterior neural structures in S. officinalis.

  5. A combined approach exploring gene function based on Worm-Human Orthology

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    Johnsen Robert

    2005-05-01

    Full Text Available Abstract Background Many aspects of the nematode Caenorhabditis elegans biology are conserved between invertebrates and vertebrates establishing this particular organism as an excellent genetic model. Because of its small size, large populations and self-fertilization of the hermaphrodite, functional predictions carried out by genetic modifications as well as RNAi screens, can be rapidly tested. Results In order to explore the function of a set of C. elegans genes of unknown function, as well as their potential functional roles in the human genome, we performed a phylogenetic analysis to select the most probable worm orthologs. A total of 13 C. elegans genes were subjected to down- regulation via RNAi and characterization of expression profiles using GFP strains. Previously unknown distinct expression patterns were observed for four of the analyzed genes, as well as four visible RNAi phenotypes. In addition, subcellular protein over-expression profiles of the human orthologs for seven out of the thirteen genes using human cells were also analyzed. Conclusion By combining a whole-organism approach using C. elegans with complementary experimental work done on human cell lines, this analysis extends currently available information on the selected set of genes.

  6. A combined approach exploring gene function based on Worm-Human Orthology

    Science.gov (United States)

    Tamas, Ivica; Hodges, Emily; Dessi, Patrick; Johnsen, Robert; Vaz Gomes, Ana

    2005-01-01

    Background Many aspects of the nematode Caenorhabditis elegans biology are conserved between invertebrates and vertebrates establishing this particular organism as an excellent genetic model. Because of its small size, large populations and self-fertilization of the hermaphrodite, functional predictions carried out by genetic modifications as well as RNAi screens, can be rapidly tested. Results In order to explore the function of a set of C. elegans genes of unknown function, as well as their potential functional roles in the human genome, we performed a phylogenetic analysis to select the most probable worm orthologs. A total of 13 C. elegans genes were subjected to down- regulation via RNAi and characterization of expression profiles using GFP strains. Previously unknown distinct expression patterns were observed for four of the analyzed genes, as well as four visible RNAi phenotypes. In addition, subcellular protein over-expression profiles of the human orthologs for seven out of the thirteen genes using human cells were also analyzed. Conclusion By combining a whole-organism approach using C. elegans with complementary experimental work done on human cell lines, this analysis extends currently available information on the selected set of genes. PMID:15877817

  7. Cloning and characterization of a FLORICAULA/LEAFY ortholog, PFL, in polygamous papaya

    Institute of Scientific and Technical Information of China (English)

    Qingyi YU; Paul H. MOORE; Henrik H. ALBERT; Adrienne H.K. ROADER; Ray MING

    2005-01-01

    The homologous genes FLORICAULA (FLO) in Antirrhinum and LEAFY (LFY) in Arabidopsis are known to regulate the initiation of flowering in these two distantly related plant species. These genes are necessary also for the expression of downstream genes that control floral organ identity. We used Arabidopsis LFY cDNA as a probe to clone and sequence a papaya ortholog of LFY, PFL. It encodes a protein that shares 61% identity with the Arabidopsis LFY gene and 71% identity with the LFYhomologs of the two woody tree species: California sycamore (Platanus racemosa) and black cottonwood (Populus trichocarpa). Despite the high sequence similarity within two conserved regions, the N-terminal proline-rich motif in papaya PFL differs from other members in the family. This difference may not affect the gene function of papaya PFL, since an equally divergent but a functional LFY ortholog NEEDLY of Pinus radiata has been reported. Genomic and BAC Southern analyses indicated that there is only one copy of PFL in the papaya genome. In situ hybridization experiments demonstrated that PFL is expressed at a relatively low level in leaf primordia,but it is expressed at a high level in the floral meristem. Quantitative PCR analyses revealed that PFL was expressed in flower buds of all three sex types - male, female, and hermaphrodite with marginal difference between hermaphrodite and unisexual flowers. These data suggest that PFL may play a similar role as LFY in flower development and has limited effect on sex differentiation in papaya.

  8. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

    DEFF Research Database (Denmark)

    Huerta-Cepas, Jaime; Szklarczyk, Damian; Forslund, Kristoffer;

    2016-01-01

    eggNOG is a public resource that provides Orthologous Groups (OGs) of proteins at different taxonomic levels, each with integrated and summarized functional annotations. Developments since the latest public release include changes to the algorithm for creating OGs across taxonomic levels, making ...

  9. Unresolved orthology and peculiar coding sequence properties of lamprey genes: the KCNA gene family as test case

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    Kuraku Shigehiro

    2011-06-01

    Full Text Available Abstract Background In understanding the evolutionary process of vertebrates, cyclostomes (hagfishes and lamprey occupy crucial positions. Resolving molecular phylogenetic relationships of cyclostome genes with gnathostomes (jawed vertebrates genes is indispensable in deciphering both the species tree and gene trees. However, molecular phylogenetic analyses, especially those including lamprey genes, have produced highly discordant results between gene families. To efficiently scrutinize this problem using partial genome assemblies of early vertebrates, we focused on the potassium voltage-gated channel, shaker-related (KCNA family, whose members are mostly single-exon. Results Seven sea lamprey KCNA genes as well as six elephant shark genes were identified, and their orthologies to bony vertebrate subgroups were assessed. In contrast to robustly supported orthology of the elephant shark genes to gnathostome subgroups, clear orthology of any sea lamprey gene could not be established. Notably, sea lamprey KCNA sequences displayed unique codon usage pattern and amino acid composition, probably associated with exceptionally high GC-content in their coding regions. This lamprey-specific property of coding sequences was also observed generally for genes outside this gene family. Conclusions Our results suggest that secondary modifications of sequence properties unique to the lamprey lineage may be one of the factors preventing robust orthology assessments of lamprey genes, which deserves further genome-wide validation. The lamprey lineage-specific alteration of protein-coding sequence properties needs to be taken into consideration in tackling the key questions about early vertebrate evolution.

  10. Mycoplasma hyopneumoniae and Mycoplasma flocculare differential domains from orthologous surface proteins induce distinct cellular immune responses in mice.

    Science.gov (United States)

    Leal, Fernanda Munhoz Dos Anjos; Virginio, Veridiana Gomes; Martello, Carolina Lumertz; Paes, Jéssica Andrade; Borges, Thiago J; Jaeger, Natália; Bonorino, Cristina; Ferreira, Henrique Bunselmeyer

    2016-07-15

    Mycoplasma hyopneumoniae and Mycoplasma flocculare are two genetically close species found in the swine respiratory tract. Despite their similarities, while M. hyopneumoniae is the causative agent of porcine enzootic pneumonia, M. flocculare is a commensal bacterium. Genomic and transcriptional comparative analyses so far failed to explain the difference in pathogenicity between these two species. We then hypothesized that such difference might be, at least in part, explained by amino acid sequence and immunological or functional differences between ortholog surface proteins. In line with that, it was verified that approximately 85% of the ortholog surface proteins from M. hyopneumoniae 7448 and M. flocculare present one or more differential domains. To experimentally assess possible immunological implications of this kind of difference, the extracellular differential domains from one pair of orthologous surface proteins (MHP7448_0612, from M. hyopneumoniae, and MF_00357, from M. flocculare) were expressed in E. coli and used to immunize mice. The recombinant polypeptides (rMHP61267-169 and rMF35767-196, respectively) induced distinct cellular immune responses. While, rMHP61267-169 induced both Th1 and Th2 responses, rMF35767-196 induced just an early pro-inflammatory response. These results indicate that immunological properties determined by differential domains in orthologous surface protein might play a role in pathogenicity, contributing to elicit specific and differential immune responses against each species.

  11. Development and bin mapping of a Rosaceae Conserved Ortholog Set (COS of markers

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    Kozik Alex

    2009-01-01

    Full Text Available Abstract Background Detailed comparative genome analyses within the economically important Rosaceae family have not been conducted. This is largely due to the lack of conserved gene-based molecular markers that are transferable among the important crop genera within the family [e.g. Malus (apple, Fragaria (strawberry, and Prunus (peach, cherry, apricot and almond]. The lack of molecular markers and comparative whole genome sequence analysis for this family severely hampers crop improvement efforts as well as QTL confirmation and validation studies. Results We identified a set of 3,818 rosaceaous unigenes comprised of two or more ESTs that correspond to single copy Arabidopsis genes. From this Rosaceae Conserved Orthologous Set (RosCOS, 1039 were selected from which 857 were used for the development of intron-flanking primers and allele amplification. This led to successful amplification and subsequent mapping of 613 RosCOS onto the Prunus TxE reference map resulting in a genome-wide coverage of 0.67 to 1.06 gene-based markers per cM per linkage group. Furthermore, the RosCOS primers showed amplification success rates from 23 to 100% across the family indicating that a substantial part of the RosCOS primers can be directly employed in other less studied rosaceaous crops. Comparisons of the genetic map positions of the RosCOS with the physical locations of the orthologs in the Populus trichocarpa genome identified regions of colinearity between the genomes of Prunus-Rosaceae and Populus-Salicaceae. Conclusion Conserved orthologous genes are extremely useful for the analysis of genome evolution among closely and distantly related species. The results presented in this study demonstrate the considerable potential of the mapped Prunus RosCOS for genome-wide marker employment and comparative whole genome studies within the Rosaceae family. Moreover, these markers will also function as useful anchor points for the genome sequencing efforts currently

  12. The Fission Yeast FANCM Ortholog Directs Non-Crossover Recombination During Meiosis

    Science.gov (United States)

    Lorenz, Alexander; Osman, Fekret; Sun, Weili; Nandi, Saikat; Steinacher, Roland; Whitby, Matthew C.

    2012-01-01

    The formation of healthy gametes depends on programmed DNA double strand breaks (DSBs), which are each repaired as a crossover (CO) or non-crossover (NCO) from a homologous template. Although most of these DSBs are repaired without giving COs, little is known about the genetic requirements of NCO-specific recombination. We show that Fml1, the Fanconi anemia complementation group M (FANCM)-ortholog of Schizosaccharomyces pombe, directs the formation of NCOs during meiosis in competition with the Mus81-dependent pro-CO pathway. We also define the Rad51/Dmc1-mediator Swi5-Sfr1 as a major determinant in biasing the recombination process in favour of Mus81, to ensure the appropriate amount of COs to guide meiotic chromosome segregation. The conservation of these proteins from yeast to Humans suggests that this interplay may be a general feature of meiotic recombination. PMID:22723423

  13. Expression and in vitro properties of guinea pig IL-5: Comparison to human and murine orthologs

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    Clay W Scott

    2000-01-01

    Full Text Available Interleukin-5 (IL-5 is a key mediator of eosinophilic inflammation. The biological role of this cytokine in an allergic airway inflammatory response has been widely demonstrated in guinea pigs, yet the interaction of guinea pig IL-5 (gpIL-5 with its receptor has not been studied. Experiments were performed to quantitate the interaction of gpIL-5 with gpIL-5r and to compare this affinity with that of hIL-5 and mIL-5 and their cognate receptors. The cross-species affinity and agonist efficacy were evaluated to see if gpIL-5r had a restricted species reactivity (as is the case with mIL-5r or did not distinguish between IL-5 orthologs (similar to hIL-5r. gpIL-5 was cloned using mRNA isolated from cells obtained by bronchoalveolar lavage. Recombinant gpIL-5 was expressed in T.ni insect cells and purified from spent media. Binding assays were performed using insect cells expressing hIL-5rαβ or gpIL-5rαβ1 as previously described (Cytokine, 12:858–866, 2000 or using B13 cells which express mIL-5r. The agonist potency and efficacy properties of each IL-5 ortholog were evaluated by quantitating the proliferative response of hum an TF-1 cells and murine B13 cells. gpIL-5 bound with high affinity to recombinant gpIL-5r as demonstrated by displacing [125I]hIL-5 (Ki = 160 pM. gpIL-5 also bound to hIL-5r with high affinity (Ki = 750 pM. hIL-5 and mIL-5 showed similar, high-affinity binding profiles to both gpIL-5r and hIL-5r. In contrast, gpIL-5 and hIL5 did not bind to the mIL-5r as demonstrated by an inability to displace [125I]mIL-5, even at 1000-fold molar excess. These differences in affinity for IL-5r orthologs correlated with bioassay results: human TF1 cells showed roughly com parable proliferative responses to guinea pig, hum an and murine IL-5 whereas murine B13 cells showed a strong preference for murine over guinea pig and human IL-5(EC50 = 1.9, 2200 and 720 pM, respectively. Recombinant gpIL-5 binds to the gpIL-5r with high affinity, similar

  14. Suiformes orthologous satellite DNAs as a hallmark of Pecari tajacu and Tayassu pecari (Tayassuidae) evolutionary rearrangements.

    Science.gov (United States)

    Adega, Filomena; Chaves, Raquel; Guedes-Pinto, Henrique

    2008-12-01

    In a broad general way, eukaryotic satellite DNA sequences are characterized by a highly dynamic molecular behavior due to concerted evolution that leads to rapid change between repeat sequences of different species, achieved by amplification of new variants during speciation or by gradual sequence evolution due to the accumulation of nucleotide substitutions. There are, although exceptions for this almost universal rule. We isolated variants from both the Mc1 and Ac2 pig (Sus scrofa, Suidae) satellite DNA families from the genomes of two Tayassuidae members: Pecari tajacu and Tayassu pecari, which have highly derived karyotypes. The presence of these sequences in both families' genomes (Suidae and Tayassuidae) implies their existence in a common ancestor, what confers to the variants the status of orthology and the approximate age of, at least 40 million years. While at the molecular composition level these orthologous sequences are highly homologous, cross-species physical mapping revealed a completely different chromosomal location in Suidae versus Tayassuidae families, most probably, reflecting the high level of divergence and chromosomes evolution pathways after radiation of each family. Detailed comparative analysis of the satellites assignment on the peccary's chromosomes revealed its co-localization with homologous evolutionary breakpoints in both species, suggesting their involvement in the rearrangement events. The complex behavior of the repeats evolution in the pig/peccaries genomes is here clearly illustrated. These sequences are molecularly preserved for a considerable period of time and display slow rates of sequence change, but show a dynamic motion behavior throughout the peccary's genomes that accompanied the great architectonic reorganization of Tayassuidae chromosomes during evolution.

  15. Drug target prediction and prioritization: using orthology to predict essentiality in parasite genomes

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    Hall Ross S

    2010-04-01

    Full Text Available Abstract Background New drug targets are urgently needed for parasites of socio-economic importance. Genes that are essential for parasite survival are highly desirable targets, but information on these genes is lacking, as gene knockouts or knockdowns are difficult to perform in many species of parasites. We examined the applicability of large-scale essentiality information from four model eukaryotes, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus and Saccharomyces cerevisiae, to discover essential genes in each of their genomes. Parasite genes that lack orthologues in their host are desirable as selective targets, so we also examined prediction of essential genes within this subset. Results Cross-species analyses showed that the evolutionary conservation of genes and the presence of essential orthologues are each strong predictors of essentiality in eukaryotes. Absence of paralogues was also found to be a general predictor of increased relative essentiality. By combining several orthology and essentiality criteria one can select gene sets with up to a five-fold enrichment in essential genes compared with a random selection. We show how quantitative application of such criteria can be used to predict a ranked list of potential drug targets from Ancylostoma caninum and Haemonchus contortus - two blood-feeding strongylid nematodes, for which there are presently limited sequence data but no functional genomic tools. Conclusions The present study demonstrates the utility of using orthology information from multiple, diverse eukaryotes to predict essential genes. The data also emphasize the challenge of identifying essential genes among those in a parasite that are absent from its host.

  16. Phyletic profiling with cliques of orthologs is enhanced by signatures of paralogy relationships.

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    Nives Skunca

    Full Text Available New microbial genomes are sequenced at a high pace, allowing insight into the genetics of not only cultured microbes, but a wide range of metagenomic collections such as the human microbiome. To understand the deluge of genomic data we face, computational approaches for gene functional annotation are invaluable. We introduce a novel model for computational annotation that refines two established concepts: annotation based on homology and annotation based on phyletic profiling. The phyletic profiling-based model that includes both inferred orthologs and paralogs-homologs separated by a speciation and a duplication event, respectively-provides more annotations at the same average Precision than the model that includes only inferred orthologs. For experimental validation, we selected 38 poorly annotated Escherichia coli genes for which the model assigned one of three GO terms with high confidence: involvement in DNA repair, protein translation, or cell wall synthesis. Results of antibiotic stress survival assays on E. coli knockout mutants showed high agreement with our model's estimates of accuracy: out of 38 predictions obtained at the reported Precision of 60%, we confirmed 25 predictions, indicating that our confidence estimates can be used to make informed decisions on experimental validation. Our work will contribute to making experimental validation of computational predictions more approachable, both in cost and time. Our predictions for 998 prokaryotic genomes include ~400000 specific annotations with the estimated Precision of 90%, ~19000 of which are highly specific-e.g. "penicillin binding," "tRNA aminoacylation for protein translation," or "pathogenesis"-and are freely available at http://gorbi.irb.hr/.

  17. Construction and analysis of tag single nucleotide polymorphism maps for six human-mouse orthologous candidate genes in type 1 diabetes

    Science.gov (United States)

    Maier, Lisa M; Smyth, Deborah J; Vella, Adrian; Payne, Felicity; Cooper, Jason D; Pask, Rebecca; Lowe, Christopher; Hulme, John; Smink, Luc J; Fraser, Heather; Moule, Carolyn; Hunter, Kara M; Chamberlain, Giselle; Walker, Neil; Nutland, Sarah; Undlien, Dag E; Rønningen, Kjersti S; Guja, Cristian; Ionescu-Tîrgovişte, Constantin; Savage, David A; Strachan, David P; Peterson, Laurence B; Todd, John A; Wicker, Linda S; Twells, Rebecca C

    2005-01-01

    Background One strategy to help identify susceptibility genes for complex, multifactorial diseases is to map disease loci in a representative animal model of the disorder. The nonobese diabetic (NOD) mouse is a model for human type 1 diabetes. Linkage and congenic strain analyses have identified several NOD mouse Idd (insulin dependent diabetes) loci, which have been mapped to small chromosome intervals, for which the orthologous regions in the human genome can be identified. Here, we have conducted re-sequencing and association analysis of six orthologous genes identified in NOD Idd loci: NRAMP1/SLC11A1 (orthologous to Nramp1/Slc11a1 in Idd5.2), FRAP1 (orthologous to Frap1 in Idd9.2), 4-1BB/CD137/TNFRSF9 (orthologous to 4-1bb/Cd137/Tnrfrsf9 in Idd9.3), CD101/IGSF2 (orthologous to Cd101/Igsf2 in Idd10), B2M (orthologous to B2m in Idd13) and VAV3 (orthologous to Vav3 in Idd18). Results Re-sequencing of a total of 110 kb of DNA from 32 or 96 type 1 diabetes cases yielded 220 single nucleotide polymorphisms (SNPs). Sixty-five SNPs, including 54 informative tag SNPs, and a microsatellite were selected and genotyped in up to 1,632 type 1 diabetes families and 1,709 cases and 1,829 controls. Conclusion None of the candidate regions showed evidence of association with type 1 diabetes (P values > 0.2), indicating that common variation in these key candidate genes does not play a major role in type 1 diabetes susceptibility in the European ancestry populations studied. PMID:15720714

  18. Construction and analysis of tag single nucleotide polymorphism maps for six human-mouse orthologous candidate genes in type 1 diabetes

    Directory of Open Access Journals (Sweden)

    Savage David A

    2005-02-01

    Full Text Available Abstract Background One strategy to help identify susceptibility genes for complex, multifactorial diseases is to map disease loci in a representative animal model of the disorder. The nonobese diabetic (NOD mouse is a model for human type 1 diabetes. Linkage and congenic strain analyses have identified several NOD mouse Idd (insulin dependent diabetes loci, which have been mapped to small chromosome intervals, for which the orthologous regions in the human genome can be identified. Here, we have conducted re-sequencing and association analysis of six orthologous genes identified in NOD Idd loci: NRAMP1/SLC11A1 (orthologous to Nramp1/Slc11a1 in Idd5.2, FRAP1 (orthologous to Frap1 in Idd9.2, 4-1BB/CD137/TNFRSF9 (orthologous to 4-1bb/Cd137/Tnrfrsf9 in Idd9.3, CD101/IGSF2 (orthologous to Cd101/Igsf2 in Idd10, B2M (orthologous to B2m in Idd13 and VAV3 (orthologous to Vav3 in Idd18. Results Re-sequencing of a total of 110 kb of DNA from 32 or 96 type 1 diabetes cases yielded 220 single nucleotide polymorphisms (SNPs. Sixty-five SNPs, including 54 informative tag SNPs, and a microsatellite were selected and genotyped in up to 1,632 type 1 diabetes families and 1,709 cases and 1,829 controls. Conclusion None of the candidate regions showed evidence of association with type 1 diabetes (P values > 0.2, indicating that common variation in these key candidate genes does not play a major role in type 1 diabetes susceptibility in the European ancestry populations studied.

  19. High-density linkage mapping and evolution of paralogs and orthologs in Salix and Populus

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    Öst Torbjörn

    2010-02-01

    Full Text Available Abstract Background Salix (willow and Populus (poplar are members of the Salicaceae family and they share many ecological as well as genetic and genomic characteristics. The interest of using willow for biomass production is growing, which has resulted in increased pressure on breeding of high yielding and resistant clones adapted to different environments. The main purpose of this work was to develop dense genetic linkage maps for mapping of traits related to yield and resistance in willow. We used the Populus trichocarpa genome to extract evenly spaced markers and mapped the orthologous loci in the willow genome. The marker positions in the two genomes were used to study genome evolution since the divergence of the two lineages some 45 mya. Results We constructed two linkage maps covering the 19 linkage groups in willow. The most detailed consensus map, S1, contains 495 markers with a total genetic distance of 2477 cM and an average distance of 5.0 cM between the markers. The S3 consensus map contains 221 markers and has a total genetic distance of 1793 cM and an average distance of 8.1 cM between the markers. We found high degree of synteny and gene order conservation between willow and poplar. There is however evidence for two major interchromosomal rearrangements involving poplar LG I and XVI and willow LG Ib, suggesting a fission or a fusion in one of the lineages, as well as five intrachromosomal inversions. The number of silent substitutions were three times lower (median: 0.12 between orthologs than between paralogs (median: 0.37 - 0.41. Conclusions The relatively slow rates of genomic change between willow and poplar mean that the genomic resources in poplar will be most useful in genomic research in willow, such as identifying genes underlying QTLs of important traits. Our data suggest that the whole-genome duplication occurred long before the divergence of the two genera, events which have until now been regarded as contemporary

  20. Expression and actions of GnIH and its orthologs in vertebrates: Current status and advanced knowledge.

    Science.gov (United States)

    Ullah, Rahim; Shen, Yi; Zhou, Yu-Dong; Huang, Ke; Fu, Jun-Fen; Wahab, Fazal; Shahab, Muhammad

    2016-10-01

    The physiology of reproduction is very complex and is regulated by multiple factors, including a number of hypothalamic neuropeptides. In last few decades, various neuropeptides have been discovered to be involved in stimulation or inhibition of reproduction. In 2000, Tsutsui and colleagues uncovered gonadotropin-inhibitory hormone (GnIH), a neuropeptide generating inhibitory drive to the reproductive axis, in the brain of Coturnix quail. Afterward, GnIH orthologs were discovered in other vertebrates from fish to mammals including human. In these vertebrates, all the discovered GnIH and its ortholgs have LPXRFamide (X=L or Q) sequence at C-terminus. GnIH orthologs of mammals and primates are also termed as RFamide-related peptide (RFRP)-1 and -3 that too have an LPXRFamide (X=L or Q) motif at their C-terminus. GnIH and its orthologs form a member of the RFamide peptide family. GnIH signals via its canonical G protein coupled receptor 147 (GPR147). Both GnIH and GPR147 are expressed in hypothalamus and other brain regions. Besides actions through the hypothalamic GnRH and kisspeptinergic neurons, GnIH-GPR147 signaling exerts inhibitory effect on the reproductive axis via pituitary gonadotropes and directly at gonadal level. Various factors including availability and quality of food, photoperiod, temperature, social interaction, various stresses and some diseases modulate GnIH-GPR147 signaling. In this review, we have discussed expression and actions of GnIH and its orthologs in vertebrates. Special emphasis is given on the role of GnIH-GPR147 signaling pathway in the regulation of reproduction. We have also reviewed and discussed currently available literature on the participation of GnIH-GPR147 signaling pathway in the stress modulation of reproduction.

  1. Identification and characterization of orthologs of AtNHX5 and AtNHX6 in Brassica napus

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    Brett Andrew Ford

    2012-09-01

    Full Text Available Improving crop species by breeding for salt tolerance or introducing salt tolerant traits is one method of increasing crop yields in saline affected areas. The model plant species Arabidopsis thaliana has been extensively studied and there is substantial information available about the function and importance of many genes and proteins involved in salt tolerance. The identification and characterization of A. thaliana orthologs in species such as Brassica napus (oilseed rape can prove difficult due to the significant genomic changes that have occurred since their divergence approximately 20 million years ago. The recently released B. rapa genome provides an excellent resource for comparative studies of Arabidopsis and the cultivated Brassica species, and facilitates the identification of Brassica species orthologs which may be of agronomic importance. Sodium hydrogen antiporter (NHX proteins transport a sodium or potassium ion in exchange for a hydrogen ion in the other direction across a membrane. In A. thaliana there are eight members of the NHX family designated AtNHX1-8 that can be sub-divided into three clades (plasma membrane (PM, intracellular class I (IC-I and intracellular class II (IC-II based on their subcellular localization. In plants, many NHX proteins are primary determinants of salt tolerance and act by transporting Na+ out of the cytosol where it would otherwise accumulate to toxic levels. Significant work has been done analyzing both PM and IC-I clade members role in salt tolerance in a variety of plant species but relatively little analysis has been described for the IC-II clade. Here we describe the identification of B. napus orthologs of AtNHX5 and AtNHX6, using the Brassica rapa genome sequence, macro- and micro-synteny analysis, comparative expression and promoter motif analysis, and highlight the value of these multiple approaches for identifying true orthologs in closely related species with multiple paralogs.

  2. Genomic structure and expression analysis of the RNase kappa family ortholog gene in the insect Ceratitis capitata.

    Science.gov (United States)

    Rampias, Theodoros N; Fragoulis, Emmanuel G; Sideris, Diamantis C

    2008-12-01

    Cc RNase is the founding member of the recently identified RNase kappa family, which is represented by a single ortholog in a wide range of animal taxonomic groups. Although the precise biological role of this protein is still unknown, it has been shown that the recombinant proteins isolated so far from the insect Ceratitis capitata and from human exhibit ribonucleolytic activity. In this work, we report the genomic organization and molecular evolution of the RNase kappa gene from various animal species, as well as expression analysis of the ortholog gene in C. capitata. The high degree of amino acid sequence similarity, in combination with the fact that exon sizes and intronic positions are extremely conserved among RNase kappa orthologs in 15 diverse genomes from sea anemone to human, imply a very significant biological function for this enzyme. In C. capitata, two forms of RNase kappa mRNA (0.9 and 1.5 kb) with various lengths of 3' UTR were identified as alternative products of a single gene, resulting from the use of different polyadenylation signals. Both transcripts are expressed in all insect tissues and developmental stages. Sequence analysis of the extended region of the longer transcript revealed the existence of three mRNA instability motifs (AUUUA) and five poly(U) tracts, whose functional importance in RNase kappa mRNA decay remains to be explored.

  3. Drosophila pico and its mammalian ortholog lamellipodin activate serum response factor and promote cell proliferation.

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    Lyulcheva, Ekaterina; Taylor, Eleanor; Michael, Magdalene; Vehlow, Anne; Tan, Shengjiang; Fletcher, Adam; Krause, Matthias; Bennett, Daimark

    2008-11-01

    MIG-10/RIAM/lamellipodin (MRL) proteins link activated Ras-GTPases with actin regulatory Ena/VASP proteins to induce local changes in cytoskeletal dynamics and cell motility. MRL proteins alter monomeric (G):filamentous (F) actin ratios, but the impact of these changes had not been fully appreciated. We report here that the Drosophila MRL ortholog, pico, is required for tissue and organismal growth. Reduction in pico levels resulted in reduced cell division rates, growth retardation, increased G:F actin ratios and lethality. Conversely, pico overexpression reduced G:F actin ratios and promoted tissue overgrowth in an epidermal growth factor (EGF) receptor (EGFR)-dependent manner. Consistently, in HeLa cells, lamellipodin was required for EGF-induced proliferation. We show that pico and lamellipodin share the ability to activate serum response factor (SRF), a transcription factor that responds to reduced G:F-actin ratios via its co-factor Mal. Genetics data indicate that mal/SRF levels are important for pico-mediated tissue growth. We propose that MRL proteins link EGFR activation to mitogenic SRF signaling via changes in actin dynamics.

  4. ATX-2, the C. elegans Ortholog of Human Ataxin-2, Regulates Centrosome Size and Microtubule Dynamics.

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    Michael D Stubenvoll

    2016-09-01

    Full Text Available Centrosomes are critical sites for orchestrating microtubule dynamics, and exhibit dynamic changes in size during the cell cycle. As cells progress to mitosis, centrosomes recruit more microtubules (MT to form mitotic bipolar spindles that ensure proper chromosome segregation. We report a new role for ATX-2, a C. elegans ortholog of Human Ataxin-2, in regulating centrosome size and MT dynamics. ATX-2, an RNA-binding protein, forms a complex with SZY-20 in an RNA-independent fashion. Depleting ATX-2 results in embryonic lethality and cytokinesis failure, and restores centrosome duplication to zyg-1 mutants. In this pathway, SZY-20 promotes ATX-2 abundance, which inversely correlates with centrosome size. Centrosomes depleted of ATX-2 exhibit elevated levels of centrosome factors (ZYG-1, SPD-5, γ-Tubulin, increasing MT nucleating activity but impeding MT growth. We show that ATX-2 influences MT behavior through γ-Tubulin at the centrosome. Our data suggest that RNA-binding proteins play an active role in controlling MT dynamics and provide insight into the control of proper centrosome size and MT dynamics.

  5. Monitoring autophagic flux using Ref(2)P, the Drosophila p62 ortholog.

    Science.gov (United States)

    DeVorkin, Lindsay; Gorski, Sharon M

    2014-09-02

    Human p62, also known as Sequestome-1 (SQSTM1), is a multifunctional scaffold protein that contains many domains, including a Phox/Bem1P (PB1) multimerization domain, an ubiquitin-associated (UBA) domain, and a light chain 3 (LC3) recognition sequence. p62 binds ubiquitinated proteins and targets them for degradation by the proteasome. In addition, p62 directly binds LC3; this may serve as a mechanism to deliver ubiquitinated proteins for degradation by autophagy. During this process, p62 itself is degraded. The inhibition of autophagy leads to the accumulation of p62, indicating that it can be used as a marker of autophagic flux. Ref(2)P (refractory to sigma P), the Drosophila ortholog of p62, is also required for the formation of ubiquitinated protein aggregates. Ref(2)P contains a putative LC3-interacting region, and genetic inhibition of autophagy in Drosophila leads to the accumulation of Ref(2)P protein levels. Thus, like p62, Ref(2)P may serve as a marker of autophagic flux. Here we provide two procedures to examine Ref(2)P protein levels in Drosophila ovaries.

  6. Drosophila Pico and Its Mammalian Ortholog Lamellipodin Activate Serum Response Factor and Promote Cell Proliferation

    Science.gov (United States)

    Lyulcheva, Ekaterina; Taylor, Eleanor; Michael, Magdalene; Vehlow, Anne; Tan, Shengjiang; Fletcher, Adam; Krause, Matthias; Bennett, Daimark

    2008-01-01

    Summary MIG-10/RIAM/lamellipodin (MRL) proteins link activated Ras-GTPases with actin regulatory Ena/VASP proteins to induce local changes in cytoskeletal dynamics and cell motility. MRL proteins alter monomeric (G):filamentous (F) actin ratios, but the impact of these changes had not been fully appreciated. We report here that the Drosophila MRL ortholog, pico, is required for tissue and organismal growth. Reduction in pico levels resulted in reduced cell division rates, growth retardation, increased G:F actin ratios and lethality. Conversely, pico overexpression reduced G:F actin ratios and promoted tissue overgrowth in an epidermal growth factor (EGF) receptor (EGFR)-dependent manner. Consistently, in HeLa cells, lamellipodin was required for EGF-induced proliferation. We show that pico and lamellipodin share the ability to activate serum response factor (SRF), a transcription factor that responds to reduced G:F-actin ratios via its co-factor Mal. Genetics data indicate that mal/SRF levels are important for pico-mediated tissue growth. We propose that MRL proteins link EGFR activation to mitogenic SRF signaling via changes in actin dynamics. PMID:19000833

  7. Inference of gene-phenotype associations via protein-protein interaction and orthology.

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    Panwen Wang

    Full Text Available One of the fundamental goals of genetics is to understand gene functions and their associated phenotypes. To achieve this goal, in this study we developed a computational algorithm that uses orthology and protein-protein interaction information to infer gene-phenotype associations for multiple species. Furthermore, we developed a web server that provides genome-wide phenotype inference for six species: fly, human, mouse, worm, yeast, and zebrafish. We evaluated our inference method by comparing the inferred results with known gene-phenotype associations. The high Area Under the Curve values suggest a significant performance of our method. By applying our method to two human representative diseases, Type 2 Diabetes and Breast Cancer, we demonstrated that our method is able to identify related Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways. The web server can be used to infer functions and putative phenotypes of a gene along with the candidate genes of a phenotype, and thus aids in disease candidate gene discovery. Our web server is available at http://jjwanglab.org/PhenoPPIOrth.

  8. Behavioral analysis of the huntingtin-associated protein 1 ortholog trak-1 in Caenorhabditis elegans.

    Science.gov (United States)

    Norflus, Fran; Bu, Jingnan; Guyton, Evon; Gutekunst, Claire-Anne

    2016-09-01

    The precise role of huntingtin-associated protein 1 (HAP1) is not known, but studies have shown that it is important for early development and survival. A Caenorhabditis elegans ortholog of HAP1, T27A3.1 (also called trak-1), has been found and is expressed in a subset of neurons. Potential behavioral functions of three knockout lines of T27A3.1 were examined. From its suspected role in mice we hypothesize that T27A3.1 might be involved in egg hatching and early growth, mechanosensation, chemosensation, sensitivity to osmolarity, and synaptic transmission. Our studies show that the knockout worms are significantly different from the wild-type (WT) worms only in the synaptic transmission test, which was measured by adding aldicarb, an acetylcholinesterase inhibitor. The change in function was determined by measuring the number of worms paralyzed. However, when the T27A3.1 worms were tested for egg hatching and early growth, mechanosensation, chemosensation, and sensitivity to osmolarity, there were no significant differences between the knockout and WT worms. © 2016 Wiley Periodicals, Inc.

  9. Morphogenesis of Strongyloides stercoralis infective larvae requires the DAF-16 ortholog FKTF-1.

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    Michelle L Castelletto

    2009-04-01

    Full Text Available Based on metabolic and morphological similarities between infective third-stage larvae of parasitic nematodes and dauer larvae of Caenorhabditis elegans, it is hypothesized that similar genetic mechanisms control the development of these forms. In the parasite Strongyloides stercoralis, FKTF-1 is an ortholog of DAF-16, a forkhead transcription factor that regulates dauer larval development in C. elegans. Using transgenesis, we investigated the role of FKTF-1 in S. stercoralis' infective larval development. In first-stage larvae, GFP-tagged recombinant FKTF-1b localizes to the pharynx and hypodermis, tissues remodeled in infective larvae. Activating and inactivating mutations at predicted AKT phosphorylation sites on FKTF-1b give constitutive cytoplasmic and nuclear localization of the protein, respectively, indicating that its post-translational regulation is similar to other FOXO-class transcription factors. Mutant constructs designed to interfere with endogenous FKTF-1b function altered the intestinal and pharyngeal development of the larvae and resulted in some transgenic larvae failing to arrest in the infective stage. Our findings indicate that FKTF-1b is required for proper morphogenesis of S. stercoralis infective larvae and support the overall hypothesis of similar regulation of dauer development in C. elegans and the formation of infective larvae in parasitic nematodes.

  10. Ohgata, the Single Drosophila Ortholog of Human Cereblon, Regulates Insulin Signaling-dependent Organismic Growth.

    Science.gov (United States)

    Wakabayashi, Satoru; Sawamura, Naoya; Voelzmann, André; Broemer, Meike; Asahi, Toru; Hoch, Michael

    2016-11-25

    Cereblon (CRBN) is a substrate receptor of the E3 ubiquitin ligase complex that is highly conserved in animals and plants. CRBN proteins have been implicated in various biological processes such as development, metabolism, learning, and memory formation, and their impairment has been linked to autosomal recessive non-syndromic intellectual disability and cancer. Furthermore, human CRBN was identified as the primary target of thalidomide teratogenicity. Data on functional analysis of CRBN family members in vivo, however, are still scarce. Here we identify Ohgata (OHGT), the Drosophila ortholog of CRBN, as a regulator of insulin signaling-mediated growth. Using ohgt mutants that we generated by targeted mutagenesis, we show that its loss results in increased body weight and organ size without changes of the body proportions. We demonstrate that ohgt knockdown in the fat body, an organ analogous to mammalian liver and adipose tissue, phenocopies the growth phenotypes. We further show that overgrowth is due to an elevation of insulin signaling in ohgt mutants and to the down-regulation of inhibitory cofactors of circulating Drosophila insulin-like peptides (DILPs), named acid-labile subunit and imaginal morphogenesis protein-late 2. The two inhibitory proteins were previously shown to be components of a heterotrimeric complex with growth-promoting DILP2 and DILP5. Our study reveals OHGT as a novel regulator of insulin-dependent organismic growth in Drosophila.

  11. Identification of novel human damage response proteins targeted through yeast orthology.

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    J Peter Svensson

    Full Text Available Studies in Saccharomyces cerevisiae show that many proteins influence cellular survival upon exposure to DNA damaging agents. We hypothesized that human orthologs of these S. cerevisiae proteins would also be required for cellular survival after treatment with DNA damaging agents. For this purpose, human homologs of S. cerevisiae proteins were identified and mapped onto the human protein-protein interaction network. The resulting human network was highly modular and a series of selection rules were implemented to identify 45 candidates for human toxicity-modulating proteins. The corresponding transcripts were targeted by RNA interference in human cells. The cell lines with depleted target expression were challenged with three DNA damaging agents: the alkylating agents MMS and 4-NQO, and the oxidizing agent t-BuOOH. A comparison of the survival revealed that the majority (74% of proteins conferred either sensitivity or resistance. The identified human toxicity-modulating proteins represent a variety of biological functions: autophagy, chromatin modifications, RNA and protein metabolism, and telomere maintenance. Further studies revealed that MMS-induced autophagy increase the survival of cells treated with DNA damaging agents. In summary, we show that damage recovery proteins in humans can be identified through homology to S. cerevisiae and that many of the same pathways are represented among the toxicity modulators.

  12. The rodent Four-jointed ortholog Fjx1 regulates dendrite extension.

    Science.gov (United States)

    Probst, Barbara; Rock, Rebecca; Gessler, Manfred; Vortkamp, Andrea; Püschel, Andreas W

    2007-12-01

    The extrinsic and intrinsic factors that regulate the size and complexity of dendritic arborizations are still poorly understood. Here we identify Fjx1, the rodent ortholog of the Drosophila planar cell polarity (PCP) protein Four-jointed (Fj), as a new inhibitory factor that regulates dendrite extension. The Drosophila gene four-jointed (fj) has been suggested to provide directional information in wing discs, but the mechanism how it acts is only poorly understood and the function of its mammalian homolog Fjx1 remains to be investigated. We analyzed the phenotype of a null mutation for mouse Fjx1. Homozygous Fjx1 mutants show an abnormal morphology of dendritic arbors in the hippocampus. In cultured hippocampal neurons from Fjx1 mutant mice, loss of Fjx1 resulted in an increase in dendrite extension and branching. Addition of Fjx1 to cultures of dissociated hippocampal neurons had the opposite effect and reduced the length of dendrites and decreased dendritic branching. Rescue experiments with cultured neurons showed that Fjx1 can act both cell-autonomously and non-autonomously. Our results identify Fjx1 as a new inhibitory factor that regulates dendrite extension.

  13. Ect2, an ortholog of Drosophila Pebble, regulates formation of growth cones in primary cortical neurons.

    Science.gov (United States)

    Tsuji, Takahiro; Higashida, Chiharu; Aoki, Yoshihiko; Islam, Mohammad Saharul; Dohmoto, Mitsuko; Higashida, Haruhiro

    2012-11-01

    In collaboration with Marshall Nirenberg, we performed in vivo RNA interference (RNAi) genome-wide screening in Drosophila embryos. Pebble has been shown to be involved in Drosophila neuronal development. We have also reported that depletion of Ect2, a mammalian ortholog of Pebble, induces differentiation in NG108-15 neuronal cells. However, the precise role of Ect2 in neuronal development has yet to be studied. Here, we confirmed in PC12 pheochromocytoma cells that inhibition of Ect2 expression by RNAi stimulated neurite outgrowth, and in the mouse embryonic cortex that Ect2 was accumulated throughout the ventricular and subventricular zones with neuronal progenitor cells. Next, the effects of Ect2 depletion were studied in primary cultures of mouse embryonic cortical neurons: Loss of Ect2 did not affect the differentiation stages of neuritogenesis, the number of neurites, or axon length, while the numbers of growth cones and growth cone-like structures were increased. Taken together, our results suggest that Ect2 contributes to neuronal morphological differentiation through regulation of growth cone dynamics.

  14. Functional analysis of alternative splicing of the FLOWERING LOCUS T orthologous gene in Chrysanthemum morifolium

    Science.gov (United States)

    Mao, Yachao; Sun, Jing; Cao, Peipei; Zhang, Rong; Fu, Qike; Chen, Sumei; Chen, Fadi; Jiang, Jiafu

    2016-01-01

    As the junction of floral development pathways, the FLOWERING LOCUS T (FT) protein called ‘florigen’ plays an important role in the process of plant flowering through signal integration. We isolated four transcripts encoding different isoforms of a FT orthologous gene CmFTL1, from Chrysanthemum morifolium cultivar ‘Jimba’. Sequence alignments suggested that the four transcripts are related to the intron 1. Expression analysis showed that four alternative splicing (AS) forms of CmFTL1 varied depending on the developmental stage of the flower. The functional complement experiment using an Arabidopsis mutant ft-10 revealed that the archetypal and AS forms of CmFTL1 had the function of complementing late flower phenotype in different levels. In addition, transgenic confirmation at transcript level showed CmFTL1 and CmFTL1ast coexist in the same tissue type at the same developmental stage, indicating a post-transcriptional modification of CmFTL1 in Arabidopsis. Moreover, ectopic expression of different AS forms in chrysanthemum resulted in the development of multiple altered phenotypes, varying degrees of early flowering. We found that an alternative splicing form (CmFTL1-astE134) without the exon 2 lacked the ability causing the earlier flower phenotype. The evidence in this study indicates that complex alternative processing of CmFTL1 transcripts in C. morifolium may be associated with flowering regulation and hold some potential for biotechnical engineering to create early-flowering phenotypes in ornamental cultivars. PMID:27917290

  15. Computational Identification of the Paralogs and Orthologs of Human Cytochrome P450 Superfamily and the Implication in Drug Discovery

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    Shu-Ting Pan

    2016-06-01

    Full Text Available The human cytochrome P450 (CYP superfamily consisting of 57 functional genes is the most important group of Phase I drug metabolizing enzymes that oxidize a large number of xenobiotics and endogenous compounds, including therapeutic drugs and environmental toxicants. The CYP superfamily has been shown to expand itself through gene duplication, and some of them become pseudogenes due to gene mutations. Orthologs and paralogs are homologous genes resulting from speciation or duplication, respectively. To explore the evolutionary and functional relationships of human CYPs, we conducted this bioinformatic study to identify their corresponding paralogs, homologs, and orthologs. The functional implications and implications in drug discovery and evolutionary biology were then discussed. GeneCards and Ensembl were used to identify the paralogs of human CYPs. We have used a panel of online databases to identify the orthologs of human CYP genes: NCBI, Ensembl Compara, GeneCards, OMA (“Orthologous MAtrix” Browser, PATHER, TreeFam, EggNOG, and Roundup. The results show that each human CYP has various numbers of paralogs and orthologs using GeneCards and Ensembl. For example, the paralogs of CYP2A6 include CYP2A7, 2A13, 2B6, 2C8, 2C9, 2C18, 2C19, 2D6, 2E1, 2F1, 2J2, 2R1, 2S1, 2U1, and 2W1; CYP11A1 has 6 paralogs including CYP11B1, 11B2, 24A1, 27A1, 27B1, and 27C1; CYP51A1 has only three paralogs: CYP26A1, 26B1, and 26C1; while CYP20A1 has no paralog. The majority of human CYPs are well conserved from plants, amphibians, fishes, or mammals to humans due to their important functions in physiology and xenobiotic disposition. The data from different approaches are also cross-validated and validated when experimental data are available. These findings facilitate our understanding of the evolutionary relationships and functional implications of the human CYP superfamily in drug discovery.

  16. Enhancing the prediction of protein pairings between interacting families using orthology information

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    Pazos Florencio

    2008-01-01

    Full Text Available Abstract Background It has repeatedly been shown that interacting protein families tend to have similar phylogenetic trees. These similarities can be used to predicting the mapping between two families of interacting proteins (i.e. which proteins from one family interact with which members of the other. The correct mapping will be that which maximizes the similarity between the trees. The two families may eventually comprise orthologs and paralogs, if members of the two families are present in more than one organism. This fact can be exploited to restrict the possible mappings, simply by impeding links between proteins of different organisms. We present here an algorithm to predict the mapping between families of interacting proteins which is able to incorporate information regarding orthologues, or any other assignment of proteins to "classes" that may restrict possible mappings. Results For the first time in methods for predicting mappings, we have tested this new approach on a large number of interacting protein domains in order to statistically assess its performance. The method accurately predicts around 80% in the most favourable cases. We also analysed in detail the results of the method for a well defined case of interacting families, the sensor and kinase components of the Ntr-type two-component system, for which up to 98% of the pairings predicted by the method were correct. Conclusion Based on the well established relationship between tree similarity and interactions we developed a method for predicting the mapping between two interacting families using genomic information alone. The program is available through a web interface.

  17. The complexity of vesicle transport factors in plants examined by orthology search.

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    Puneet Paul

    Full Text Available Vesicle transport is a central process to ensure protein and lipid distribution in eukaryotic cells. The current knowledge on the molecular components and mechanisms of this process is majorly based on studies in Saccharomyces cerevisiae and Arabidopsis thaliana, which revealed 240 different proteinaceous factors either experimentally proven or predicted to be involved in vesicle transport. In here, we performed an orthologue search using two different algorithms to identify the components of the secretory pathway in yeast and 14 plant genomes by using the 'core-set' of 240 factors as bait. We identified 4021 orthologues and (co-orthologues in the discussed plant species accounting for components of COP-II, COP-I, Clathrin Coated Vesicles, Retromers and ESCRTs, Rab GTPases, Tethering factors and SNAREs. In plants, we observed a significantly higher number of (co-orthologues than yeast, while only 8 tethering factors from yeast seem to be absent in the analyzed plant genomes. To link the identified (co-orthologues to vesicle transport, the domain architecture of the proteins from yeast, genetic model plant A. thaliana and agriculturally relevant crop Solanum lycopersicum has been inspected. For the orthologous groups containing (co-orthologues from yeast, A. thaliana and S. lycopersicum, we observed the same domain architecture for 79% (416/527 of the (co-orthologues, which documents a very high conservation of this process. Further, publically available tissue-specific expression profiles for a subset of (co-orthologues found in A. thaliana and S. lycopersicum suggest that some (co-orthologues are involved in tissue-specific functions. Inspection of localization of the (co-orthologues based on available proteome data or localization predictions lead to the assignment of plastid- as well as mitochondrial localized (co-orthologues of vesicle transport factors and the relevance of this is discussed.

  18. Identification of Putative Ortholog Gene Blocks Involved in Gestant and Lactating Mammary Gland Development: A Rodent Cross-Species Microarray Transcriptomics Approach

    Science.gov (United States)

    Rodríguez-Cruz, Maricela; Coral-Vázquez, Ramón M.; Hernández-Stengele, Gabriel; Sánchez, Raúl; Salazar, Emmanuel; Sanchez-Muñoz, Fausto; Encarnación-Guevara, Sergio; Ramírez-Salcedo, Jorge

    2013-01-01

    The mammary gland (MG) undergoes functional and metabolic changes during the transition from pregnancy to lactation, possibly by regulation of conserved genes. The objective was to elucidate orthologous genes, chromosome clusters and putative conserved transcriptional modules during MG development. We analyzed expression of 22,000 transcripts using murine microarrays and RNA samples of MG from virgin, pregnant, and lactating rats by cross-species hybridization. We identified 521 transcripts differentially expressed; upregulated in early (78%) and midpregnancy (89%) and early lactation (64%), but downregulated in mid-lactation (61%). Putative orthologous genes were identified. We mapped the altered genes to orthologous chromosomal locations in human and mouse. Eighteen sets of conserved genes associated with key cellular functions were revealed and conserved transcription factor binding site search entailed possible coregulation among all eight block sets of genes. This study demonstrates that the use of heterologous array hybridization for screening of orthologous gene expression from rat revealed sets of conserved genes arranged in chromosomal order implicated in signaling pathways and functional ontology. Results demonstrate the utilization power of comparative genomics and prove the feasibility of using rodent microarrays to identification of putative coexpressed orthologous genes involved in the control of human mammary gland development. PMID:24288657

  19. Identification of Putative Ortholog Gene Blocks Involved in Gestant and Lactating Mammary Gland Development: A Rodent Cross-Species Microarray Transcriptomics Approach

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    Maricela Rodríguez-Cruz

    2013-01-01

    Full Text Available The mammary gland (MG undergoes functional and metabolic changes during the transition from pregnancy to lactation, possibly by regulation of conserved genes. The objective was to elucidate orthologous genes, chromosome clusters and putative conserved transcriptional modules during MG development. We analyzed expression of 22,000 transcripts using murine microarrays and RNA samples of MG from virgin, pregnant, and lactating rats by cross-species hybridization. We identified 521 transcripts differentially expressed; upregulated in early (78% and midpregnancy (89% and early lactation (64%, but downregulated in mid-lactation (61%. Putative orthologous genes were identified. We mapped the altered genes to orthologous chromosomal locations in human and mouse. Eighteen sets of conserved genes associated with key cellular functions were revealed and conserved transcription factor binding site search entailed possible coregulation among all eight block sets of genes. This study demonstrates that the use of heterologous array hybridization for screening of orthologous gene expression from rat revealed sets of conserved genes arranged in chromosomal order implicated in signaling pathways and functional ontology. Results demonstrate the utilization power of comparative genomics and prove the feasibility of using rodent microarrays to identification of putative coexpressed orthologous genes involved in the control of human mammary gland development.

  20. From zebrafish heart jogging genes to mouse and human orthologs: using Gene Ontology to investigate mammalian heart development.

    Science.gov (United States)

    Khodiyar, Varsha K; Howe, Doug; Talmud, Philippa J; Breckenridge, Ross; Lovering, Ruth C

    2013-01-01

    For the majority of organs in developing vertebrate embryos, left-right asymmetry is controlled by a ciliated region; the left-right organizer node in the mouse and human, and the Kuppfer's vesicle in the zebrafish. In the zebrafish, laterality cues from the Kuppfer's vesicle determine asymmetry in the developing heart, the direction of 'heart jogging' and the direction of 'heart looping'.  'Heart jogging' is the term given to the process by which the symmetrical zebrafish heart tube is displaced relative to the dorsal midline, with a leftward 'jog'. Heart jogging is not considered to occur in mammals, although a leftward shift of the developing mouse caudal heart does occur prior to looping, which may be analogous to zebrafish heart jogging. Previous studies have characterized 30 genes involved in zebrafish heart jogging, the majority of which have well defined orthologs in mouse and human and many of these orthologs have been associated with early mammalian heart development.    We undertook manual curation of a specific set of genes associated with heart development and we describe the use of Gene Ontology term enrichment analyses to examine the cellular processes associated with heart jogging.  We found that the human, mouse and zebrafish 'heart jogging orthologs' are involved in similar organ developmental processes across the three species, such as heart, kidney and nervous system development, as well as more specific cellular processes such as cilium development and function. The results of these analyses are consistent with a role for cilia in the determination of left-right asymmetry of many internal organs, in addition to their known role in zebrafish heart jogging.    This study highlights the importance of model organisms in the study of human heart development, and emphasises both the conservation and divergence of developmental processes across vertebrates, as well as the limitations of this approach.

  1. Chemically engineering ligand selectivity at the free fatty acid receptor 2 based on pharmacological variation between species orthologs

    Science.gov (United States)

    Hudson, Brian D.; Christiansen, Elisabeth; Tikhonova, Irina G.; Grundmann, Manuel; Kostenis, Evi; Adams, David R.; Ulven, Trond; Milligan, Graeme

    2012-01-01

    When it is difficult to develop selective ligands within a family of related G-protein-coupled receptors (GPCRs), chemically engineered receptors activated solely by synthetic ligands (RASSLs) are useful alternatives for probing receptor function. In the present work, we explored whether a RASSL of the free fatty acid receptor 2 (FFA2) could be developed on the basis of pharmacological variation between species orthologs. For this, bovine FFA2 was characterized, revealing distinct ligand selectivity compared with human FFA2. Homology modeling and mutational analysis demonstrated a single mutation in human FFA2 of C4.57G resulted in a human FFA2 receptor with ligand selectivity similar to the bovine receptor. This was exploited to generate human FFA2-RASSL by the addition of a second mutation at a known orthosteric ligand interaction site, H6.55Q. The resulting FFA2-RASSL displayed a >100-fold loss of activity to endogenous ligands, while responding to the distinct ligand sorbic acid with pEC50 values for inhibition of cAMP, 5.83 ± 0.11; Ca2+ mobilization, 4.63 ± 0.05; ERK phosphorylation, 5.61 ± 0.06; and dynamic mass redistribution, 5.35 ± 0.06. This FFA2-RASSL will be useful in future studies on this receptor and demonstrates that exploitation of pharmacological variation between species orthologs is a powerful method to generate novel chemically engineered GPCRs.—Hudson, B. D., Christiansen, E., Tikhonova, I. G., Grundmann, M., Kostenis, E., Adams, D. R., Ulven, T., Milligan, G. Chemically engineering ligand selectivity at the free fatty acid receptor 2 based on pharmacological variation between species orthologs. PMID:22919070

  2. ZmPep1, an ortholog of Arabidopsis elicitor peptide 1, regulates maize innate immunity and enhances disease resistance.

    Science.gov (United States)

    Huffaker, Alisa; Dafoe, Nicole J; Schmelz, Eric A

    2011-03-01

    ZmPep1 is a bioactive peptide encoded by a previously uncharacterized maize (Zea mays) gene, ZmPROPEP1. ZmPROPEP1 was identified by sequence similarity as an ortholog of the Arabidopsis (Arabidopsis thaliana) AtPROPEP1 gene, which encodes the precursor protein of elicitor peptide 1 (AtPep1). Together with its receptors, AtPEPR1 and AtPEPR2, AtPep1 functions to activate and amplify innate immune responses in Arabidopsis and enhances resistance to both Pythium irregulare and Pseudomonas syringae. Candidate orthologs to the AtPROPEP1 gene have been identified from a variety of crop species; however, prior to this study, activities of the respective peptides encoded by these orthologs were unknown. Expression of the ZmPROPEP1 gene is induced by fungal infection and treatment with jasmonic acid or ZmPep1. ZmPep1 activates de novo synthesis of the hormones jasmonic acid and ethylene and induces the expression of genes encoding the defense proteins endochitinase A, PR-4, PRms, and SerPIN. ZmPep1 also stimulates the expression of Benzoxazineless1, a gene required for the biosynthesis of benzoxazinoid defenses, and the accumulation of 2-hydroxy-4,7-dimethoxy-1,4-benzoxazin-3-one glucoside in leaves. To ascertain whether ZmPep1-induced defenses affect resistance, maize plants were pretreated with the peptide prior to infection with fungal pathogens. Based on cell death and lesion severity, ZmPep1 pretreatment was found to enhance resistance to both southern leaf blight and anthracnose stalk rot caused by Cochliobolis heterostrophus and Colletotrichum graminicola, respectively. We present evidence that peptides belonging to the Pep family have a conserved function across plant species as endogenous regulators of innate immunity and may have potential for enhancing disease resistance in crops.

  3. Subtractive hybridization identifies chick-cripto, a novel EGF-CFC ortholog expressed during gastrulation, neurulation and early cardiogenesis.

    Science.gov (United States)

    Colas, J F; Schoenwolf, G C

    2000-09-19

    EGF-CFC genes encode a novel class of extracellular, membrane-associated proteins that notably play an important role during vertebrate gastrulation. Whereas the two cysteine-rich domains that characterize these proteins, namely the extracellular EGF-like and the CFC domain, are known to be encoded by two evolutionarily conserved exons, it is generally assumed, based on weak primary sequence identity, that the remaining parts of the protein differ among vertebrates, suggesting that known members of the EGF-CFC family do not represent true orthologs. Here, by characterizing the full cDNA and genomic sequences of a new EGF-CFC gene in chick, and by comparing them with their counterparts in human (CRIPTO), mouse (cripto and cryptic), Xenopus (FRL-1) and zebrafish (one-eyed pinhead), we show that all EGF-CFC genes share an identical genomic organization over the entire coding region. Not only are the central two exons (coding for the EGF-like and CFC motifs) conserved, but also conserved are the total number of exons, their size, their intron phase and their correlation with discrete protein modules, in particular those modules that allow the EGF-CFC motif to become membrane-associated. Therefore, despite apparent divergence between their 5' and 3'-terminal exons, all known CRIPTO-related genes are structurally orthologous. We named this novel ortholog in bird, chick-cripto. We report the mRNA distribution of chick-cripto, which begins in the epiblast of the gastrula, with a pattern similar to EGF-CFC genes of other vertebrates.

  4. On the artefactual parasitic eubacteria clan in conditioned logdet phylogenies: heterotachy and ortholog identification artefacts as explanations

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    Bryant David

    2010-11-01

    Full Text Available Abstract Background Phylogenetic reconstruction methods based on gene content often place all the parasitic and endosymbiotic eubacteria (parasites for short together in a clan. Many other lines of evidence point to this parasites clan being an artefact. This artefact could be a consequence of the methods used to construct ortholog databases (due to some unknown bias, the methods used to estimate the phylogeny, or both. We test the idea that the parasites clan is an ortholog identification artefact by analyzing three different ortholog databases (COG, TRIBES, and OFAM, which were constructed using different methods, and are thus unlikely to share the same biases. In each case, we estimate a phylogeny using an improved version of the conditioned logdet distance method. If the parasites clan appears in trees from all three databases, it is unlikely to be an ortholog identification artefact. Accelerated loss of a subset of gene families in parasites (a form of heterotachy may contribute to the difficulty of estimating a phylogeny from gene content data. We test the idea that heterotachy is the underlying reason for the estimation of an artefactual parasites clan by applying two different mixture models (phylogenetic and non-phylogenetic, in combination with conditioned logdet. In these models, there are two categories of gene families, one of which has accelerated loss in parasites. Distances are estimated separately from each category by conditioned logdet. This should reduce the tendency for tree estimation methods to group the parasites together, if heterotachy is the underlying reason for estimation of the parasites clan. Results The parasites clan appears in conditioned logdet trees estimated from all three databases. This makes it less likely to be an artefact of database construction. The non-phylogenetic mixture model gives trees without a parasites clan. However, the phylogenetic mixture model still results in a tree with a parasites clan

  5. Comparative analysis of function and interaction of transcription factors in nematodes: Extensive conservation of orthology coupled to rapid sequence evolution

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    Singh Rama S

    2008-08-01

    Full Text Available Abstract Background Much of the morphological diversity in eukaryotes results from differential regulation of gene expression in which transcription factors (TFs play a central role. The nematode Caenorhabditis elegans is an established model organism for the study of the roles of TFs in controlling the spatiotemporal pattern of gene expression. Using the fully sequenced genomes of three Caenorhabditid nematode species as well as genome information from additional more distantly related organisms (fruit fly, mouse, and human we sought to identify orthologous TFs and characterized their patterns of evolution. Results We identified 988 TF genes in C. elegans, and inferred corresponding sets in C. briggsae and C. remanei, containing 995 and 1093 TF genes, respectively. Analysis of the three gene sets revealed 652 3-way reciprocal 'best hit' orthologs (nematode TF set, approximately half of which are zinc finger (ZF-C2H2 and ZF-C4/NHR types and HOX family members. Examination of the TF genes in C. elegans and C. briggsae identified the presence of significant tandem clustering on chromosome V, the majority of which belong to ZF-C4/NHR family. We also found evidence for lineage-specific duplications and rapid evolution of many of the TF genes in the two species. A search of the TFs conserved among nematodes in Drosophila melanogaster, Mus musculus and Homo sapiens revealed 150 reciprocal orthologs, many of which are associated with important biological processes and human diseases. Finally, a comparison of the sequence, gene interactions and function indicates that nematode TFs conserved across phyla exhibit significantly more interactions and are enriched in genes with annotated mutant phenotypes compared to those that lack orthologs in other species. Conclusion Our study represents the first comprehensive genome-wide analysis of TFs across three nematode species and other organisms. The findings indicate substantial conservation of transcription

  6. Identification and complete sequencing of novel human transcripts through the use of mouse orthologs and testis cDNA sequences

    DEFF Research Database (Denmark)

    Ferreira, Elisa N; Pires, Lilian C; Parmigiani, Raphael B;

    2004-01-01

    The correct identification of all human genes, and their derived transcripts, has not yet been achieved, and it remains one of the major aims of the worldwide genomics community. Computational programs suggest the existence of 30,000 to 40,000 human genes. However, definitive gene identification...... can only be achieved by experimental approaches. We used two distinct methodologies, one based on the alignment of mouse orthologous sequences to the human genome, and another based on the construction of a high-quality human testis cDNA library, in an attempt to identify new human transcripts within...

  7. Chemically engineering ligand selectivity at the free fatty acid receptor 2 based on pharmacological variation between species orthologs

    DEFF Research Database (Denmark)

    Hudson, Brian D; Christiansen, Elisabeth; Tikhonova, Irina G

    2012-01-01

    When it is difficult to develop selective ligands within a family of related G-protein-coupled receptors (GPCRs), chemically engineered receptors activated solely by synthetic ligands (RASSLs) are useful alternatives for probing receptor function. In the present work, we explored whether a RASSL...... on this receptor and demonstrates that exploitation of pharmacological variation between species orthologs is a powerful method to generate novel chemically engineered GPCRs.-Hudson, B. D., Christiansen, E., Tikhonova, I. G., Grundmann, M., Kostenis, E., Adams, D. R., Ulven, T., Milligan, G. Chemically engineering...

  8. A search of Brassica SI-involved orthologs in buckwheat leads to novel buckwheat sequence identification: MLPK possibly involved in SI response

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    Banović Bojana

    2010-01-01

    Full Text Available Self-incompatibility (SI systems, gamethophytic (GSI and sporophytic (SSI, prevent self-pollination in angiosperms. Buckwheat displays heteromorphic SSI, with pollination allowed only between different flower morphs - thrum and pin. The physiology of thrum and pin morph SI responses are entirely different, resembling homomorphic Brassica SSI and Prunus GSI responses, respectively. Considering angiosperm species may share ancestral SI genes, we examined the presence of Brassica and Prunus SI-involved gene orthologs in the buckwheat genome. We did not find evidence of SRK, SLG and SP11 Brassica or S-RNase and SFB Prunus orthologs in the buckwheat genome, but we found a Brassica MLPK ortholog. We report the partial nucleotide sequence of the buckwheat MLPK and discuss the possible implications of this finding.

  9. Systemic acquired resistance in soybean is regulated by two proteins, Orthologous to Arabidopsis NPR1

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    Sandhu Devinder

    2009-08-01

    Full Text Available Abstract Background Systemic acquired resistance (SAR is induced in non-inoculated leaves following infection with certain pathogenic strains. SAR is effective against many pathogens. Salicylic acid (SA is a signaling molecule of the SAR pathway. The development of SAR is associated with the induction of pathogenesis related (PR genes. Arabidopsis non-expressor of PR1 (NPR1 is a regulatory gene of the SA signal pathway 123. SAR in soybean was first reported following infection with Colletotrichum trancatum that causes anthracnose disease. We investigated if SAR in soybean is regulated by a pathway, similar to the one characterized in Arabidopsis. Results Pathogenesis-related gene GmPR1 is induced following treatment of soybean plants with the SAR inducer, 2,6-dichloroisonicotinic acid (INA or infection with the oomycete pathogen, Phytophthora sojae. In P. sojae-infected plants, SAR was induced against the bacterial pathogen, Pseudomonas syringae pv. glycinea. Soybean GmNPR1-1 and GmNPR1-2 genes showed high identities to Arabidopsis NPR1. They showed similar expression patterns among the organs, studied in this investigation. GmNPR1-1 and GmNPR1-2 are the only soybean homologues of NPR1and are located in homoeologous regions. In GmNPR1-1 and GmNPR1-2 transformed Arabidopsis npr1-1 mutant plants, SAR markers: (i PR-1 was induced following INA treatment and (ii BGL2 following infection with Pseudomonas syringae pv. tomato (Pst, and SAR was induced following Pst infection. Of the five cysteine residues, Cys82, Cys150, Cys155, Cys160, and Cys216 involved in oligomer-monomer transition in NPR1, Cys216 in GmNPR1-1 and GmNPR1-2 proteins was substituted to Ser and Leu, respectively. Conclusion Complementation analyses in Arabidopsis npr1-1 mutants revealed that homoeologous GmNPR1-1 and GmNPR1-2 genes are orthologous to Arabidopsis NPR1. Therefore, SAR pathway in soybean is most likely regulated by GmNPR1 genes. Substitution of Cys216 residue, essential

  10. Extracellular Ionic Locks Determine Variation in Constitutive Activity and Ligand Potency between Species Orthologs of the Free Fatty Acid Receptors FFA2 and FFA3*

    Science.gov (United States)

    Hudson, Brian D.; Tikhonova, Irina G.; Pandey, Sunil K.; Ulven, Trond; Milligan, Graeme

    2012-01-01

    Free fatty acid receptors 2 and 3 (FFA2 and FFA3) are G protein-coupled receptors for short chain free fatty acids (SCFAs). They respond to the same set of endogenous ligands but with distinct rank-order of potency such that acetate (C2) has been described as FFA2-selective, whereas propionate (C3) is non-selective. Although C2 was confirmed to be selective for human FFA2 over FFA3, this ligand was not selective between the mouse orthologs. Moreover, although C3 was indeed not selective between the human orthologs, it displayed clear selectivity for mouse FFA3 over mouse FFA2. This altered selectivity to C2 and C3 resulted from broad differences in SCFAs potency at the mouse orthologs. In studies to define the molecular basis for these observations, marked variation in ligand-independent constitutive activity was identified using a [35S]GTPγS assay. The orthologs with higher potency for the SCFAs, human FFA2 and mouse FFA3, displayed high constitutive activity in this assay, whereas the orthologs with lower potency for the agonist ligands, mouse FFA2 and human FFA3, did not. Sequence alignments of the second extracellular loop identified single negatively charged residues in FFA2 and FFA3 not conserved between species and predicted to form ionic lock interactions with arginine residues within the FFA2 or FFA3 agonist binding pocket to regulate constitutive activity and SCFA potency. Reciprocal mutation of these residues between species orthologs resulted in the induction (or repression) of constitutive activity and in most cases also yielded corresponding changes in SCFA potency. PMID:23066016

  11. 'Ca. Liberibacter asiaticus' proteins orthologous with pSymA-encoded proteins of Sinorhizobium meliloti: hypothetical roles in plant host interaction.

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    L David Kuykendall

    Full Text Available Sinorhizobium meliloti strain 1021, a nitrogen-fixing, root-nodulating bacterial microsymbiont of alfalfa, has a 3.5 Mbp circular chromosome and two megaplasmids including 1.3 Mbp pSymA carrying nonessential 'accessory' genes for nitrogen fixation (nif, nodulation and host specificity (nod. A related bacterium, psyllid-vectored 'Ca. Liberibacter asiaticus,' is an obligate phytopathogen with a reduced genome that was previously analyzed for genes orthologous to genes on the S. meliloti circular chromosome. In general, proteins encoded by pSymA genes are more similar in sequence alignment to those encoded by S. meliloti chromosomal orthologs than to orthologous proteins encoded by genes carried on the 'Ca. Liberibacter asiaticus' genome. Only two 'Ca. Liberibacter asiaticus' proteins were identified as having orthologous proteins encoded on pSymA but not also encoded on the chromosome of S. meliloti. These two orthologous gene pairs encode a Na(+/K+ antiporter (shared with intracellular pathogens of the family Bartonellacea and a Co++, Zn++ and Cd++ cation efflux protein that is shared with the phytopathogen Agrobacterium. Another shared protein, a redox-regulated K+ efflux pump may regulate cytoplasmic pH and homeostasis. The pSymA and 'Ca. Liberibacter asiaticus' orthologs of the latter protein are more highly similar in amino acid alignment compared with the alignment of the pSymA-encoded protein with its S. meliloti chromosomal homolog. About 182 pSymA encoded proteins have sequence similarity (≤ E-10 with 'Ca. Liberibacter asiaticus' proteins, often present as multiple orthologs of single 'Ca. Liberibacter asiaticus' proteins. These proteins are involved with amino acid uptake, cell surface structure, chaperonins, electron transport, export of bioactive molecules, cellular homeostasis, regulation of gene expression, signal transduction and synthesis of amino acids and metabolic cofactors. The presence of multiple orthologs defies mutational

  12. cdc-25.4, a Caenorhabditis elegans Ortholog of cdc25, Is Required for Male Mating Behavior

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    Sangmi Oh

    2016-12-01

    Full Text Available Cell division cycle 25 (cdc25 is an evolutionarily conserved phosphatase that promotes cell cycle progression. Among the four cdc25 orthologs in Caenorhabditis elegans, we found that cdc-25.4 mutant males failed to produce outcrossed progeny. This was not caused by defects in sperm development, but by defects in male mating behavior. The cdc-25.4 mutant males showed various defects during male mating, including contact response, backing, turning, and vulva location. Aberrant turning behavior was the most prominent defect in the cdc-25.4 mutant males. We also found that cdc-25.4 is expressed in many neuronal cells throughout development. The turning defect in cdc-25.4 mutant males was recovered by cdc-25.4 transgenic expression in neuronal cells, suggesting that cdc-25.4 functions in neurons for male mating. However, the neuronal morphology of cdc-25.4 mutant males appeared to be normal, as examined with several neuronal markers. Also, RNAi depletion of wee-1.3, a C. elegans ortholog of Wee1/Myt1 kinase, failed to suppress the mating defects of cdc-25.4 mutant males. These findings suggest that, for successful male mating, cdc-25.4 does not target cell cycles that are required for neuronal differentiation and development. Rather, cdc-25.4 likely regulates noncanonical substrates in neuronal cells.

  13. Pairwise comparison of orthologous olfactory receptor genes between two sympatric sibling sea kraits of the genus Laticauda in Vanuatu.

    Science.gov (United States)

    Kishida, Takushi; Hayano, Azusa; Inoue-Murayama, Miho; Hikida, Tsutomu

    2013-06-01

    Olfaction-based reproductive isolation is widely observed in animals, but little is known about the genetic basis of such isolation mechanisms. Two species of sibling amphibious sea snakes, Laticauda colubrina and L. frontalis live in Vanuatu sympatrically and syntopically, but no natural hybrids have been reported. Adult females of both taxa possess distinctive lipids in the skin, and male L. frontalis distinguishes conspecific females based on olfactory cues. To shed light on the molecular basis of the evolution of olfaction-based isolation mechanisms, olfactory receptor (OR) gene repertoires of both taxa were identified using pyrosequencing-based technology, and orthologous OR gene sets were identified. Few species-specific gene duplications or species-specific gene losses were found. However, the nonsynonymous-to-synonymous substitution rate ratio was relatively higher between orthologous OR genes of L. frontalis and L. colubrina, indicating that L. frontalis and L. colubrina have evolved to possess different olfactory senses. We suggest that L. frontalis and L. colubrina have evolved allopatrically, and this may be a byproduct of the allopatric evolution, and that this dissimilarity may function as a premating isolation barrier, since L. frontalis has returned to the ancestral range (Vanuatu).

  14. ANCAC: amino acid, nucleotide, and codon analysis of COGs – a tool for sequence bias analysis in microbial orthologs

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    Meiler Arno

    2012-09-01

    Full Text Available Abstract Background The COG database is the most popular collection of orthologous proteins from many different completely sequenced microbial genomes. Per definition, a cluster of orthologous groups (COG within this database exclusively contains proteins that most likely achieve the same cellular function. Recently, the COG database was extended by assigning to every protein both the corresponding amino acid and its encoding nucleotide sequence resulting in the NUCOCOG database. This extended version of the COG database is a valuable resource connecting sequence features with the functionality of the respective proteins. Results Here we present ANCAC, a web tool and MySQL database for the analysis of amino acid, nucleotide, and codon frequencies in COGs on the basis of freely definable phylogenetic patterns. We demonstrate the usefulness of ANCAC by analyzing amino acid frequencies, codon usage, and GC-content in a species- or function-specific context. With respect to amino acids we, at least in part, confirm the cognate bias hypothesis by using ANCAC’s NUCOCOG dataset as the largest one available for that purpose thus far. Conclusions Using the NUCOCOG datasets, ANCAC connects taxonomic, amino acid, and nucleotide sequence information with the functional classification via COGs and provides a GUI for flexible mining for sequence-bias. Thereby, to our knowledge, it is the only tool for the analysis of sequence composition in the light of physiological roles and phylogenetic context without requirement of substantial programming-skills.

  15. Orthologs of Human Disease Associated Genes and RNAi Analysis of Silencing Insulin Receptor Gene in Bombyx mori

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    Zan Zhang

    2014-10-01

    Full Text Available The silkworm, Bombyx mori L., is an important economic insect that has been domesticated for thousands of years to produce silk. It is our great interest to investigate the possibility of developing the B. mori as human disease model. We searched the orthologs of human disease associated genes in the B. mori by bi-directional best hits of BLAST and confirmed by searching the OrthoDB. In total, 5006 genes corresponding to 1612 kinds of human diseases had orthologs in the B. mori, among which, there are 25 genes associated with diabetes mellitus. Of these, we selected the insulin receptor gene of the B. mori (Bm-INSR to study its expression in different tissues and at different developmental stages and tissues. Quantitative PCR showed that Bm-INSR was highly expressed in the Malpighian tubules but expressed at low levels in the testis. It was highly expressed in the 3rd and 4th instar larvae, and adult. We knocked down Bm-INSR expression using RNA interference. The abundance of Bm-INSR transcripts were dramatically reduced to ~4% of the control level at 6 days after dsRNA injection and the RNAi-treated B. mori individuals showed apparent growth inhibition and malformation such as abnormal body color in black, which is the typical symptom of diabetic patients. Our results demonstrate that B. mori has potential use as an animal model for diabetic mellitus research.

  16. Frequent and recent retrotransposition of orthologous genes plays a role in the evolution of sperm glycolytic enzymes

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    de Villena Fernando

    2010-05-01

    Full Text Available Abstract Background The central metabolic pathway of glycolysis converts glucose to pyruvate, with the net production of 2 ATP and 2 NADH per glucose molecule. Each of the ten reactions in this pathway is typically catalyzed by multiple isozymes encoded by a multigene family. Several isozymes in this pathway are expressed only during spermatogenesis, and gene targeting studies indicate that they are essential for sperm function and male fertility in mouse. At least three of the novel glycolytic isozymes are encoded by retrogenes (Pgk2, Aldoart1, and Aldoart2. Their restricted expression profile suggests that retrotransposition may play a significant role in the evolution of sperm glycolytic enzymes. Results We conducted a comprehensive genomic analysis of glycolytic enzymes in the human and mouse genomes and identified several intronless copies for all enzymes in the pathway, except Pfk. Within each gene family, a single orthologous gene was typically retrotransposed frequently and independently in both species. Several retroposed sequences maintained open reading frames (ORFs and/or provided evidence of alternatively spliced exons. We analyzed expression of sequences with ORFs and Gpi1 transcript in mouse spermatogenic cells. Conclusions Our analysis detected frequent, recent, and lineage-specific retrotransposition of orthologous glycolytic enzymes in the human and mouse genomes. Retrotransposition events are associated with LINE/LTR and genomic integration is random. We found evidence for the alternative splicing of parent genes. Many retroposed sequences have maintained ORFs, suggesting a functional role for these genes.

  17. ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes

    Energy Technology Data Exchange (ETDEWEB)

    Novichkov, Pavel S.; Ratnere, Igor; Wolf, Yuri I.; Koonin, Eugene V.; Dubchak, Inna

    2009-07-23

    The database of Alignable Tight Genomic Clusters (ATGCs) consists of closely related genomes of archaea and bacteria, and is a resource for research into prokaryotic microevolution. Construction of a data set with appropriate characteristics is a major hurdle for this type of studies. With the current rate of genome sequencing, it is difficult to follow the progress of the field and to determine which of the available genome sets meet the requirements of a given research project, in particular, with respect to the minimum and maximum levels of similarity between the included genomes. Additionally, extraction of specific content, such as genomic alignments or families of orthologs, from a selected set of genomes is a complicated and time-consuming process. The database addresses these problems by providing an intuitive and efficient web interface to browse precomputed ATGCs, select appropriate ones and access ATGC-derived data such as multiple alignments of orthologous proteins, matrices of pairwise intergenomic distances based on genome-wide analysis of synonymous and nonsynonymous substitution rates and others. The ATGC database will be regularly updated following new releases of the NCBI RefSeq. The database is hosted by the Genomics Division at Lawrence Berkeley National laboratory and is publicly available at http://atgc.lbl.gov.

  18. Cloning, expression and purification of orthologous membrane proteins: a general protocol for preparation of the histidine sensor kinase ETR1 from different species.

    Science.gov (United States)

    Classen, Elisa; Groth, Georg

    2012-03-01

    Orthologous proteins do not necessarily share the same function in all species and those sharing the same function might employ a modified catalytic mechanism. Thus, comparative analysis of homologous or orthologous proteins from different organisms can provide detailed information on the function and the mechanism of an entire protein family. The sensor kinase ETR1 from Arabidopsis thaliana has been well characterized by genetic, physiological and biochemical studies. However, as further model plants are coming into focus for plant hormone research, a general protocol for isolation and purification of orthologous ETR1 proteins seems instrumental for a detailed molecular analysis of this protein family. In this study, we describe the native purification of recombinant ETR1 from Arabidopsis thaliana by mild solubilization with the zwitter-ionic detergent Fos-Choline-14 and single-step purification by immobilized metal ion affinity chromatography. The same protocol was successfully applied for the purification of the orthologous proteins from the moss Physcomitrella patens subsp. patens and the tomato Lycopersicon esculentum. The successful transfer of the purification protocol to proteins of the same family which share sequence identity of 63-80% only suggests that this protocol presents a general purification strategy which is likely to apply also to the purification of other members of the sensor histidine kinase family.

  19. Functional evolution of a multigene family: orthologous and paralogous pheromone receptor genes in the turnip moth, Agrotis segetum.

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    Dan-Dan Zhang

    Full Text Available Lepidopteran pheromone receptors (PRs, for which orthologies are evident among closely related species, provide an intriguing example of gene family evolution in terms of how new functions may arise. However, only a limited number of PRs have been functionally characterized so far and thus evolutionary scenarios suffer from elements of speculation. In this study we investigated the turnip moth Agrotis segetum, in which female moths produce a mixture of chemically related pheromone components that elicit specific responses from receptor cells on male antennae. We cloned nine A. segetum PR genes and the Orco gene by degenerate primer based RT-PCR. The nine PR genes, named as AsegOR1 and AsegOR3-10, fall into four distinct orthologous clusters of known lepidopteran PRs, of which one contains six paralogues. The paralogues are under relaxed selective pressure, contrasting with the purifying selection on other clusters. We identified the receptors AsegOR9, AsegOR4 and AsegOR5, specific for the respective homologous pheromone components (Z-5-decenyl, (Z-7-dodecenyl and (Z-9-tetradecenyl acetates, by two-electrode voltage clamp recording from Xenopus laevis oocytes co-expressing Orco and each PR candidate. These receptors occur in three different orthologous clusters. We also found that the six paralogues with high sequence similarity vary dramatically in ligand selectivity and sensitivity. Different from AsegOR9, AsegOR6 showed a relatively large response to the behavioural antagonist (Z-5-decenol, and a small response to (Z-5-decenyl acetate. AsegOR1 was broadly tuned, but most responsive to (Z-5-decenyl acetate, (Z-7-dodecenyl acetate and the behavioural antagonist (Z-8-dodecenyl acetate. AsegOR8 and AsegOR7, which differ from AsegOR6 and AsegOR1 by 7 and 10 aa respectively, showed much lower sensitivities. AsegOR10 showed only small responses to all the tested compounds. These results suggest that new receptors arise through gene duplication, and

  20. The trehalose utilization gene thuA ortholog in Mesorhizobium loti does not influence competitiveness for nodulation on Lotus spp.

    Science.gov (United States)

    Ampomah, Osei Yaw; Jensen, John Beck

    2014-03-01

    Competitiveness for nodulation is a desirable trait in rhizobia strains used as inoculant. In Sinorhizobium meliloti 1021 mutation in either of the trehalose utilization genes thuA or thuB influences its competitiveness for root colonization and nodule occupancy depending on the interacting host. We have therefore investigated whether mutation in the thuA ortholog in Mesorhizobium loti MAFF303099 also leads to a similar competitive phenotype on its hosts. The results show that M. loti thuA mutant Ml7023 was symbiotically effective and was as competitive as the wild type in colonization and nodule occupancy on Lotus corniculatus and Lotus japonicus. The thuA gene in M. loti was not induced during root colonization or in the infection threads unlike in S. meliloti, despite its induction by trehalose and high osmolarity in in vitro assays.

  1. Patterns of structural dynamics in RACK1 protein retained throughout evolution: A hydrogen-deuterium exchange study of three orthologs

    Science.gov (United States)

    Tarnowski, Krzysztof; Fituch, Kinga; Szczepanowski, Roman H; Dadlez, Michal; Kaus-Drobek, Magdalena

    2014-01-01

    RACK1 is a member of the WD repeat family of proteins and is involved in multiple fundamental cellular processes. An intriguing feature of RACK1 is its ability to interact with at least 80 different protein partners. Thus, the structural features enabling such interactomic flexibility are of great interest. Several previous studies of the crystal structures of RACK1 orthologs described its detailed architecture and confirmed predictions that RACK1 adopts a seven-bladed β-propeller fold. However, this did not explain its ability to bind to multiple partners. We performed hydrogen-deuterium (H-D) exchange mass spectrometry on three orthologs of RACK1 (human, yeast, and plant) to obtain insights into the dynamic properties of RACK1 in solution. All three variants retained similar patterns of deuterium uptake, with some pronounced differences that can be attributed to RACK1's divergent biological functions. In all cases, the most rigid structural elements were confined to B-C turns and, to some extent, strands B and C, while the remaining regions retained much flexibility. We also compared the average rate constants for H-D exchange in different regions of RACK1 and found that amide protons in some regions exchanged at least 1000-fold faster than in others. We conclude that its evolutionarily retained structural architecture might have allowed RACK1 to accommodate multiple molecular partners. This was exemplified by our additional analysis of yeast RACK1 dimer, which showed stabilization, as well as destabilization, of several interface regions upon dimer formation. PMID:24591271

  2. Critical role of the virus-encoded microRNA-155 ortholog in the induction of Marek's disease lymphomas.

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    Yuguang Zhao

    2011-02-01

    Full Text Available Notwithstanding the well-characterised roles of a number of oncogenes in neoplastic transformation, microRNAs (miRNAs are increasingly implicated in several human cancers. Discovery of miRNAs in several oncogenic herpesviruses such as KSHV has further highlighted the potential of virus-encoded miRNAs to contribute to their oncogenic capabilities. Nevertheless, despite the identification of several possible cancer-related genes as their targets, the direct in vivo role of virus-encoded miRNAs in neoplastic diseases such as those induced by KSHV is difficult to demonstrate in the absence of suitable models. However, excellent natural disease models of rapid-onset Marek's disease (MD lymphomas in chickens allow examination of the oncogenic potential of virus-encoded miRNAs. Using viruses modified by reverse genetics of the infectious BAC clone of the oncogenic RB-1B strain of MDV, we show that the deletion of the six-miRNA cluster 1 from the viral genome abolished the oncogenicity of the virus. This loss of oncogenicity appeared to be primarily due to the single miRNA within the cluster, miR-M4, the ortholog of cellular miR-155, since its deletion or a 2-nucleotide mutation within its seed region was sufficient to inhibit the induction of lymphomas. The definitive role of this miR-155 ortholog in oncogenicity was further confirmed by the rescue of oncogenic phenotype by revertant viruses that expressed either the miR-M4 or the cellular homolog gga-miR-155. This is the first demonstration of the direct in vivo role of a virus-encoded miRNA in inducing tumors in a natural infection model. Furthermore, the use of viruses deleted in miRNAs as effective vaccines against virulent MDV challenge, enables the prospects of generating genetically defined attenuated vaccines.

  3. Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression

    Directory of Open Access Journals (Sweden)

    Vandepoele Klaas

    2009-06-01

    Full Text Available Abstract Background Large-scale identification of the interrelationships between different components of the cell, such as the interactions between proteins, has recently gained great interest. However, unraveling large-scale protein-protein interaction maps is laborious and expensive. Moreover, assessing the reliability of the interactions can be cumbersome. Results In this study, we have developed a computational method that exploits the existing knowledge on protein-protein interactions in diverse species through orthologous relations on the one hand, and functional association data on the other hand to predict and filter protein-protein interactions in Arabidopsis thaliana. A highly reliable set of protein-protein interactions is predicted through this integrative approach making use of existing protein-protein interaction data from yeast, human, C. elegans and D. melanogaster. Localization, biological process, and co-expression data are used as powerful indicators for protein-protein interactions. The functional repertoire of the identified interactome reveals interactions between proteins functioning in well-conserved as well as plant-specific biological processes. We observe that although common mechanisms (e.g. actin polymerization and components (e.g. ARPs, actin-related proteins exist between different lineages, they are active in specific processes such as growth, cancer metastasis and trichome development in yeast, human and Arabidopsis, respectively. Conclusion We conclude that the integration of orthology with functional association data is adequate to predict protein-protein interactions. Through this approach, a high number of novel protein-protein interactions with diverse biological roles is discovered. Overall, we have predicted a reliable set of protein-protein interactions suitable for further computational as well as experimental analyses.

  4. Patterns of structural dynamics in RACK1 protein retained throughout evolution: a hydrogen-deuterium exchange study of three orthologs.

    Science.gov (United States)

    Tarnowski, Krzysztof; Fituch, Kinga; Szczepanowski, Roman H; Dadlez, Michal; Kaus-Drobek, Magdalena

    2014-05-01

    RACK1 is a member of the WD repeat family of proteins and is involved in multiple fundamental cellular processes. An intriguing feature of RACK1 is its ability to interact with at least 80 different protein partners. Thus, the structural features enabling such interactomic flexibility are of great interest. Several previous studies of the crystal structures of RACK1 orthologs described its detailed architecture and confirmed predictions that RACK1 adopts a seven-bladed β-propeller fold. However, this did not explain its ability to bind to multiple partners. We performed hydrogen-deuterium (H-D) exchange mass spectrometry on three orthologs of RACK1 (human, yeast, and plant) to obtain insights into the dynamic properties of RACK1 in solution. All three variants retained similar patterns of deuterium uptake, with some pronounced differences that can be attributed to RACK1's divergent biological functions. In all cases, the most rigid structural elements were confined to B-C turns and, to some extent, strands B and C, while the remaining regions retained much flexibility. We also compared the average rate constants for H-D exchange in different regions of RACK1 and found that amide protons in some regions exchanged at least 1000-fold faster than in others. We conclude that its evolutionarily retained structural architecture might have allowed RACK1 to accommodate multiple molecular partners. This was exemplified by our additional analysis of yeast RACK1 dimer, which showed stabilization, as well as destabilization, of several interface regions upon dimer formation.

  5. A novel firmicute protein family related to the actinobacterial resuscitation-promoting factors by non-orthologous domain displacement

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    Finan Christopher L

    2005-03-01

    Full Text Available Abstract Background In Micrococcus luteus growth and resuscitation from starvation-induced dormancy is controlled by the production of a secreted growth factor. This autocrine resuscitation-promoting factor (Rpf is the founder member of a family of proteins found throughout and confined to the actinobacteria (high G + C Gram-positive bacteria. The aim of this work was to search for and characterise a cognate gene family in the firmicutes (low G + C Gram-positive bacteria and obtain information about how they may control bacterial growth and resuscitation. Results In silico analysis of the accessory domains of the Rpf proteins permitted their classification into several subfamilies. The RpfB subfamily is related to a group of firmicute proteins of unknown function, represented by YabE of Bacillus subtilis. The actinobacterial RpfB and firmicute YabE proteins have very similar domain structures and genomic contexts, except that in YabE, the actinobacterial Rpf domain is replaced by another domain, which we have called Sps. Although totally unrelated in both sequence and secondary structure, the Rpf and Sps domains fulfil the same function. We propose that these proteins have undergone "non-orthologous domain displacement", a phenomenon akin to "non-orthologous gene displacement" that has been described previously. Proteins containing the Sps domain are widely distributed throughout the firmicutes and they too fall into a number of distinct subfamilies. Comparative analysis of the accessory domains in the Rpf and Sps proteins, together with their weak similarity to lytic transglycosylases, provide clear evidence that they are muralytic enzymes. Conclusions The results indicate that the firmicute Sps proteins and the actinobacterial Rpf proteins are cognate and that they control bacterial culturability via enzymatic modification of the bacterial cell envelope.

  6. Characterization of structural and free energy properties of promoters associated with Primary and Operon TSS in Helicobacter pylori genome and their orthologs

    Indian Academy of Sciences (India)

    Aditya Kumar; Manju Bansal

    2012-07-01

    Promoter regions in the genomes of all domains of life show similar trends in several structural properties such as stability, bendability, curvature, etc. In current study we analysed the stability and bendability of various classes of promoter regions (based on the recent identification of different classes of transcription start sites) of Helicobacter pylori 26695 strain. It is found that primary TSS and operon-associated TSS promoters show significantly strong features in their promoter regions. DNA free-energy-based promoter prediction tool PromPredict was used to annotate promoters of different classes, and very high recall values (∼80%) are obtained for primary TSS. Orthologous genes from other strains of H. pylori show conservation of structural properties in promoter regions as well as coding regions. PromPredict annotates promoters of orthologous genes with very high recall and precision.

  7. SymGRASS: a database of sugarcane orthologous genes involved in arbuscular mycorrhiza and root nodule symbiosis

    Science.gov (United States)

    2013-01-01

    Background The rationale for gathering information from plants procuring nitrogen through symbiotic interactions controlled by a common genetic program for a sustainable biofuel production is the high energy demanding application of synthetic nitrogen fertilizers. We curated sequence information publicly available for the biofuel plant sugarcane, performed an analysis of the common SYM pathway known to control symbiosis in other plants, and provide results, sequences and literature links as an online database. Methods Sugarcane sequences and informations were downloaded from the nucEST database, cleaned and trimmed with seqclean, assembled with TGICL plus translating mapping method, and annotated. The annotation is based on BLAST searches against a local formatted plant Uniprot90 generated with CD-HIT for functional assignment, rpsBLAST to CDD database for conserved domain analysis, and BLAST search to sorghum's for Gene Ontology (GO) assignment. Gene expression was normalized according the Unigene standard, presented as ESTs/100 kb. Protein sequences known in the SYM pathway were used as queries to search the SymGRASS sequence database. Additionally, antimicrobial peptides described in the PhytAMP database served as queries to retrieve and generate expression profiles of these defense genes in the libraries compared to the libraries obtained under symbiotic interactions. Results We describe the SymGRASS, a database of sugarcane orthologous genes involved in arbuscular mycorrhiza (AM) and root nodule (RN) symbiosis. The database aggregates knowledge about sequences, tissues, organ, developmental stages and experimental conditions, and provides annotation and level of gene expression for sugarcane transcripts and SYM orthologous genes in sugarcane through a web interface. Several candidate genes were found for all nodes in the pathway, and interestingly a set of symbiosis specific genes was found. Conclusions The knowledge integrated in SymGRASS may guide studies on

  8. Construction and analysis of tag single nucleotide polymorphism maps for six human-mouse orthologous candidate genes in type 1 diabetes

    OpenAIRE

    Savage David A; Ionescu-Tîrgovişte Constantin; Guja Cristian; Rønningen Kjersti S; Undlien Dag E; Nutland Sarah; Walker Neil; Chamberlain Giselle; Hunter Kara M; Moule Carolyn; Fraser Heather; Smink Luc J; Hulme John; Lowe Christopher; Pask Rebecca

    2005-01-01

    Abstract Background One strategy to help identify susceptibility genes for complex, multifactorial diseases is to map disease loci in a representative animal model of the disorder. The nonobese diabetic (NOD) mouse is a model for human type 1 diabetes. Linkage and congenic strain analyses have identified several NOD mouse Idd (insulin dependent diabetes) loci, which have been mapped to small chromosome intervals, for which the orthologous regions in the human genome can be identified. Here, w...

  9. Three loblolly pine CesA genes expressed in developing xylem are orthologous to secondary cell wall CesA genes of angiosperms.

    Science.gov (United States)

    Nairn, C Joseph; Haselkorn, Tamara

    2005-06-01

    Specific plant cellulose synthases (CesA), encoded by a multigene family, are necessary for secondary wall synthesis in vascular tissues and are critical to wood production. We obtained full-length clones for the three CesAs that are highly expressed in developing xylem and examined their phylogenetic relationships and expression patterns in loblolly pine tissues. Full-length CesA clones were isolated from cDNA of developing loblolly pine (Pinus taeda) xylem and phylogenetic inferences made from plant CesA protein sequences. Expression of the three genes was examined by Northern blot analysis and semiquantitative RT-PCR. Each of three PtCesA genes is orthologous to one of the three angiosperm secondary cell wall CesAs. The PtCesAs are coexpressed in tissues of loblolly pine with tissues undergoing secondary cell wall biosynthesis showing the highest levels of expression. Phylogenetic and expression analyses suggest that functional roles for these loblolly pine CesAs are analogous to those of orthologs in angiosperm taxa. Based upon evidence from this and other studies, we suggest division of seed plant CesA genes into six major paralogous groups, each containing orthologs from various taxa. Available evidence suggests that paralogous CesA genes and their distinct functional roles evolved before the divergence of gymnosperm and angiosperm lineages.

  10. Rye Pm8 and wheat Pm3 are orthologous genes and show evolutionary conservation of resistance function against powdery mildew.

    Science.gov (United States)

    Hurni, Severine; Brunner, Susanne; Buchmann, Gabriele; Herren, Gerhard; Jordan, Tina; Krukowski, Patricia; Wicker, Thomas; Yahiaoui, Nabila; Mago, Rohit; Keller, Beat

    2013-12-01

    The improvement of wheat through breeding has relied strongly on the use of genetic material from related wild and domesticated grass species. The 1RS chromosome arm from rye was introgressed into wheat and crossed into many wheat lines, as it improves yield and fungal disease resistance. Pm8 is a powdery mildew resistance gene on 1RS which, after widespread agricultural cultivation, is now widely overcome by adapted mildew races. Here we show by homology-based cloning and subsequent physical and genetic mapping that Pm8 is the rye orthologue of the Pm3 allelic series of mildew resistance genes in wheat. The cloned gene was functionally validated as Pm8 by transient, single-cell expression analysis and stable transformation. Sequence analysis revealed a complex mosaic of ancient haplotypes among Pm3- and Pm8-like genes from different members of the Triticeae. These results show that the two genes have evolved independently after the divergence of the species 7.5 million years ago and kept their function in mildew resistance. During this long time span the co-evolving pathogens have not overcome these genes, which is in strong contrast to the breakdown of Pm8 resistance since its introduction into commercial wheat 70 years ago. Sequence comparison revealed that evolutionary pressure acted on the same subdomains and sequence features of the two orthologous genes. This suggests that they recognize directly or indirectly the same pathogen effectors that have been conserved in the powdery mildews of wheat and rye.

  11. Open source tool for prediction of genome wide protein-protein interaction network based on ortholog information

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    Pedamallu Chandra Sekhar

    2010-08-01

    Full Text Available Abstract Background Protein-protein interactions are crucially important for cellular processes. Knowledge of these interactions improves the understanding of cell cycle, metabolism, signaling, transport, and secretion. Information about interactions can hint at molecular causes of diseases, and can provide clues for new therapeutic approaches. Several (usually expensive and time consuming experimental methods can probe protein - protein interactions. Data sets, derived from such experiments make the development of prediction methods feasible, and make the creation of protein-protein interaction network predicting tools possible. Methods Here we report the development of a simple open source program module (OpenPPI_predictor that can generate a putative protein-protein interaction network for target genomes. This tool uses the orthologous interactome network data from a related, experimentally studied organism. Results Results from our predictions can be visualized using the Cytoscape visualization software, and can be piped to downstream processing algorithms. We have employed our program to predict protein-protein interaction network for the human parasite roundworm Brugia malayi, using interactome data from the free living nematode Caenorhabditis elegans. Availability The OpenPPI_predictor source code is available from http://tools.neb.com/~posfai/.

  12. The ABCs of eye color in Tribolium castaneum: orthologs of the Drosophila white, scarlet, and brown Genes.

    Science.gov (United States)

    Grubbs, Nathaniel; Haas, Sue; Beeman, Richard W; Lorenzen, Marcé D

    2015-03-01

    In Drosophila melanogaster, each of the three paralogous ABC transporters, White, Scarlet and Brown, is required for normal pigmentation of the compound eye. We have cloned the three orthologous genes from the beetle Tribolium castaneum. Conceptual translations of Tribolium white (Tcw), scarlet (Tcst), and brown (Tcbw) are 51, 48, and 32% identical to their respective Drosophila counterparts. We have identified loss-of-eye-pigment strains that bear mutations in Tcw and Tcst: the Tcw gene in the ivory (i) strain carries a single-base transversion, which leads to an E → D amino-acid substitution in the highly conserved Walker B motif, while the Tcst gene in the pearl (p) strain has a deletion resulting in incorporation of a premature stop codon. In light of these findings, the mutant strains i and p are herein renamed white(ivory) (w(i)) and scarlet(pearl) (st(p)), respectively. In addition, RNA inhibition of Tcw and Tcst recapitulates the mutant phenotypes, confirming the roles of these genes in normal eye pigmentation, while RNA interference of Tcbw provides further evidence that it has no role in eye pigmentation in Tribolium. We also consider the evolutionary implications of our findings.

  13. The COP1 ortholog PPS regulates the juvenile-adult and vegetative-reproductive phase changes in rice.

    Science.gov (United States)

    Tanaka, Nobuhiro; Itoh, Hironori; Sentoku, Naoki; Kojima, Mikiko; Sakakibara, Hitoshi; Izawa, Takeshi; Itoh, Jun-Ichi; Nagato, Yasuo

    2011-06-01

    Because plant reproductive development occurs only in adult plants, the juvenile-to-adult phase change is an indispensable part of the plant life cycle. We identified two allelic mutants, peter pan syndrome-1 (pps-1) and pps-2, that prolong the juvenile phase in rice (Oryza sativa) and showed that rice PPS is an ortholog of Arabidopsis thaliana CONSTITUTIVE PHOTOMORPHOGENIC1. The pps-1 mutant exhibits delayed expression of miR156 and miR172 and the suppression of GA biosynthetic genes, reducing the GA(3) content in this mutant. In spite of its prolonged juvenile phase, the pps-1 mutant flowers early, and this is associated with derepression of RAP1B expression in pps-1 plants independently of the Hd1-Hd3a/RFT1 photoperiodic pathway. PPS is strongly expressed in the fourth and fifth leaves, suggesting that it regulates the onset of the adult phase downstream of MORI1 and upstream of miR156 and miR172. Its ability to regulate the vegetative phase change and the time of flowering suggests that rice PPS acquired novel functions during the evolution of rice/monocots.

  14. Makorin ortholog LEP-2 regulates LIN-28 stability to promote the juvenile-to-adult transition in Caenorhabditis elegans.

    Science.gov (United States)

    Herrera, R Antonio; Kiontke, Karin; Fitch, David H A

    2016-03-01

    The heterochronic genes lin-28, let-7 and lin-41 regulate fundamental developmental transitions in animals, such as stemness versus differentiation and juvenile versus adult states. We identify a new heterochronic gene, lep-2, in Caenorhabditis elegans. Mutations in lep-2 cause a delay in the juvenile-to-adult transition, with adult males retaining pointed, juvenile tail tips, and displaying defective sexual behaviors. In both sexes, lep-2 mutants fail to cease molting or produce an adult cuticle. We find that LEP-2 post-translationally regulates LIN-28 by promoting LIN-28 protein degradation. lep-2 encodes the sole C. elegans ortholog of the Makorin (Mkrn) family of proteins. Like lin-28 and other heterochronic pathway members, vertebrate Mkrns are involved in developmental switches, including the timing of pubertal onset in humans. Based on shared roles, conservation and the interaction between lep-2 and lin-28 shown here, we propose that Mkrns, together with other heterochronic genes, constitute an evolutionarily ancient conserved module regulating switches in development.

  15. p53 inhibits autophagy by interacting with the human ortholog of yeast Atg17, RB1CC1/FIP200.

    Science.gov (United States)

    Morselli, Eugenia; Shen, Shensi; Ruckenstuhl, Christoph; Bauer, Maria Anna; Mariño, Guillermo; Galluzzi, Lorenzo; Criollo, Alfredo; Michaud, Mickael; Maiuri, Maria Chiara; Chano, Tokuhiro; Madeo, Frank; Kroemer, Guido

    2011-08-15

    The tumor suppressor protein p53 tonically suppresses autophagy when it is present in the cytoplasm. This effect is phylogenetically conserved from mammals to nematodes, and human p53 can inhibit autophagy in yeast, as we show here. Bioinformatic investigations of the p53 interactome in relationship to the autophagy-relevant protein network underscored the possible relevance of a direct molecular interaction between p53 and the mammalian ortholog of the essential yeast autophagy protein Atg17, namely RB1-inducible coiled-coil protein 1 (RB1CC1), also called FAK family kinase-interacting protein of 200 KDa (FIP200). Mutational analyses revealed that a single point mutation in p53 (K382R) abolished its capacity to inhibit autophagy upon transfection into p53-deficient human colon cancer or yeast cells. In conditions in which wild-type p53 co-immunoprecipitated with RB1CC1/FIP200, p53 (K382R) failed to do so, underscoring the importance of the physical interaction between these proteins for the control of autophagy. In conclusion, p53 regulates autophagy through a direct molecular interaction with RB1CC1/FIP200, a protein that is essential for the very apical step of autophagy initiation.

  16. Genetic variation in the Solanaceae fruit bearing species lulo and tree tomato revealed by Conserved Ortholog (COSII markers

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    Felix Enciso-Rodríguez

    2010-01-01

    Full Text Available The Lulo or naranjilla (Solanum quitoense Lam. and the tree tomato or tamarillo (Solanum betaceum Cav. Sendt. are both Andean tropical fruit species with high nutritional value and the potential for becoming premium products in local and export markets. Herein, we present a report on the genetic characterization of 62 accessions of lulos (n = 32 and tree tomatoes (n = 30 through the use of PCR-based markers developed from single-copy conserved orthologous genes (COSII in other Solanaceae (Asterid species. We successfully PCR amplified a set of these markers for lulos (34 out of 46 initially tested and tree tomatoes (26 out of 41 for molecular studies. Six polymorphic COSII markers were found in lulo with a total of 47 alleles and five polymorphic markers in tree tomato with a total of 39 alleles in the two populations. Further genetic analyses indicated a high population structure (with F ST > 0.90, which may be a result of low migration between populations, adaptation to various niches and the number of markers evaluated. We propose COSII markers as sound tools for molecular studies, conservation and the breeding of these two fruit species.

  17. Serine- and threonine/valine-dependent activation of PDK and Tor orthologs converge on Sch9 to promote aging.

    Science.gov (United States)

    Mirisola, Mario G; Taormina, Giusi; Fabrizio, Paola; Wei, Min; Hu, Jia; Longo, Valter D

    2014-02-01

    Dietary restriction extends longevity in organisms ranging from bacteria to mice and protects primates from a variety of diseases, but the contribution of each dietary component to aging is poorly understood. Here we demonstrate that glucose and specific amino acids promote stress sensitization and aging through the differential activation of the Ras/cAMP/PKA, PKH1/2 and Tor/S6K pathways. Whereas glucose sensitized cells through a Ras-dependent mechanism, threonine and valine promoted cellular sensitization and aging primarily by activating the Tor/S6K pathway and serine promoted sensitization via PDK1 orthologs Pkh1/2. Serine, threonine and valine activated a signaling network in which Sch9 integrates TORC1 and Pkh signaling via phosphorylation of threonines 570 and 737 and promoted intracellular relocalization and transcriptional inhibition of the stress resistance protein kinase Rim15. Because of the conserved pro-aging role of nutrient and growth signaling pathways in higher eukaryotes, these results raise the possibility that similar mechanisms contribute to aging in mammals.

  18. Ectopic expression of TrPI, a Taihangia rupestris (Rosaceae) PI ortholog, causes modifications of vegetative architecture in Arabidopsis.

    Science.gov (United States)

    Lü, Shanhua; Fan, Yinglun; Liu, Like; Liu, Shujun; Zhang, Wenhui; Meng, Zheng

    2010-12-15

    In eudicotyledonous model plants, the B-function genes encode a pair of partner MADS-domain proteins, APETALA3 (AP3) and PISTILLATA (PI) in Arabidopsis and DEFICIENS (DEF) and GLOBOSA (GLO) in Antirrhinum. These proteins, which must form heterodimers to function, are required to specify petal and stamen identity during flower development. Here, we report cloning and characterization of TrPI (Taihangia rupestris PISTILLATA), a PI/GLO-like gene from the core eudicot species Taihangia rupestris (Rosaceae). DNA gel blot analysis showed that TrPI is a single copy gene in the T. rupestris genome. Quantitative RT-PCR and in situ hybridization analyses revealed that TrPI is transcribed in both the vegetative and reproductive organs at different levels. Ectopic expression of TrPI in Arabidopsis caused severe modifications in vegetative plant architecture, including rosette leaves and cauline leaves arranged in a non-spiral phyllotaxy, and a flattened primary inflorescence stem that produced two or three offshoots at the base, middle or top. Moreover, we show that the TrPI gene is capable of rescuing pi-1 mutant phenotypes. Yeast two-hybrid assays showed that TrPI forms homodimers. Taken together, these results show that TrPI might function in regulating plant architecture in addition to its function as a floral organ identity gene in T. rupestris, suggesting that the TrPI protein has biochemical features that distinguish it from the well-studied orthologs, PI and GLO.

  19. Host-species transferrin receptor 1 orthologs are cellular receptors for nonpathogenic new world clade B arenaviruses.

    Directory of Open Access Journals (Sweden)

    Jonathan Abraham

    2009-04-01

    Full Text Available The ability of a New World (NW clade B arenavirus to enter cells using human transferrin receptor 1 (TfR1 strictly correlates with its ability to cause hemorrhagic fever. Amapari (AMAV and Tacaribe (TCRV, two nonpathogenic NW clade B arenaviruses that do not use human TfR1, are closely related to the NW arenaviruses that cause hemorrhagic fevers. Here we show that pseudotyped viruses bearing the surface glycoprotein (GP of AMAV or TCRV can infect cells using the TfR1 orthologs of several mammalian species, including those of their respective natural hosts, the small rodent Neacomys spinosus and the fruit bat Artibeus jamaicensis. Mutation of one residue in human TfR1 makes it a functional receptor for TCRV, and mutation of four residues makes it a functional receptor for AMAV. Our data support an in vivo role for TfR1 in the replication of most, if not all, NW clade B arenaviruses, and suggest that with modest changes in their GPs the nonpathogenic arenaviruses could use human TfR1 and emerge as human pathogens.

  20. A role in immunity for Arabidopsis cysteine protease RD21, the ortholog of the tomato immune protease C14.

    Directory of Open Access Journals (Sweden)

    Takayuki Shindo

    Full Text Available Secreted papain-like Cys proteases are important players in plant immunity. We previously reported that the C14 protease of tomato is targeted by cystatin-like EPIC proteins that are secreted by the oomycete pathogen Phytophthora infestans (Pinf during infection. C14 has been under diversifying selection in wild potato species coevolving with Pinf and reduced C14 levels result in enhanced susceptibility for Pinf. Here, we investigated the role C14-EPIC-like interactions in the natural pathosystem of Arabidopsis with the oomycete pathogen Hyaloperonospora arabidopsidis (Hpa. In contrast to the Pinf-solanaceae pathosystem, the C14 orthologous protease of Arabidopsis, RD21, does not evolve under diversifying selection in Arabidopsis, and rd21 null mutants do not show phenotypes upon compatible and incompatible Hpa interactions, despite the evident lack of a major leaf protease. Hpa isolates express highly conserved EPIC-like proteins during infections, but it is unknown if these HpaEPICs can inhibit RD21 and one of these HpaEPICs even lacks the canonical cystatin motifs. The rd21 mutants are unaffected in compatible and incompatible interactions with Pseudomonas syringae pv. tomato, but are significantly more susceptible for the necrotrophic fungal pathogen Botrytis cinerea, demonstrating that RD21 provides immunity to a necrotrophic pathogen.

  1. DNA microarray data integration by ortholog gene analysis reveals potential molecular mechanisms of estrogen-dependent growth of human uterine fibroids

    Directory of Open Access Journals (Sweden)

    Shou Jianyong

    2007-04-01

    Full Text Available Abstract Background Uterine fibroids or leiomyoma are a common benign smooth muscle tumor. The tumor growth is well known to be estrogen-dependent. However, the molecular mechanisms of its estrogen-dependency is not well understood. Methods Differentially expressed genes in human uterine fibroids were either retrieved from published papers or from our own statistical analysis of downloaded array data. Probes for the same genes on different Affymetrix chips were mapped based on probe comparison information provided by Affymetrix. Genes identified by two or three array studies were submitted for ortholog analysis. Human and rat ortholog genes were identified by using ortholog gene databases, HomoloGene and TOGA and were confirmed by synteny analysis with MultiContigView tool in the Ensembl genome browser. Results By integrated analysis of three recently published DNA microarray studies with human tissue, thirty-eight genes were found to be differentially expressed in the same direction in fibroid compared to adjacent uterine myometrium by at least two research groups. Among these genes, twelve with rat orthologs were identified as estrogen-regulated from our array study investigating uterine expression in ovariectomized rats treated with estrogen. Functional and pathway analyses of the twelve genes suggested multiple molecular mechanisms for estrogen-dependent cell survival and tumor growth. Firstly, estrogen increased expression of the anti-apoptotic PCP4 gene and suppressed the expression of growth inhibitory receptors PTGER3 and TGFBR2. Secondly, estrogen may antagonize PPARγ signaling, thought to inhibit fibroid growth and survival, at two points in the PPAR pathway: 1 through increased ANXA1 gene expression which can inhibit phospholipase A2 activity and in turn decrease arachidonic acid synthesis, and 2 by decreasing L-PGDS expression which would reduce synthesis of PGJ2, an endogenous ligand for PPARγ. Lastly, estrogen affects retinoic

  2. Mouse FGF15 is the ortholog of human and chick FGF19, but is not uniquely required for otic induction.

    Science.gov (United States)

    Wright, Tracy J; Ladher, Raj; McWhirter, John; Murre, Cornelis; Schoenwolf, Gary C; Mansour, Suzanne L

    2004-05-01

    The inner ear develops from an ectodermal placode that is specified by inductive signals from the adjacent neurectoderm and underlying mesoderm. In chick, fibroblast growth factor (Fgf)-19 is expressed in mesoderm underlying the presumptive otic placode, and human FGF19 induces expression of otic markers in a tissue explant containing neural plate and surface ectoderm. We show here that mouse Fgf15 is the sequence homolog of chick and human Fgf19/FGF19. In addition, we show that FGF15, like FGF19, is sufficient to induce expression of otic markers in a chick explant assay, suggesting that these FGFs are orthologs. Mouse embryos lacking Fgf15, however, do not have otic abnormalities at E9.5-E10.5, suggesting that Fgf15 is not uniquely required for otic induction or early patterning of the otocyst. To compare FGF15 and FGF19 signaling components and assess where signals potentially redundant with FGF15 might function, we determined the expression patterns of Fgf15 and Fgf19. Unlike Fgf19, Fgf15 is not expressed in mesoderm underlying the presumptive otic placode, but is expressed in the adjacent neurectoderm. Fgfr4, which encodes the likely receptor for both FGF19 and FGF15, is expressed in the neurectoderm of both species, and is also expressed in the mesoderm only in chick. These results suggest the hypotheses that during otic induction, FGF19 signals in either an autocrine fashion to the mesoderm or a paracrine fashion to the neurectoderm, whereas FGF15 signals in an autocrine fashion to the neurectoderm. Thus, the FGFs that signal to the neurectoderm are the best potential candidates for redundancy with FGF15 during mouse otic development.

  3. Fermitins, the orthologs of mammalian Kindlins, regulate the development of a functional cardiac syncytium in Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    James H Catterson

    Full Text Available The vertebrate Kindlins are an evolutionarily conserved family of proteins critical for integrin signalling and cell adhesion. Kindlin-2 (KIND2 is associated with intercalated discs in mice, suggesting a role in cardiac syncytium development; however, deficiency of Kind2 leads to embryonic lethality. Morpholino knock-down of Kind2 in zebrafish has a pleiotropic effect on development that includes the heart. It therefore remains unclear whether cardiomyocyte Kind2 expression is required for cardiomyocyte junction formation and the development of normal cardiac function. To address this question, the expression of Fermitin 1 and Fermitin 2 (Fit1, Fit2, the two Drosophila orthologs of Kind2, was silenced in Drosophila cardiomyocytes. Heart development was assessed in adult flies by immunological methods and videomicroscopy. Silencing both Fit1 and Fit2 led to a severe cardiomyopathy characterised by the failure of cardiomyocytes to develop as a functional syncytium and loss of synchrony between cardiomyocytes. A null allele of Fit1 was generated but this had no impact on the heart. Similarly, the silencing of Fit2 failed to affect heart function. In contrast, the silencing of Fit2 in the cardiomyocytes of Fit1 null flies disrupted syncytium development, leading to severe cardiomyopathy. The data definitively demonstrate a role for Fermitins in the development of a functional cardiac syncytium in Drosophila. The findings also show that the Fermitins can functionally compensate for each other in order to control syncytium development. These findings support the concept that abnormalities in cardiomyocyte KIND2 expression or function may contribute to cardiomyopathies in humans.

  4. Drosophila Brat and Human Ortholog TRIM3 Maintain Stem Cell Equilibrium and Suppress Brain Tumorigenesis by Attenuating Notch Nuclear Transport.

    Science.gov (United States)

    Mukherjee, Subhas; Tucker-Burden, Carol; Zhang, Changming; Moberg, Kenneth; Read, Renee; Hadjipanayis, Costas; Brat, Daniel J

    2016-04-15

    Cancer stem cells exert enormous influence on neoplastic behavior, in part by governing asymmetric cell division and the balance between self-renewal and multipotent differentiation. Growth is favored by deregulated stem cell division, which enhances the self-renewing population and diminishes the differentiation program. Mutation of a single gene in Drosophila, Brain Tumor (Brat), leads to disrupted asymmetric cell division resulting in dramatic neoplastic proliferation of neuroblasts and massive larval brain overgrowth. To uncover the mechanisms relevant to deregulated cell division in human glioma stem cells, we first developed a novel adult Drosophila brain tumor model using brat-RNAi driven by the neuroblast-specific promoter inscuteable Suppressing Brat in this population led to the accumulation of actively proliferating neuroblasts and a lethal brain tumor phenotype. brat-RNAi caused upregulation of Notch signaling, a node critical for self-renewal, by increasing protein expression and enhancing nuclear transport of Notch intracellular domain (NICD). In human glioblastoma, we demonstrated that the human ortholog of Drosophila Brat, tripartite motif-containing protein 3 (TRIM3), similarly suppressed NOTCH1 signaling and markedly attenuated the stem cell component. We also found that TRIM3 suppressed nuclear transport of active NOTCH1 (NICD) in glioblastoma and demonstrated that these effects are mediated by direct binding of TRIM3 to the Importin complex. Together, our results support a novel role for Brat/TRIM3 in maintaining stem cell equilibrium and suppressing tumor growth by regulating NICD nuclear transport. Cancer Res; 76(8); 2443-52. ©2016 AACR.

  5. Both STING and MAVS fish orthologs contribute to the induction of interferon mediated by RIG-I.

    Directory of Open Access Journals (Sweden)

    Stéphane Biacchesi

    Full Text Available Viral infections are detected in most cases by the host innate immune system through pattern-recognition receptors (PRR, the sensors for pathogen-associated molecular patterns (PAMPs, which induce the production of cytokines, such as type I interferons (IFN. Recent identification in mammalian and teleost fish of cytoplasmic viral RNA sensors, RIG-I-like receptors (RLRs, and their mitochondrial adaptor: the mitochondrial antiviral signaling (MAVS protein, also called IPS-1, highlight their important role in the induction of IFN at the early stage of a virus infection. More recently, an endoplasmic reticulum (ER adaptor: the stimulator of interferon genes (STING protein, also called MITA, ERIS and MPYS, has been shown to play a pivotal role in response to both non-self-cytosolic RNA and dsDNA. In this study, we cloned STING cDNAs from zebrafish and showed that it was an ortholog to mammalian STING. We demonstrated that overexpression of this ER protein in fish cells led to a constitutive induction of IFN and interferon-stimulated genes (ISGs. STING-overexpressing cells were almost fully protected against RNA virus infection with a strong inhibition of both DNA and RNA virus replication. In addition, we found that together with MAVS, STING was an important player in the RIG-I IFN-inducing pathway. This report provides the demonstration that teleost fish possess a functional RLR pathway in which MAVS and STING are downstream signaling molecules of RIG-I. The Sequences presented in this article have been submitted to GenBank under accession numbers: Zebrafish STING (HE856619; EPC STING (HE856620; EPC IRF3 (HE856621; EPC IFN promoter (HE856618.

  6. Mitochondrial localization of the threonine peptidase PfHslV, a ClpQ ortholog in Plasmodium falciparum.

    Science.gov (United States)

    Tschan, Serena; Kreidenweiss, Andrea; Stierhof, York-Dieter; Sessler, Nicole; Fendel, Rolf; Mordmüller, Benjamin

    2010-11-01

    Plasmodium falciparum belongs to a group of eukaryotes expressing an ortholog of the prokaryotic T1-threonine peptidase, heat shock locus V (HslV). Bacterial HslV is a particularly well studied protease, due to its structural and biochemical similarity to the eukaryotic proteasome. Plasmodium falciparum HslV (PfHslV) is expressed in schizonts and merozoites of the asexual blood stage. Strong sequence conservation between plasmodial species, absence of HslV homologs in the human genome, and availability of specific inhibitors led us to explore its function and potential use as a drug target. In a first step, we investigated localization of PfHslV, using a bioinformatics approach and a transgenic P. falciparum line expressing a PfHslV-enhanced yellow fluorescent protein (EYFP) fusion protein from the endogenous pfhslV locus. PfHslV-EYFP was found in the mitochondrial matrix under fluorescence and immunoelectron microscopy. Endogenous, non-modified PfHslV was present in purified mitochondria and interference with mitochondrial membrane potential by drug treatment led to impairment of PfHslV processing. Import of heterologous EYFP into the plasmodial mitochondrion is mediated by the N-terminal 37 amino acids of PfHslV. PfHslV's targeting sequence is also functional in human cells, demonstrating strong conservation of mitochondrial targeting in eukaryotes. In conclusion, our data shows that PfHslV is located to the plasmodial mitochondrion and presumably has vital function within this organelle which makes it an attractive target for interventions.

  7. A neonatal encephalopathy with seizures in standard poodle dogs with a missense mutation in the canine ortholog of ATF2.

    Science.gov (United States)

    Chen, Xuhua; Johnson, Gary S; Schnabel, Robert D; Taylor, Jeremy F; Johnson, Gayle C; Parker, Heidi G; Patterson, Edward E; Katz, Martin L; Awano, Tomoyuki; Khan, Shahwanaz; O'Brien, Dennis P

    2008-02-01

    Neonatal encephalopathy with seizures (NEWS) is a previously undescribed autosomal recessive disease of standard poodle puppies. Affected puppies are small and weak at birth. Many die in their first week of life. Those surviving past 1 week develop ataxia, a whole-body tremor, and, by 4 to 6 weeks of age, severe generalized clonic-tonic seizures. None have survived to 7 weeks of age. Cerebella from affected puppies were reduced in size and often contained dysplastic foci consisting of clusters of intermixed granule and Purkinje neurons. We used deoxyribonucleic acid samples from related standard poodles to map the NEWS locus to a 2.87-Mb segment of CFA36, which contains the canine ortholog of ATF2. This gene encodes activating transcription factor 2 (ATF-2), which participates in the cellular responses to a wide variety of stimuli. We amplified and sequenced all coding regions of canine ATF2 from a NEWS-affected puppy and identified a T > G transversion that predicts a methionine-to-arginine missense mutation at amino acid position 51. Methionine-51 lies within a hydrophobic docking site for mitogen-activated protein kinases that activate ATF-2 so the arginine substitution is likely to interfere with ATF-2 activation. All 20 NEWS-affected puppies in the standard poodle family were homozygous for the mutant G allele. The 58 clinically normal family members were either G/T heterozygotes or homozygous for the ancestral T allele. There are no previous reports of spontaneous ATF2 mutations in people or animals; however, atf2-knockout mice have cerebellar lesions that are similar to those in puppies with NEWS.

  8. Saccharomyces cerevisiae Bat1 and Bat2 aminotransferases have functionally diverged from the ancestral-like Kluyveromyces lactis orthologous enzyme.

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    Maritrini Colón

    Full Text Available BACKGROUND: Gene duplication is a key evolutionary mechanism providing material for the generation of genes with new or modified functions. The fate of duplicated gene copies has been amply discussed and several models have been put forward to account for duplicate conservation. The specialization model considers that duplication of a bifunctional ancestral gene could result in the preservation of both copies through subfunctionalization, resulting in the distribution of the two ancestral functions between the gene duplicates. Here we investigate whether the presumed bifunctional character displayed by the single branched chain amino acid aminotransferase present in K. lactis has been distributed in the two paralogous genes present in S. cerevisiae, and whether this conservation has impacted S. cerevisiae metabolism. PRINCIPAL FINDINGS: Our results show that the KlBat1 orthologous BCAT is a bifunctional enzyme, which participates in the biosynthesis and catabolism of branched chain aminoacids (BCAAs. This dual role has been distributed in S. cerevisiae Bat1 and Bat2 paralogous proteins, supporting the specialization model posed to explain the evolution of gene duplications. BAT1 is highly expressed under biosynthetic conditions, while BAT2 expression is highest under catabolic conditions. Bat1 and Bat2 differential relocalization has favored their physiological function, since biosynthetic precursors are generated in the mitochondria (Bat1, while catabolic substrates are accumulated in the cytosol (Bat2. Under respiratory conditions, in the presence of ammonium and BCAAs the bat1Δ bat2Δ double mutant shows impaired growth, indicating that Bat1 and Bat2 could play redundant roles. In K. lactis wild type growth is independent of BCAA degradation, since a Klbat1Δ mutant grows under this condition. CONCLUSIONS: Our study shows that BAT1 and BAT2 differential expression and subcellular relocalization has resulted in the distribution of the

  9. The powdery mildew resistance gene Pm8 derived from rye is suppressed by its wheat ortholog Pm3.

    Science.gov (United States)

    Hurni, Severine; Brunner, Susanne; Stirnweis, Daniel; Herren, Gerhard; Peditto, David; McIntosh, Robert A; Keller, Beat

    2014-09-01

    The powdery mildew resistance gene Pm8 derived from rye is located on a 1BL.1RS chromosome translocation in wheat. However, some wheat lines with this translocation do not show resistance to isolates of the wheat powdery mildew pathogen avirulent to Pm8 due to an unknown genetically dominant suppression mechanism. Here we show that lines with suppressed Pm8 activity contain an intact and expressed Pm8 gene. Therefore, the absence of Pm8 function in certain 1BL.1RS-containing wheat lines is not the result of gene loss or mutation but is based on suppression. The wheat gene Pm3, an ortholog of rye Pm8, suppressed Pm8-mediated powdery mildew resistance in lines containing Pm8 in a transient single-cell expression assay. This result was further confirmed in transgenic lines with combined Pm8 and Pm3 transgenes. Expression analysis revealed that suppression is not the result of gene silencing, either in wheat 1BL.1RS translocation lines carrying Pm8 or in transgenic genotypes with both Pm8 and Pm3 alleles. In addition, a similar abundance of the PM8 and PM3 proteins in single or double homozygous transgenic lines suggested that a post-translational mechanism is involved in suppression of Pm8. Co-expression of Pm8 and Pm3 genes in Nicotiana benthamiana leaves followed by co-immunoprecipitation analysis showed that the two proteins interact. Therefore, the formation of a heteromeric protein complex might result in inefficient or absent signal transmission for the defense reaction. These data provide a molecular explanation for the suppression of resistance genes in certain genetic backgrounds and suggest ways to circumvent it in future plant breeding.

  10. New species of Ehrlichia isolated from Rhipicephalus (Boophilus microplus shows an ortholog of the E. canis major immunogenic glycoprotein gp36 with a new sequence of tandem repeats

    Directory of Open Access Journals (Sweden)

    Cruz Alejandro Cabezas

    2012-12-01

    Full Text Available Abstract Background Ehrlichia species are the etiological agents of emerging and life-threatening tick-borne human zoonoses that inflict serious and fatal infections in companion animals and livestock. The aim of this paper was to phylogeneticaly characterise a new species of Ehrlichia isolated from Rhipicephalus (Boophilus microplus from Minas Gerais, Brazil. Methods The agent was isolated from the hemolymph of Rhipicephalus (B. microplus engorged females that had been collected from naturally infested cattle in a farm in the state of Minas Gerais, Brazil. This agent was then established and cultured in IDE8 tick cells. The molecular and phylogenetic analysis was based on 16S rRNA, groEL, dsb, gltA and gp36 genes. We used the maximum likelihood method to construct the phylogenetic trees. Results The phylogenetic trees based on 16S rRNA, groEL, dsb and gltA showed that the Ehrlichia spp isolated in this study falls in a clade separated from any previously reported Ehrlichia spp. The molecular analysis of the ortholog of gp36, the major immunoreactive glycoproteins in E. canis and ortholog of the E. chaffeensis gp47, showed a unique tandem repeat of 9 amino acids (VPAASGDAQ when compared with those reported for E. canis, E. chaffeensis and the related mucin-like protein in E. ruminantium. Conclusions Based on the molecular and phylogenetic analysis of the 16S rRNA, groEL, dsb and gltA genes we concluded that this tick-derived microorganism isolated in Brazil is a new species, named E. mineirensis (UFMG-EV, with predicted novel antigenic properties in the gp36 ortholog glycoprotein. Further studies on this new Ehrlichia spp should address questions about its transmissibility by ticks and its pathogenicity for mammalian hosts.

  11. Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer

    Directory of Open Access Journals (Sweden)

    Wolf Yuri I

    2012-12-01

    Full Text Available Abstract Background Collections of Clusters of Orthologous Genes (COGs provide indispensable tools for comparative genomic analysis, evolutionary reconstruction and functional annotation of new genomes. Initially, COGs were made for all complete genomes of cellular life forms that were available at the time. However, with the accumulation of thousands of complete genomes, construction of a comprehensive COG set has become extremely computationally demanding and prone to error propagation, necessitating the switch to taxon-specific COG collections. Previously, we reported the collection of COGs for 41 genomes of Archaea (arCOGs. Here we present a major update of the arCOGs and describe evolutionary reconstructions to reveal general trends in the evolution of Archaea. Results The updated version of the arCOG database incorporates 91% of the pangenome of 120 archaea (251,032 protein-coding genes altogether into 10,335 arCOGs. Using this new set of arCOGs, we performed maximum likelihood reconstruction of the genome content of archaeal ancestral forms and gene gain and loss events in archaeal evolution. This reconstruction shows that the last Common Ancestor of the extant Archaea was an organism of greater complexity than most of the extant archaea, probably with over 2,500 protein-coding genes. The subsequent evolution of almost all archaeal lineages was apparently dominated by gene loss resulting in genome streamlining. Overall, in the evolution of Archaea as well as a representative set of bacteria that was similarly analyzed for comparison, gene losses are estimated to outnumber gene gains at least 4 to 1. Analysis of specific patterns of gene gain in Archaea shows that, although some groups, in particular Halobacteria, acquire substantially more genes than others, on the whole, gene exchange between major groups of Archaea appears to be largely random, with no major ‘highways’ of horizontal gene transfer. Conclusions The updated collection

  12. The tailless ortholog nhr-67 regulates patterning of gene expression and morphogenesis in the C. elegans vulva.

    Science.gov (United States)

    Fernandes, Jolene S; Sternberg, Paul W

    2007-04-27

    Regulation of spatio-temporal gene expression in diverse cell and tissue types is a critical aspect of development. Progression through Caenorhabditis elegans vulval development leads to the generation of seven distinct vulval cell types (vulA, vulB1, vulB2, vulC, vulD, vulE, and vulF), each with its own unique gene expression profile. The mechanisms that establish the precise spatial patterning of these mature cell types are largely unknown. Dissection of the gene regulatory networks involved in vulval patterning and differentiation would help us understand how cells generate a spatially defined pattern of cell fates during organogenesis. We disrupted the activity of 508 transcription factors via RNAi and assayed the expression of ceh-2, a marker for vulB fate during the L4 stage. From this screen, we identified the tailless ortholog nhr-67 as a novel regulator of gene expression in multiple vulval cell types. We find that one way in which nhr-67 maintains cell identity is by restricting inappropriate cell fusion events in specific vulval cells, namely vulE and vulF. nhr-67 exhibits a dynamic expression pattern in the vulval cells and interacts with three other transcriptional regulators cog-1 (Nkx6.1/6.2), lin-11 (LIM), and egl-38 (Pax2/5/8) to generate the composite expression patterns of their downstream targets. We provide evidence that egl-38 regulates gene expression in vulB1, vulC, vulD, vulE, as well as vulF cells. We demonstrate that the pairwise interactions between these regulatory genes are complex and vary among the seven cell types. We also discovered a striking regulatory circuit that affects a subset of the vulval lineages: cog-1 and nhr-67 inhibit both one another and themselves. We postulate that the differential levels and combinatorial patterns of lin-11, cog-1, and nhr-67 expression are a part of a regulatory code for the mature vulval cell types.

  13. The tailless ortholog nhr-67 regulates patterning of gene expression and morphogenesis in the C. elegans vulva.

    Directory of Open Access Journals (Sweden)

    Jolene S Fernandes

    2007-04-01

    Full Text Available Regulation of spatio-temporal gene expression in diverse cell and tissue types is a critical aspect of development. Progression through Caenorhabditis elegans vulval development leads to the generation of seven distinct vulval cell types (vulA, vulB1, vulB2, vulC, vulD, vulE, and vulF, each with its own unique gene expression profile. The mechanisms that establish the precise spatial patterning of these mature cell types are largely unknown. Dissection of the gene regulatory networks involved in vulval patterning and differentiation would help us understand how cells generate a spatially defined pattern of cell fates during organogenesis. We disrupted the activity of 508 transcription factors via RNAi and assayed the expression of ceh-2, a marker for vulB fate during the L4 stage. From this screen, we identified the tailless ortholog nhr-67 as a novel regulator of gene expression in multiple vulval cell types. We find that one way in which nhr-67 maintains cell identity is by restricting inappropriate cell fusion events in specific vulval cells, namely vulE and vulF. nhr-67 exhibits a dynamic expression pattern in the vulval cells and interacts with three other transcriptional regulators cog-1 (Nkx6.1/6.2, lin-11 (LIM, and egl-38 (Pax2/5/8 to generate the composite expression patterns of their downstream targets. We provide evidence that egl-38 regulates gene expression in vulB1, vulC, vulD, vulE, as well as vulF cells. We demonstrate that the pairwise interactions between these regulatory genes are complex and vary among the seven cell types. We also discovered a striking regulatory circuit that affects a subset of the vulval lineages: cog-1 and nhr-67 inhibit both one another and themselves. We postulate that the differential levels and combinatorial patterns of lin-11, cog-1, and nhr-67 expression are a part of a regulatory code for the mature vulval cell types.

  14. Identification and characterization of the Non-race specific Disease Resistance 1 (NDR1 orthologous protein in coffee

    Directory of Open Access Journals (Sweden)

    Mongrand Sébastien

    2011-10-01

    Full Text Available Abstract Background Leaf rust, which is caused by the fungus Hemileia vastatrix (Pucciniales, is a devastating disease that affects coffee plants (Coffea arabica L.. Disadvantages that are associated with currently developed phytoprotection approaches have recently led to the search for alternative strategies. These include genetic manipulations that constitutively activate disease resistance signaling pathways. However, molecular actors of such pathways still remain unknown in C. arabica. In this study, we have isolated and characterized the coffee NDR1 gene, whose Arabidopsis ortholog is a well-known master regulator of the hypersensitive response that is dependent on coiled-coil type R-proteins. Results Two highly homologous cDNAs coding for putative NDR1 proteins were identified and cloned from leaves of coffee plants. One of the candidate coding sequences was then expressed in the Arabidopsis knock-out null mutant ndr1-1. Upon a challenge with a specific strain of the bacterium Pseudomonas syringae (DC3000::AvrRpt2, analysis of both macroscopic symptoms and in planta microbial growth showed that the coffee cDNA was able to restore the resistance phenotype in the mutant genetic background. Thus, the cDNA was dubbed CaNDR1a (standing for Coffea arabica Non-race specific Disease Resistance 1a. Finally, biochemical and microscopy data were obtained that strongly suggest the mechanistic conservation of the NDR1-driven function within coffee and Arabidopsis plants. Using a transient expression system, it was indeed shown that the CaNDR1a protein, like its Arabidopsis counterpart, is localized to the plasma membrane, where it is possibly tethered by means of a GPI anchor. Conclusions Our data provide molecular and genetic evidence for the identification of a novel functional NDR1 homolog in plants. As a key regulator initiating hypersensitive signalling pathways, CaNDR1 gene(s might be target(s of choice for manipulating the coffee innate immune

  15. Tyrosine-phosphorylated Ehrlichia chaffeensis and Ehrlichia canis tandem repeat orthologs contain a major continuous cross-reactive antibody epitope in lysine-rich repeats.

    Science.gov (United States)

    McBride, Jere W; Zhang, Xiaofeng; Wakeel, Abdul; Kuriakose, Jeeba A

    2011-08-01

    A small subset of major immunoreactive proteins have been identified in Ehrlichia chaffeensis and Ehrlichia canis, including three molecularly and immunologically characterized pairs of immunoreactive tandem repeat protein (TRP) orthologs with major continuous species-specific epitopes within acidic tandem repeats (TR) that stimulate strong antibody responses during infection. In this study, we identified a fourth major immunoreactive TR-containing ortholog pair and defined a major cross-reactive epitope in homologous nonidentical 24-amino-acid lysine-rich TRs. Antibodies from patients and dogs with ehrlichiosis reacted strongly with recombinant TR regions, and epitopes were mapped to the N-terminal TR region (18 amino acids) in E. chaffeensis and the complete TR (24 amino acids) in E. canis. Two less-dominant epitopes were mapped to adjacent glutamate/aspartate-rich and aspartate/tyrosine-rich regions in the acidic C terminus of E. canis TRP95 but not in E. chaffeensis TRP75. Major immunoreactive proteins in E. chaffeensis (75-kDa) and E. canis (95-kD) whole-cell lysates and supernatants were identified with TR-specific antibodies. Consistent with other ehrlichial TRPs, the TRPs identified in ehrlichial whole-cell lysates and the recombinant proteins migrated abnormally slow electrophoretically a characteristic that was demonstrated with the positively charged TR and negatively charged C-terminal domains. E. chaffeensis TRP75 and E. canis TRP95 were immunoprecipitated with anti-pTyr antibody, demonstrating that they are tyrosine phosphorylated during infection of the host cell.

  16. OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs

    Science.gov (United States)

    Zdobnov, Evgeny M.; Tegenfeldt, Fredrik; Kuznetsov, Dmitry; Waterhouse, Robert M.; Simão, Felipe A.; Ioannidis, Panagiotis; Seppey, Mathieu; Loetscher, Alexis; Kriventseva, Evgenia V.

    2017-01-01

    OrthoDB is a comprehensive catalog of orthologs, genes inherited by extant species from a single gene in their last common ancestor. In 2016 OrthoDB reached its 9th release, growing to over 22 million genes from over 5000 species, now adding plants, archaea and viruses. In this update we focused on usability of this fast-growing wealth of data: updating the user and programmatic interfaces to browse and query the data, and further enhancing the already extensive integration of available gene functional annotations. Collating functional annotations from over 100 resources, and enabled us to propose descriptive titles for 87% of ortholog groups. Additionally, OrthoDB continues to provide computed evolutionary annotations and to allow user queries by sequence homology. The OrthoDB resource now enables users to generate publication-quality comparative genomics charts, as well as to upload, analyze and interactively explore their own private data. OrthoDB is available from http://orthodb.org. PMID:27899580

  17. An ortholog of farA of Aspergillus nidulans is implicated in the transcriptional activation of genes involved in fatty acid utilization in the yeast Yarrowia lipolytica

    Energy Technology Data Exchange (ETDEWEB)

    Poopanitpan, Napapol; Kobayashi, Satoshi; Fukuda, Ryouichi; Horiuchi, Hiroyuki [Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657 (Japan); Ohta, Akinori, E-mail: aaohta@mail.ecc.u-tokyo.ac.jp [Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657 (Japan)

    2010-11-26

    Research highlights: {yields} POR1 is a Yarrowia lipolytica ortholog of farA involved in fatty acid response in A. nidulans. {yields} Deletion of POR1 caused growth defects on fatty acids. {yields} {Delta}por1 strain exhibited defects in the induction of genes involved in fatty acid utilization. -- Abstract: The yeast Yarrowia lipolytica effectively utilizes hydrophobic substrates such as fatty acids and n-alkanes. To identify a gene(s) regulating fatty acid utilization in Y. lipolytica, we first studied homologous genes to OAF1 and PIP2 of Saccharomyces cerevisiae, but their disruption did not change growth on oleic acid at all. We next characterized a Y. lipolytica gene, POR1 (primary oleate regulator 1), an ortholog of farA encoding a transcriptional activator that regulates fatty acid utilization in Aspergillus nidulans. The deletion mutant of POR1 was defective in the growth on various fatty acids, but not on glucose, glycerol, or n-hexadecane. It exhibited slight defect on n-decane. The transcriptional induction of genes involved in {beta}-oxidation and peroxisome proliferation by oleate was distinctly diminished in the {Delta}por1 strains. These data suggest that POR1 encodes a transcriptional activator widely regulating fatty acid metabolism in Y. lipolytica.

  18. Characterization of gana-1, a Caenorhabditis elegans gene encoding a single ortholog of vertebrate α-galactosidase and α-N-acetylgalactosaminidase

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    Kostrouchová Marta

    2005-01-01

    Full Text Available Abstract Background Human α-galactosidase A (α-GAL and α-N-acetylgalactosaminidase (α-NAGA are presumed to share a common ancestor. Deficiencies of these enzymes cause two well-characterized human lysosomal storage disorders (LSD – Fabry (α-GAL deficiency and Schindler (α-NAGA deficiency diseases. Caenorhabditis elegans was previously shown to be a relevant model organism for several late endosomal/lysosomal membrane proteins associated with LSDs. The aim of this study was to identify and characterize C. elegans orthologs to both human lysosomal luminal proteins α-GAL and α-NAGA. Results BlastP searches for orthologs of human α-GAL and α-NAGA revealed a single C. elegans gene (R07B7.11 with homology to both human genes (α-galactosidase and α-N-acetylgalactosaminidase – gana-1. We cloned and sequenced the complete gana-1 cDNA and elucidated the gene organization. Phylogenetic analyses and homology modeling of GANA-1 based on the 3D structure of chicken α-NAGA, rice α-GAL and human α-GAL suggest a close evolutionary relationship of GANA-1 to both human α-GAL and α-NAGA. Both α-GAL and α-NAGA enzymatic activities were detected in C. elegans mixed culture homogenates. However, α-GAL activity on an artificial substrate was completely inhibited by the α-NAGA inhibitor, N-acetyl-D-galactosamine. A GANA-1::GFP fusion protein expressed from a transgene, containing the complete gana-1 coding region and 3 kb of its hypothetical promoter, was not detectable under the standard laboratory conditions. The GFP signal was observed solely in a vesicular compartment of coelomocytes of the animals treated with Concanamycin A (CON A or NH4Cl, agents that increase the pH of the cellular acidic compartment. Immunofluorescence detection of the fusion protein using polyclonal anti-GFP antibody showed a broader and coarsely granular cytoplasmic expression pattern in body wall muscle cells, intestinal cells, and a vesicular compartment of

  19. Expression of chick Fgf19 and mouse Fgf15 orthologs is regulated in the developing brain by Fgf8 and Shh.

    Science.gov (United States)

    Gimeno, L; Martinez, S

    2007-08-01

    Fibroblast growth factors (Fgfs) constitute a family of signaling molecules that play essential roles in development. We have studied the expression pattern of mouse Fgf15 in the developing brain. Fgf19 is another member of the FGF family that has been suggested as the chick and human ortholog of mouse and rat Fgf15. Here, we compare the expression pattern during neural development of chick Fgf19 with mouse Fgf15. Unlike Fgf15, Fgf19 presents an expression in the isthmic alar plate, diencephalic and mesencephalic parabasal plates, hindbrain basal plate, as well as in the zona limitans intrathalamica (zli). Moreover, we explored the regulation between Fgf19 and the signaling molecules of the isthmic and zli organizers: Fgf8 and Shh, respectively. Considering the possibility that Fgf19 plays a similar role in humans and chicks, this finding could explain the significant diencephalic phenotypic differences between humans and mice in models and diseases where the Shh pathway is affected.

  20. Tomato Cutin Deficient 1 (CD1) and putative orthologs comprise an ancient family of cutin synthase‐like (CUS) proteins that are conserved among land plants

    DEFF Research Database (Denmark)

    Yeats, Trevor H.; Huang, Wenlin; Chatterjee, Subhasish;

    2014-01-01

    The aerial epidermis of all land plants is covered with a hydrophobic cuticle that provides essential protection from desiccation, and so its evolution is believed to have been prerequisite for terrestrial colonization. A major structural component of apparently all plant cuticles is cutin......, a polyester of hydroxy fatty acids; however, despite its ubiquity, the details of cutin polymeric structure and the mechanisms of its formation and remodeling are not well understood. We recently reported that cutin polymerization in tomato (Solanum lycopersicum) fruit occurs via transesterification...... of hydroxyacylglycerol precursors, catalyzed by the GDSL‐motif lipase/hydrolase family protein (GDSL) Cutin Deficient 1 (CD1). Here, we present additional biochemical characterization of CD1 and putative orthologs from Arabidopsis thaliana and the moss Physcomitrella patens, which represent a distinct clade of cutin...

  1. Two Poplar Glycosyltransferase Genes, PdGATL1.1 and PdGATL1.2, Are Functional Orthologs to PARVUS/AtGATL 1 in Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    Yingzhen Kong; Gongke Zhou; Utku Avci; Xiaogang Gu; Chelsea Jones; Yanbin Yin; Ying Xu; Michael G. Hahn

    2009-01-01

    Several genes in Arabidopsis, including PARVUS/AtGATL1, have been implicated in xylan synthesis. However, the biosynthesis of xylan in woody plants, where this polysaccharide is a major component of wood, is poorly understood. Here, we characterize two Populus genes, PdGATL1.1 and PdGATL1.2, the closest orthologs to the Arabidopsis PARVUS/GATL 1 gene, with respect to their gene expression in poplar, their sub-cellular localization, and their ability to complement the parvus mutation in Arabidopsis. Overexpression of the two poplar genes in the parvus mutant rescued most of the defects caused by the parvus mutation, including morphological changes, collapsed xylem, and altered cell wall mono-saccharide composition. Quantitative RT-PCR showed that PdGATL1.1 is expressed most strongly in developing xylem of poplar. In contrast, PdGATL1.2 is expressed much more uniformly in leaf, shoot tip, cortex, phloem, and xylem, and the transcript level of PdGATL1.2 is much lower than that of PdGATL1.1 in all tissues examined. Sub-cellular localization experi-ments showed that these two proteins are localized to both ER and Golgi in comparison with marker proteins resident to these sub-cellular compartments. Our data indicate that PdGATLI.1 and PdGATL1.2 are functional orthologs of PARVUS/ GATL1 and can play a role in xylan synthesis, but may also have role(s) in the synthesis of other wall polymers.

  2. A functional EDS1 ortholog is differentially regulated in powdery mildew resistant and susceptible grapevines and complements an Arabidopsis eds1 mutant.

    Science.gov (United States)

    Gao, Fei; Shu, Xiaomei; Ali, Mohammad Babar; Howard, Susanne; Li, Nan; Winterhagen, Patrick; Qiu, Wenping; Gassmann, Walter

    2010-04-01

    Vitis vinifera (grapevine) is the most economically important deciduous fruit crop, but cultivated grapevine varieties lack adequate innate immunity to a range of devastating diseases. To identify genetic resources for grapevine innate immunity and understand pathogen defense pathways in a woody perennial plant, we focus in this study on orthologs of the central Arabidopsis thaliana defense regulator ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1). The family of EDS1-like genes is expanded in grapevine, and members of this family were previously found to be constitutively upregulated in the resistant variety 'Norton' of the North American grapevine species Vitis aestivalis, while they were induced by Erysiphe necator, the causal agent of grapevine powdery mildew (PM), in the susceptible V. vinifera variety 'Cabernet Sauvignon'. Here, we determine the responsiveness of individual EDS1-like genes in grapevine to PM and salicylic acid, and find that EDS1-like paralogs are differentially regulated in 'Cabernet Sauvignon', while two are constitutively upregulated in 'Norton'. Sequencing of VvEDS1 and VaEDS1 cDNA and genomic clones revealed high conservation in the protein-encoding sequence and some divergence of the promoter sequence in the two grapevine varieties. Complementation of the Arabidopsis eds1-1 mutant showed that the EDS1-like gene with highest predicted amino acid sequence similarity to AtEDS1 from either grapevine varieties is a functional ortholog of AtEDS1. Together, our analyses show that differential susceptibility to PM is correlated with differences in EDS1 expression, not differences in EDS1 function, between resistant 'Norton' and susceptible 'Cabernet Sauvignon'.

  3. Identification and characterization of the soybean IPK1 ortholog of a low phytic acid mutant reveals an exon-excluding splice-site mutation.

    Science.gov (United States)

    Yuan, Feng-Jie; Zhu, Dan-Hua; Tan, Yuan-Yuan; Dong, De-Kun; Fu, Xu-Jun; Zhu, Shen-Long; Li, Bai-Quan; Shu, Qing-Yao

    2012-11-01

    Phytic acid (myo-inositol 1, 2, 3, 4, 5, 6 hexakisphosphate) is an important constituent of soybean meal. Since phytic acid and its mineral salts (phytates) are almost indigestible for monogastrics, their abundance in grain food/feed causes nutritional and environmental problems; interest in breeding low phytic acid has therefore increased considerably. Based on gene mapping and the characteristics of inositol polyphosphates profile in the seeds of a soybean mutant line Gm-lpa-ZC-2, the soybean ortholog of inositol 1,3,4,5,6 pentakisphosphate (InsP(5)) 2-kinase (IPK1), which transforms InsP(5) into phytic acid, was first hypothesized as the candidate gene responsible for the low phytic acid alteration in Gm-lpa-ZC-2. One IPK1 ortholog (Glyma14g07880, GmIPK1) was then identified in the mapped region on chromosome 14. Sequencing revealed a G → A point mutation in the genomic DNA sequence and the exclusion of the entire fifth exon in the cDNA sequence of GmIPK1 in Gm-lpa-ZC-2 compared with its wild-type progenitor Zhechun No. 3. The excluded exon encodes 37 amino acids that spread across two conserved IPK1 motifs. Furthermore, complete co-segregation of low phytic acid phenotype with the G → A mutation was observed in the F(2) population of ZC-lpa x Zhexiandou No. 4 (a wild-type cultivar). Put together, the G → A point mutation affected the pre-mRNA splicing and resulted in the exclusion of the fifth exon of GmIPK1 which is expected to disrupt the GmIPK1 functionality, leading to low phytic acid level in Gm-lpa-ZC-2. Gm-lpa-ZC-2, would be a good germplasm source in low phytic acid soybean breeding.

  4. Two maize END-1 orthologs, BETL9 and BETL9like, are transcribed in a non-overlapping spatial pattern on the outer surface of the developing endosperm

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    Joaquín eRoyo

    2014-05-01

    Full Text Available In the course of a project aimed to isolate transfer cells-specific genes in maize endosperm we have identified the BETL9 gene. BETL9 encodes for a small protein very similar in sequence to the product of the barley transfer cell-specific gene end-1. Both BETL9 and END-1 proteins are lipid transfer proteins, but their function is currently unknown. In situ hybridization analysis confirms that the BETL9 gene is exclusively transcribed in the basal endosperm transfer cell layer during seed development since 10 days after pollination. However, immunolocalization data indicates that the BETL9 protein accumulates in the maternal placento-chalaza cells located just beside the transfer cell layer. This suggests that the BETL9 protein should be transported to the maternal side to exert its, still unknown, function. In addition, we have identified a second maize gene very similar in sequence to BETL9 and we have named it BETL9like. In situ hybridization shows that BETL9like is also specifically transcribed in the developing maize endosperm within the same time frame that BETL9, but in this case it is exclusively expressed in the aleurone cell layer. Consequently, the BETL9 and BETL9like genes are transcribed in a non-overlapping pattern on the outer surface of the maize endosperm. The BETL9 and BETL9like promoter sequences, fused to the GUS reporter gen, accurately reflected the expression pattern observed for the genes in maize. Finally, we have identified in the Arabidopsis genome a set of four genes orthologous to BETL9 and BETL9like and analysed the activity of their promoters in Arabidopsis transgenic plants carrying fusions of their promoter sequences to the GUS reporter. As in the case of the maize genes, the Arabidopsis orthologs showed highly complementary expression patterns.

  5. Rescue of Drosophila Melanogaster l(2)35Aa lethality is only mediated by polypeptide GalNAc-transferase pgant35A, but not by the evolutionary conserved human ortholog GalNAc-transferase-T11

    DEFF Research Database (Denmark)

    Bennett, Eric P; Chen, Ya-Wen; Schwientek, Tilo;

    2010-01-01

    conserved family of genes encoding polypeptide GalNAc-transferases. Phylogenetic and functional analyses have proposed that subfamilies of orthologous GalNAc-transferase genes are conserved in species, suggesting that they serve distinct functions in vivo. Based on sequence alignments, pgant35A and human......)35Aa lethality. By use of genetic "domain swapping" experiments we demonstrate, that lack of rescue was not caused by inappropriate sub-cellular targeting of functionally active GalNAc-T11. Collectively our results show, that fly embryogenesis specifically requires functional pgant35A......, and that the presence of this gene product during fly embryogenesis is functionally distinct from other Drosophila GalNAc-transferase isoforms and from the proposed human ortholog GALNT11....

  6. Transcriptional activity and nuclear localization of Cabut, the Drosophila ortholog of vertebrate TGF-β-inducible early-response gene (TIEG proteins.

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    Yaiza Belacortu

    Full Text Available BACKGROUND: Cabut (Cbt is a C(2H(2-class zinc finger transcription factor involved in embryonic dorsal closure, epithelial regeneration and other developmental processes in Drosophila melanogaster. Cbt orthologs have been identified in other Drosophila species and insects as well as in vertebrates. Indeed, Cbt is the Drosophila ortholog of the group of vertebrate proteins encoded by the TGF-ß-inducible early-response genes (TIEGs, which belong to Sp1-like/Krüppel-like family of transcription factors. Several functional domains involved in transcriptional control and subcellular localization have been identified in the vertebrate TIEGs. However, little is known of whether these domains and functions are also conserved in the Cbt protein. METHODOLOGY/PRINCIPAL FINDINGS: To determine the transcriptional regulatory activity of the Drosophila Cbt protein, we performed Gal4-based luciferase assays in S2 cells and showed that Cbt is a transcriptional repressor and able to regulate its own expression. Truncated forms of Cbt were then generated to identify its functional domains. This analysis revealed a sequence similar to the mSin3A-interacting repressor domain found in vertebrate TIEGs, although located in a different part of the Cbt protein. Using β-Galactosidase and eGFP fusion proteins, we also showed that Cbt contains the bipartite nuclear localization signal (NLS previously identified in TIEG proteins, although it is non-functional in insect cells. Instead, a monopartite NLS, located at the amino terminus of the protein and conserved across insects, is functional in Drosophila S2 and Spodoptera exigua Sec301 cells. Last but not least, genetic interaction and immunohistochemical assays suggested that Cbt nuclear import is mediated by Importin-α2. CONCLUSIONS/SIGNIFICANCE: Our results constitute the first characterization of the molecular mechanisms of Cbt-mediated transcriptional control as well as of Cbt nuclear import, and demonstrate the

  7. Rescue of Drosophila Melanogaster l(2)35Aa lethality is only mediated by polypeptide GalNAc-transferase pgant35A, but not by the evolutionary conserved human ortholog GalNAc-transferase-T11.

    Science.gov (United States)

    Bennett, Eric P; Chen, Ya-Wen; Schwientek, Tilo; Mandel, Ulla; Schjoldager, Katrine ter-Borch Gram; Cohen, Stephen M; Clausen, Henrik

    2010-05-01

    The Drosophila l(2)35Aa gene encodes a UDP-N-acetylgalactosamine: Polypeptide N-acetylgalactosaminyltransferase, essential for embryogenesis and development (J. Biol. Chem. 277, 22623-22638; J. Biol. Chem. 277, 22616-22). l(2)35Aa, also known as pgant35A, is a member of a large evolutionarily conserved family of genes encoding polypeptide GalNAc-transferases. Phylogenetic and functional analyses have proposed that subfamilies of orthologous GalNAc-transferase genes are conserved in species, suggesting that they serve distinct functions in vivo. Based on sequence alignments, pgant35A and human GALNT11 are thought to belong to a distinct subfamily. Recent in vitro studies have shown that pgant35A and pgant7, encoding enzymes from different subfamilies, prefer different acceptor substrates, whereas the orthologous pgant35A and human GALNT11 gene products possess, 1) conserved substrate preferences and 2) similar acceptor site preferences in vitro. In line with the in vitro pgant7 studies, we show that l(2)35Aa lethality is not rescued by ectopic pgant7 expression. Remarkably and in contrast to this observation, the human pgant35A ortholog, GALNT11, was shown not to support rescue of the l(2)35Aa lethality. By use of genetic "domain swapping" experiments we demonstrate, that lack of rescue was not caused by inappropriate sub-cellular targeting of functionally active GalNAc-T11. Collectively our results show, that fly embryogenesis specifically requires functional pgant35A, and that the presence of this gene product during fly embryogenesis is functionally distinct from other Drosophila GalNAc-transferase isoforms and from the proposed human ortholog GALNT11.

  8. X-ray crystallographic studies of the extracellular domain of the first plant ATP receptor, DORN1, and the orthologous protein from Camelina sativa

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    Li, Zhijie; Chakraborty, Sayan; Xu, Guozhou (NCSU)

    2016-10-26

    Does not respond to nucleotides 1 (DORN1) has recently been identified as the first membrane-integral plant ATP receptor, which is required for ATP-induced calcium response, mitogen-activated protein kinase activation and defense responses inArabidopsis thaliana. In order to understand DORN1-mediated ATP sensing and signal transduction, crystallization and preliminary X-ray studies were conducted on the extracellular domain of DORN1 (atDORN1-ECD) and that of an orthologous protein,Camelina sativalectin receptor kinase I.9 (csLecRK-I.9-ECD or csI.9-ECD). A variety of deglycosylation strategies were employed to optimize the glycosylated recombinant atDORN1-ECD for crystallization. In addition, the glycosylated csI.9-ECD protein was crystallized at 291 K. X-ray diffraction data were collected at 4.6 Å resolution from a single crystal. The crystal belonged to space groupC222 orC2221, with unit-cell parametersa= 94.7,b= 191.5,c= 302.8 Å. These preliminary studies have laid the foundation for structural determination of the DORN1 and I.9 receptor proteins, which will lead to a better understanding of the perception and function of extracellular ATP in plants.

  9. Identification of single-copy orthologous genes between Physalis and Solanum lycopersicum and analysis of genetic diversity in Physalis using molecular markers.

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    Jingli Wei

    Full Text Available The genus Physalis includes a number of commercially important edible and ornamental species. Its high nutritional value and potential medicinal properties leads to the increased commercial interest in the products of this genus worldwide. However, lack of molecular markers prevents the detailed study of genetics and phylogeny in Physalis, which limits the progress of breeding. In the present study, we compared the DNA sequences between Physalis and tomato, and attempted to analyze genetic diversity in Physalis using tomato markers. Blasting 23180 DNA sequences derived from Physalis against the International Tomato Annotation Group (ITAG Release2.3 Predicted CDS (SL2.40 discovered 3356 single-copy orthologous genes between them. A total of 38 accessions from at least six species of Physalis were subjected to genetic diversity analysis using 97 tomato markers and 25 SSR markers derived from P. peruviana. Majority (73.2% of tomato markers could amplify DNA fragments from at least one accession of Physalis. Diversity in Physalis at molecular level was also detected. The average Nei's genetic distance between accessions was 0.3806 with a range of 0.2865 to 0.7091. These results indicated Physalis and tomato had similarity at both molecular marker and DNA sequence levels. Therefore, the molecular markers developed in tomato can be used in genetic study in Physalis.

  10. Identification of single-copy orthologous genes between Physalis and Solanum lycopersicum and analysis of genetic diversity in Physalis using molecular markers.

    Science.gov (United States)

    Wei, Jingli; Hu, Xiaorong; Yang, Jingjing; Yang, Wencai

    2012-01-01

    The genus Physalis includes a number of commercially important edible and ornamental species. Its high nutritional value and potential medicinal properties leads to the increased commercial interest in the products of this genus worldwide. However, lack of molecular markers prevents the detailed study of genetics and phylogeny in Physalis, which limits the progress of breeding. In the present study, we compared the DNA sequences between Physalis and tomato, and attempted to analyze genetic diversity in Physalis using tomato markers. Blasting 23180 DNA sequences derived from Physalis against the International Tomato Annotation Group (ITAG) Release2.3 Predicted CDS (SL2.40) discovered 3356 single-copy orthologous genes between them. A total of 38 accessions from at least six species of Physalis were subjected to genetic diversity analysis using 97 tomato markers and 25 SSR markers derived from P. peruviana. Majority (73.2%) of tomato markers could amplify DNA fragments from at least one accession of Physalis. Diversity in Physalis at molecular level was also detected. The average Nei's genetic distance between accessions was 0.3806 with a range of 0.2865 to 0.7091. These results indicated Physalis and tomato had similarity at both molecular marker and DNA sequence levels. Therefore, the molecular markers developed in tomato can be used in genetic study in Physalis.

  11. The sinR ortholog PGN_0088 encodes a transcriptional regulator that inhibits polysaccharide synthesis in Porphyromonas gingivalis ATCC 33277 biofilms.

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    Reiko Yamamoto

    Full Text Available Biofilm-forming cells are distinct from well characterized planktonic cells and aggregate in the extracellular matrix, the so-called extracellular polymeric substances (EPS. The sinR gene of Bacillus subtilis encodes a transcriptional regulator that is known to be involved in the biosynthesis of EPS in biofilms. Porphyromonas gingivalis inhabits the subgingival and extraradicular biofilm of humans and is one of the primary pathogens that cause progressive marginal and refractory apical periodontitis. Furthermore, P. gingivalis possesses PGN_0088, which encodes a putative ortholog of B. subtilis sinR. Here, we investigated the role of PGN_0088 (sinR on biofilm formation. P. gingivalis strains formed biofilms on saliva-coated glass surfaces in phosphate buffered saline. Quantitative analysis indicated that the biofilm of the sinR null mutant consisted of dense exopolysaccharide. Microscopic observations showed that the increased levels of exopolysaccharide produced by the sinR mutant changed the morphology of the EPS to a mesh-liked structure. Furthermore, physical analyses suggested that the enrichment of exopolysaccharide in the EPS enhanced the resistance of the biofilm to hydrodynamic shear force. The results presented here demonstrate sinR plays important roles in the ability of P. gingivalis strain ATCC 33277 to act as a negative mediator of exopolysaccharide accumulation and is indirectly associated with the structure of the EPS and the force of its adhesion to surfaces.

  12. Very high conservation between Cyp6a2 from Drosophila melanogaster and its ortholog Cyp6a26 from D. Simulans

    Institute of Scientific and Technical Information of China (English)

    SOPHIE TAR(E)S; LAURY ARTHAUD; ALEXANDRA BRUN-BARALE; DIDIER CROCHARD; JEAN-MARC BRIDE; MARCEL AMICHOT

    2007-01-01

    Although Drosophila simulans is closely related to D. melanogaster, very fewcytochrome P450 genes have been studied in this species until now. As Cyp6a2 from D.melanogaster is a major gene implicated in the detoxification of xenobiotic molecules, wedecided to look for its ortholog in D. simulans. The isolated gene, Cyp6a26, presentsstructural characteristics very similar to those of Cyp6a2: an identical size of 1590-bpcomprising two exons separated by a 69-bp intron and a nucleotide sequence homology of95%. Many putative transcriptionally important motifs were identified in the upstreamDNAs of the two genes but only 16 elements are in common positions. Treatment of flies withphenobarbital leads to an increased production of Cyp6a26 mRNAs. The expression ofCyp6a26 mRNAs varies following developmental stages in the same manner as Cyp6a2.Immunohistochemistry experiments of phenobarbital-treated adult drosophila show that thespatial expression pattern of the two proteins is also conserved between the two species. Allthese data argue in favor of the conservation of the function of these homologous genesbetween the two Drosophila species.

  13. Efficient Generation of Gene-Modified Pigs Harboring Precise Orthologous Human Mutation via CRISPR/Cas9-Induced Homology-Directed Repair in Zygotes.

    Science.gov (United States)

    Zhou, Xiaoyang; Wang, Lulu; Du, Yinan; Xie, Fei; Li, Liang; Liu, Yu; Liu, Chuanhong; Wang, Shiqiang; Zhang, Shibing; Huang, Xingxu; Wang, Yong; Wei, Hong

    2016-01-01

    Precise genetic mutation of model animals is highly valuable for functional investigation of human mutations. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9)-induced homology-directed repair (HDR) is usually used for precise genetic mutation, being limited by the relatively low efficiency compared with that of non-homologous end joining (NHEJ). Although inhibition of NHEJ was shown to enhance HDR-derived mutation, in this work, without inhibition of NHEJ, we first generated gene-modified pigs harboring precise orthologous human mutation (Sox10 c.A325>T) via CRISPR/Cas9-induced HDR in zygotes using single-strand oligo DNA (ssODN) as template with an efficiency as high as 80%, indicating that pig zygotes exhibited high activities of HDR relative to NHEJ and were highly amendable to genetic mutation via CIRSPR/Cas9-induced HDR. Besides, we found a higher concentration of ssODN remarkably reduced HDR-derived mutation in pig zygotes, suggesting a possible balance for optimal HDR-derived mutation in zygotes between the excessive accessibility to HDR templates and the activities of HDR relative to NHEJ which appeared to be negatively correlated to ssODN concentration. In addition, the HDR-derived mutation, as well as those from NHEJ, extensively integrated into various tissues including gonad of founder pig without detected off-targeting, suggesting CRISPR/Cas9-induced HDR in zygotes is a reliable approach for precise genetic mutation in pigs.

  14. The structure of YqeH: An AtNOS1/AtNOA1 ortholog that couples GTP hydrolysis to molecular recognition

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    Sudhamsu, J.; Lee, G.I.; Klessig, D.F.; Crane, B.R. (Cornell); (Boyce)

    2009-03-27

    AtNOS1/AtNOA1 was identified as a nitric oxide-generating enzyme in plants, but that function has recently been questioned. To resolve issues surrounding AtNOA1 activity, we report the biochemical properties and a 2.36 {angstrom} resolution crystal structure of a bacterial AtNOA1 ortholog (YqeH). Geobacillus YqeH fused to a putative AtNOA1 leader peptide complements growth and morphological defects of Atnoa1 mutant plants. YqeH does not synthesize nitric oxide from L-arginine but rather hydrolyzes GTP. The YqeH structure reveals a circularly permuted GTPase domain and an unusual C-terminal {beta}-domain. A small N-terminal domain, disordered in the structure, binds zinc. Structural homology among the C-terminal domain, the RNA-binding regulator TRAP, and the hypoxia factor pVHL define a recognition module for peptides and nucleic acids. TRAP residues important for RNA binding are conserved by the YqeH C-terminal domain, whose positioning is coupled to GTP hydrolysis. YqeH and AtNOA1 probably act as G-proteins that regulate nucleic acid recognition and not as nitric-oxide synthases.

  15. An Induced Chromosomal Translocation in Soybean Disrupts a KASI Ortholog and Is Associated with a High-Sucrose and Low-Oil Seed Phenotype

    Science.gov (United States)

    Dobbels, Austin A.; Michno, Jean-Michel; Campbell, Benjamin W.; Virdi, Kamaldeep S.; Stec, Adrian O.; Muehlbauer, Gary J.; Naeve, Seth L.; Stupar, Robert M.

    2017-01-01

    Mutagenesis is a useful tool in many crop species to induce heritable genetic variability for trait improvement and gene discovery. In this study, forward screening of a soybean fast neutron (FN) mutant population identified an individual that produced seed with nearly twice the amount of sucrose (8.1% on dry matter basis) and less than half the amount of oil (8.5% on dry matter basis) as compared to wild type. Bulked segregant analysis (BSA), comparative genomic hybridization, and genome resequencing were used to associate the seed composition phenotype with a reciprocal translocation between chromosomes 8 and 13. In a backcross population, the translocation perfectly cosegregated with the seed composition phenotype and exhibited non-Mendelian segregation patterns. We hypothesize that the translocation is responsible for the altered seed composition by disrupting a β-ketoacyl-[acyl carrier protein] synthase 1 (KASI) ortholog. KASI is a core fatty acid synthesis enzyme that is involved in the conversion of sucrose into oil in developing seeds. This finding may lead to new research directions for developing soybean cultivars with modified carbohydrate and oil seed composition. PMID:28235823

  16. Deletion of the Ustilago maydis ortholog of the Aspergillus sporulation regulator medA affects mating and virulence through pheromone response.

    Science.gov (United States)

    Chacko, Nadia; Gold, Scott

    2012-06-01

    Mating of compatible haploid cells of Ustilago maydis is essential for infection and disease development in the host. For mating and subsequent filamentous growth and pathogenicity, the transcription factor, prf1 is necessary. Prf1 is in turn regulated by the cAMP and MAPK pathways and other regulators like rop1 and hap1. Here we describe the identification of another putative Prf1 regulator, med1, the ortholog of the Aspergillus nidulans medusa (medA) transcription factor and show that it is required for mating and full virulence in U. maydis. med1 deletion mutants show both pre- and post-mating defects and are unresponsive to external pheromone. The expression of prf1 is down-regulated in Δmed1 compared to the wild type, suggesting that med1 is upstream of prf1. Additionally, indicative of a role in secondary metabolism regulation, deletion of the med1 gene de-represses the production of glycolipids in U. maydis.

  17. The Caenorhabditis elegans iodotyrosine deiodinase ortholog SUP-18 functions through a conserved channel SC-box to regulate the muscle two-pore domain potassium channel SUP-9.

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    Ignacio Perez de la Cruz

    2014-02-01

    Full Text Available Loss-of-function mutations in the Caenorhabditis elegans gene sup-18 suppress the defects in muscle contraction conferred by a gain-of-function mutation in SUP-10, a presumptive regulatory subunit of the SUP-9 two-pore domain K(+ channel associated with muscle membranes. We cloned sup-18 and found that it encodes the C. elegans ortholog of mammalian iodotyrosine deiodinase (IYD, an NADH oxidase/flavin reductase that functions in iodine recycling and is important for the biosynthesis of thyroid hormones that regulate metabolism. The FMN-binding site of mammalian IYD is conserved in SUP-18, which appears to require catalytic activity to function. Genetic analyses suggest that SUP-10 can function with SUP-18 to activate SUP-9 through a pathway that is independent of the presumptive SUP-9 regulatory subunit UNC-93. We identified a novel evolutionarily conserved serine-cysteine-rich region in the C-terminal cytoplasmic domain of SUP-9 required for its specific activation by SUP-10 and SUP-18 but not by UNC-93. Since two-pore domain K(+ channels regulate the resting membrane potentials of numerous cell types, we suggest that the SUP-18 IYD regulates the activity of the SUP-9 channel using NADH as a coenzyme and thus couples the metabolic state of muscle cells to muscle membrane excitability.

  18. Inhibition of human high-affinity copper importer Ctr1 orthologous in the nervous system of Drosophila ameliorates Aβ42-induced Alzheimer's disease-like symptoms.

    Science.gov (United States)

    Lang, Minglin; Fan, Qiangwang; Wang, Lei; Zheng, Yajun; Xiao, Guiran; Wang, Xiaoxi; Wang, Wei; Zhong, Yi; Zhou, Bing

    2013-11-01

    Disruption of copper homeostasis has been implicated in Alzheimer's disease (AD) during the last 2 decades; however, whether copper is a friend or a foe is controversial. Within a genetically tractable Drosophila AD model, we manipulated the expression of human high-affinity copper importer orthologous in Drosophila to explore the in vivo roles of copper ions in the development of AD. We found that inhibition of Ctr1C expression by RNAi in Aβ-expressing flies significantly reduced copper accumulation in the brains of the flies as well as ameliorating neurodegeneration, enhancing climbing ability, and prolonging lifespan. Interestingly, Ctr1C inhibition led to a significant increase in higher-molecular-weight Aβ42 forms in brain lysates, whereas it was accompanied by a trend of decreased expression of amyloid-β degradation proteases (including NEP1-3 and IDE) with age and reduced Cu-Aβ interaction-induced oxidative stress in Ctr1C RNAi flies. Similar results were obtained from inhibiting another copper importer Ctr1B and overexpressing a copper exporter DmATP7 in the nervous system of AD flies. These results imply that copper may play a causative role in developing AD, as either Aβ oligomers or aggregates were less toxic in a reduced copper environment or one with less copper binding. Early manipulation of brain copper uptake can have a great effect on Aβ pathology.

  19. Tomato Cutin Deficient 1 (CD1) and putative orthologs comprise an ancient family of cutin synthase-like (CUS) proteins that are conserved among land plants.

    Science.gov (United States)

    Yeats, Trevor H; Huang, Wenlin; Chatterjee, Subhasish; Viart, Hélène M-F; Clausen, Mads H; Stark, Ruth E; Rose, Jocelyn K C

    2014-03-01

    The aerial epidermis of all land plants is covered with a hydrophobic cuticle that provides essential protection from desiccation, and so its evolution is believed to have been prerequisite for terrestrial colonization. A major structural component of apparently all plant cuticles is cutin, a polyester of hydroxy fatty acids; however, despite its ubiquity, the details of cutin polymeric structure and the mechanisms of its formation and remodeling are not well understood. We recently reported that cutin polymerization in tomato (Solanum lycopersicum) fruit occurs via transesterification of hydroxyacylglycerol precursors, catalyzed by the GDSL-motif lipase/hydrolase family protein (GDSL) Cutin Deficient 1 (CD1). Here, we present additional biochemical characterization of CD1 and putative orthologs from Arabidopsis thaliana and the moss Physcomitrella patens, which represent a distinct clade of cutin synthases within the large GDSL superfamily. We demonstrate that members of this ancient and conserved family of cutin synthase-like (CUS) proteins act as polyester synthases with negligible hydrolytic activity. Moreover, solution-state NMR analysis indicates that CD1 catalyzes the formation of primarily linear cutin oligomeric products in vitro. These results reveal a conserved mechanism of cutin polyester synthesis in land plants, and suggest that elaborations of the linear polymer, such as branching or cross-linking, may require additional, as yet unknown, factors.

  20. Functional and spatial analysis of C. elegans SYG-1 and SYG-2, orthologs of the Neph/nephrin cell adhesion module directing selective synaptogenesis.

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    Nicola Wanner

    Full Text Available The assembly of specific synaptic connections represents a prime example of cellular recognition. Members of the Ig superfamily are among the most ancient proteins represented in the genomes of both mammalian and invertebrate organisms, where they constitute a trans-synaptic adhesion system. The correct connectivity patterns of the highly conserved immunoglobulin superfamily proteins nephrin and Neph1 are crucial for the assembly of functional neuronal circuits and the formation of the kidney slit diaphragm, a synapse-like structure forming the filtration barrier. Here, we utilize the nematode C. elegans model for studying the requirements of synaptic specificity mediated by nephrin-Neph proteins. In C. elegans, the nephrin/Neph1 orthologs SYG-2 and SYG-1 form intercellular contacts strictly in trans between epithelial guidepost cells and neurons specifying the localization of synapses. We demonstrate a functional conservation between mammalian nephrin and SYG-2. Expression of nephrin effectively compensated loss of syg-2 function in C. elegans and restored defective synaptic connectivity further establishing the C. elegans system as a valuable model for slit diaphragm proteins. Next, we investigated the effect of SYG-1 and SYG-2 trans homodimerization respectively. Strikingly, synapse assembly could be induced by homophilic SYG-1 but not SYG-2 binding indicating a critical role of SYG-1 intracellular signalling for morphogenetic events and pointing toward the dynamic and stochastic nature of extra- and intracellular nephrin-Neph interactions to generate reproducible patterns of synaptic connectivity.

  1. Identification and characterization of RcMADS1, an AGL24 ortholog from the holoparasitic plant Rafflesia cantleyi Solms-Laubach (Rafflesiaceae.

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    Rengasamy Ramamoorthy

    Full Text Available Rafflesia, a holoparasitic genus that produces the largest flower in the world is characterized by the absence of leaves, stem and other macroscopic organs. To better understand the molecular regulation of flower development in this genus we isolated and characterized a floral MADS-box gene, namely, RcMADS1 from Rafflesia cantleyi. Heterologous expression analysis in Arabidopsis was chosen because Rafflesia is not amenable to genetic manipulations. RcMADS1 shares sequence similarity with AGAMOUS-LIKE 24 (AGL24 and SHORT VEGETATIVE PHASE (SVP of Arabidopsis. Ectopic expression of RcMADS1 in Arabidopsis caused early flowering and conversion of sepals and petals into leaf-like structures, and carpels into inflorescences. In 35S::RcMADS1 plants SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1, a downstream target gene of AGL24, was upregulated. 35S::RcMADS1 plants exhibit early flowering and conversion of the floral meristem into inflorescence meristem, as in 35S::AGL24 plants. Similar to AGL24, RcMADS1 could rescue the late flowering phenotypes of agl24-1 and FRIGIDA, but not the early flowering of svp-41. Based on these results, we propose that RcMADS1 is a functional ortholog of Arabidopsis AGL24.

  2. Ect2, an ortholog of Drosophila's pebble, negatively regulates neurite outgrowth in neuroblastoma × glioma hybrid NG108-15 cells.

    Science.gov (United States)

    Tsuji, Takahiro; Higashida, Chiharu; Yoshida, Yasumasa; Islam, Mohammad Saharul; Dohmoto, Mitsuko; Koizumi, Keita; Higashida, Haruhiro

    2011-07-01

    To identify genes required for brain development, we previously performed in vivo RNA interference (RNAi) screening in Drosophila embryos. We identified pebble as a gene that disrupts development of the Drosophila nervous system. Although pebble has been shown to be involved in neuronal development of Drosophila in several screens, the involvement of Ect2, a mammalian ortholog of pebble, in mammalian neuronal development has not been addressed. To examine the role of Ect2 in neuronal differentiation, we performed Ect2 RNAi in the mouse neuroblastoma × rat glioma NG108-15 cell line. Depletion of Ect2 resulted in an increased proportion of binucleate cells and morphological differentiation of NG108-15 cells characterized by the outgrowth of neurites. These morphological changes were correlated with an increased level of acetylcholine esterase mRNA. In addition, expression of Ect2 was decreased in differentiated NG108-15 cells induced by dibutyryl cyclic AMP. These findings indicate that Ect2 negatively regulates the differentiation of NG108-15 cells and suggest that Ect2 may play a role in neuronal differentiation and brain development in vivo.

  3. A novel DFNA36 mutation in TMC1 orthologous to the Beethoven (Bth) mouse associated with autosomal dominant hearing loss in a Chinese family.

    Science.gov (United States)

    Zhao, Yali; Wang, Dayong; Zong, Liang; Zhao, Feifan; Guan, Liping; Zhang, Peng; Shi, Wei; Lan, Lan; Wang, Hongyang; Li, Qian; Han, Bing; Yang, Ling; Jin, Xin; Wang, Jian; Wang, Jun; Wang, Qiuju

    2014-01-01

    Mutations in the transmembrane channel-like gene 1 (TMC1) can cause both DFNA36 and DFNB7/11 hearing loss. More than thirty DFNB7/11 mutations have been reported, but only three DFNA36 mutations were reported previously. In this study, we found a large Chinese family with 222 family members showing post-lingual, progressive sensorineural hearing loss which were consistent with DFNA36 hearing loss. Auditory brainstem response (ABR) test of the youngest patient showed a special result with nearly normal threshold but prolonged latency, decreased amplitude, and the abnormal waveform morphology. Exome sequencing of the proband found four candidate variants in known hearing loss genes. Sanger sequencing in all family members found a novel variant c.1253T>A (p.M418K) in TMC1 at DFNA36 that co-segregated with the phenotype. This mutation in TMC1 is orthologous to the mutation found in the hearing loss mouse model named Bth ten years ago. In another 51 Chinese autosomal dominant hearing loss families, we screened the segments containing the dominant mutations of TMC1 and no functional variants were found. TMC1 is expressed in the hair cells in inner ear. Given the already known roles of TMC1 in the mechanotransduction in the cochlea and its expression in inner ear, our results may provide an interesting perspective into its function in inner ear.

  4. A novel DFNA36 mutation in TMC1 orthologous to the Beethoven (Bth mouse associated with autosomal dominant hearing loss in a Chinese family.

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    Yali Zhao

    Full Text Available Mutations in the transmembrane channel-like gene 1 (TMC1 can cause both DFNA36 and DFNB7/11 hearing loss. More than thirty DFNB7/11 mutations have been reported, but only three DFNA36 mutations were reported previously. In this study, we found a large Chinese family with 222 family members showing post-lingual, progressive sensorineural hearing loss which were consistent with DFNA36 hearing loss. Auditory brainstem response (ABR test of the youngest patient showed a special result with nearly normal threshold but prolonged latency, decreased amplitude, and the abnormal waveform morphology. Exome sequencing of the proband found four candidate variants in known hearing loss genes. Sanger sequencing in all family members found a novel variant c.1253T>A (p.M418K in TMC1 at DFNA36 that co-segregated with the phenotype. This mutation in TMC1 is orthologous to the mutation found in the hearing loss mouse model named Bth ten years ago. In another 51 Chinese autosomal dominant hearing loss families, we screened the segments containing the dominant mutations of TMC1 and no functional variants were found. TMC1 is expressed in the hair cells in inner ear. Given the already known roles of TMC1 in the mechanotransduction in the cochlea and its expression in inner ear, our results may provide an interesting perspective into its function in inner ear.

  5. AtbHLH29 of Arabidopsis thaliana is a functional ortholog of tomato FER involved in controlling iron acquisition in strategy I plants

    Institute of Scientific and Technical Information of China (English)

    You Xi YUAN; Juan ZHANG; Dao Wen WANG; Hong Qing LING

    2005-01-01

    AtbHLH29 of Arabidopsis, encoding a bHLH protein, reveals a high similarity to the tomato FER which is proposed as a transcriptional regulator involved in controlling the iron deficiency responses and the iron uptake in tomato. For identification of its biological functions, AtbHLH29 was introduced into the genome of the tomato FER mutant T3238fer mediated by Agrobacterium tumefaciencs. Transgenic plants were regenerated and the stable integration of AtbHLH29 into their genomes was confirmed by Southern hybridization. Molecular analysis demonstrated that expression of the exogenous AtbHLH29 of Arabidopsis in roots of the FER mutant T3238fer enabled to complement the defect functions of FER. The transgenic plants regained the ability to activate the whole iron deficiency responses and showed normal growth as the wild type under iron-limiting stress. Our transformation data demonstrate that AtbHLH29 is a functional ortholog of the tomato FER and can completely replace FER in controlling the effective iron acquisition in tomato.Except of iron, FER protein was directly or indirectly involved in manganese homeostasis due to that loss functions of FER in T3238fer resulted in strong reduction of Mn content in leaves and the defect function on Mn accumulation in leaves was complemented by expression of AtbHLH29 in the transgenic plants. Identification of the similar biological functions of FER and AtbHLH29, which isolated from two systematically wide-diverged "strategy I" plants, suggests that FER might be a universal gene presented in all strategy I plants in controlling effective iron acquisition system in roots.

  6. A mutation in the FAM36A gene, the human ortholog of COX20, impairs cytochrome c oxidase assembly and is associated with ataxia and muscle hypotonia.

    Science.gov (United States)

    Szklarczyk, Radek; Wanschers, Bas F J; Nijtmans, Leo G; Rodenburg, Richard J; Zschocke, Johannes; Dikow, Nicola; van den Brand, Mariël A M; Hendriks-Franssen, Marthe G M; Gilissen, Christian; Veltman, Joris A; Nooteboom, Marco; Koopman, Werner J H; Willems, Peter H G M; Smeitink, Jan A M; Huynen, Martijn A; van den Heuvel, Lambertus P

    2013-02-15

    The mitochondrial respiratory chain complex IV (cytochrome c oxidase) is a multi-subunit enzyme that transfers electrons from cytochrome c to molecular oxygen, yielding water. Its biogenesis requires concerted expression of mitochondria- and nuclear-encoded subunits and assembly factors. In this report, we describe a homozygous missense mutation in FAM36A from a patient who displays ataxia and muscle hypotonia. The FAM36A gene is a remote, putative ortholog of the fungal complex IV assembly factor COX20. Messenger RNA (mRNA) and protein co-expression analyses support the involvement of FAM36A in complex IV function in mammals. The c.154A>C mutation in the FAM36A gene, a mutation that is absent in sequenced exomes, leads to a reduced activity and lower levels of complex IV and its protein subunits. The FAM36A protein is nearly absent in patient's fibroblasts. Cells affected by the mutation accumulate subassemblies of complex IV that contain COX1 but are almost devoid of COX2 protein. We observe co-purification of FAM36A and COX2 proteins, supporting that the FAM36A defect hampers the early step of complex IV assembly at the incorporation of the COX2 subunit. Lentiviral complementation of patient's fibroblasts with wild-type FAM36A increases the complex IV activity as well as the amount of holocomplex IV and of individual subunits. These results establish the function of the human gene FAM36A/COX20 in complex IV assembly and support a causal role of the gene in complex IV deficiency.

  7. A motif-based search in bacterial genomes identifies the ortholog of the small RNA Yfr1 in all lineages of cyanobacteria

    Directory of Open Access Journals (Sweden)

    Axmann Ilka M

    2007-10-01

    Full Text Available Abstract Background Non-coding RNAs (ncRNA are regulators of gene expression in all domains of life. They control growth and differentiation, virulence, motility and various stress responses. The identification of ncRNAs can be a tedious process due to the heterogeneous nature of this molecule class and the missing sequence similarity of orthologs, even among closely related species. The small ncRNA Yfr1 has previously been found in the Prochlorococcus/Synechococcus group of marine cyanobacteria. Results Here we show that screening available genome sequences based on an RNA motif and followed by experimental analysis works successfully in detecting this RNA in all lineages of cyanobacteria. Yfr1 is an abundant ncRNA between 54 and 69 nt in size that is ubiquitous for cyanobacteria except for two low light-adapted strains of Prochlorococcus, MIT 9211 and SS120, in which it must have been lost secondarily. Yfr1 consists of two predicted stem-loop elements separated by an unpaired sequence of 16–20 nucleotides containing the ultraconserved undecanucleotide 5'-ACUCCUCACAC-3'. Conclusion Starting with an ncRNA previously found in a narrow group of cyanobacteria only, we show here the highly specific and sensitive identification of its homologs within all lineages of cyanobacteria, whereas it was not detected within the genome sequences of E. coli and of 7 other eubacteria belonging to the alpha-proteobacteria, chlorobiaceae and spirochaete. The integration of RNA motif prediction into computational pipelines for the detection of ncRNAs in bacteria appears as a promising step to improve the quality of such predictions.

  8. The role of the RACK1 ortholog Cpc2p in modulating pheromone-induced cell cycle arrest in fission yeast.

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    Magdalena Mos

    Full Text Available The detection and amplification of extracellular signals requires the involvement of multiple protein components. In mammalian cells the receptor of activated C kinase (RACK1 is an important scaffolding protein for signal transduction networks. Further, it also performs a critical function in regulating the cell cycle by modulating the G1/S transition. Many eukaryotic cells express RACK1 orthologs, with one example being Cpc2p in the fission yeast Schizosaccharomyces pombe. In contrast to RACK1, Cpc2p has been described to positively regulate, at the ribosomal level, cells entry into M phase. In addition, Cpc2p controls the stress response pathways through an interaction with Msa2p, and sexual development by modulating Ran1p/Pat1p. Here we describe investigations into the role, which Cpc2p performs in controlling the G protein-mediated mating response pathway. Despite structural similarity to Gβ-like subunits, Cpc2p appears not to function at the G protein level. However, upon pheromone stimulation, cells overexpressing Cpc2p display substantial cell morphology defects, disorientation of septum formation and a significantly protracted G1 arrest. Cpc2p has the potential to function at multiple positions within the pheromone response pathway. We provide a mechanistic interpretation of this novel data by linking Cpc2p function, during the mating response, with its previous described interactions with Ran1p/Pat1p. We suggest that overexpressing Cpc2p prolongs the stimulated state of pheromone-induced cells by increasing ste11 gene expression. These data indicate that Cpc2p regulates the pheromone-induced cell cycle arrest in fission yeast by delaying cells entry into S phase.

  9. Caenorhabditis elegans AGXT-1 is a mitochondrial and temperature-adapted ortholog of peroxisomal human AGT1: New insights into between-species divergence in glyoxylate metabolism.

    Science.gov (United States)

    Mesa-Torres, Noel; Calvo, Ana C; Oppici, Elisa; Titelbaum, Nicholas; Montioli, Riccardo; Miranda-Vizuete, Antonio; Cellini, Barbara; Salido, Eduardo; Pey, Angel L

    2016-09-01

    In humans, glyoxylate is an intermediary product of metabolism, whose concentration is finely balanced. Mutations in peroxisomal alanine:glyoxylate aminotransferase (hAGT1) cause primary hyperoxaluria type 1 (PH1), which results in glyoxylate accumulation that is converted to toxic oxalate. In contrast, glyoxylate is used by the nematode Caenorhabditis elegans through a glyoxylate cycle to by-pass the decarboxylation steps of the tricarboxylic acid cycle and thus contributing to energy production and gluconeogenesis from stored lipids. To investigate the differences in glyoxylate metabolism between humans and C. elegans and to determine whether the nematode might be a suitable model for PH1, we have characterized here the predicted nematode ortholog of hAGT1 (AGXT-1) and compared its molecular properties with those of the human enzyme. Both enzymes form active PLP-dependent dimers with high specificity towards alanine and glyoxylate, and display similar three-dimensional structures. Interestingly, AGXT-1 shows 5-fold higher activity towards the alanine/glyoxylate pair than hAGT1. Thermal and chemical stability of AGXT-1 is lower than that of hAGT1, suggesting temperature-adaptation of the nematode enzyme linked to the lower optimal growth temperature of C. elegans. Remarkably, in vivo experiments demonstrate the mitochondrial localization of AGXT-1 in contrast to the peroxisomal compartmentalization of hAGT1. Our results support the view that the different glyoxylate metabolism in the nematode is associated with the divergent molecular properties and subcellular localization of the alanine:glyoxylate aminotransferase activity.

  10. Maize multiple archesporial cells 1 (mac1), an ortholog of rice TDL1A, modulates cell proliferation and identity in early anther development.

    Science.gov (United States)

    Wang, Chung-Ju Rachel; Nan, Guo-Ling; Kelliher, Timothy; Timofejeva, Ljudmilla; Vernoud, Vanessa; Golubovskaya, Inna N; Harper, Lisa; Egger, Rachel; Walbot, Virginia; Cande, W Zacheus

    2012-07-01

    To ensure fertility, complex somatic and germinal cell proliferation and differentiation programs must be executed in flowers. Loss-of-function of the maize multiple archesporial cells 1 (mac1) gene increases the meiotically competent population and ablates specification of somatic wall layers in anthers. We report the cloning of mac1, which is the ortholog of rice TDL1A. Contrary to prior studies in rice and Arabidopsis in which mac1-like genes were inferred to act late to suppress trans-differentiation of somatic tapetal cells into meiocytes, we find that mac1 anthers contain excess archesporial (AR) cells that proliferate at least twofold more rapidly than normal prior to tapetal specification, suggesting that MAC1 regulates cell proliferation. mac1 transcript is abundant in immature anthers and roots. By immunolocalization, MAC1 protein accumulates preferentially in AR cells with a declining radial gradient that could result from diffusion. By transient expression in onion epidermis, we demonstrate experimentally that MAC1 is secreted, confirming that the predicted signal peptide domain in MAC1 leads to secretion. Insights from cytology and double-mutant studies with ameiotic1 and absence of first division1 mutants confirm that MAC1 does not affect meiotic cell fate; it also operates independently of an epidermal, Ocl4-dependent pathway that regulates proliferation of subepidermal cells. MAC1 both suppresses excess AR proliferation and is responsible for triggering periclinal division of subepidermal cells. We discuss how MAC1 can coordinate the temporal and spatial pattern of cell proliferation in maize anthers.

  11. AtbHLH29 of Arabidopsis thaliana is a functional ortholog of tomato FER involved in controlling iron acquisition in strategy I plants.

    Science.gov (United States)

    Yuan, You Xi; Zhang, Juan; Wang, Dao Wen; Ling, Hong Qing

    2005-08-01

    AtbHLH29 of Arabidopsis, encoding a bHLH protein, reveals a high similarity to the tomato FER which is proposed as a transcriptional regulator involved in controlling the iron deficiency responses and the iron uptake in tomato. For identification of its biological functions, AtbHLH29 was introduced into the genome of the tomato FER mutant T3238fer mediated by Agrobacterium tumefaciencs. Transgenic plants were regenerated and the stable integration of AtbHLH29 into their genomes was confirmed by Southern hybridization. Molecular analysis demonstrated that expression of the exogenous AtbHLH29 of Arabidopsis in roots of the FER mutant T3238fer enabled to complement the defect functions of FER. The transgenic plants regained the ability to activate the whole iron deficiency responses and showed normal growth as the wild type under iron-limiting stress. Our transformation data demonstrate that AtbHLH29 is a functional ortholog of the tomato FER and can completely replace FER in controlling the effective iron acquisition in tomato. Except of iron, FER protein was directly or indirectly involved in manganese homeostasis due to that loss functions of FER in T3238fer resulted in strong reduction of Mn content in leaves and the defect function on Mn accumulation in leaves was complemented by expression of AtbHLH29 in the transgenic plants. Identification of the similar biological functions of FER and AtbHLH29, which isolated from two systematically wide-diverged "strategy I" plants, suggests that FER might be a universal gene presented in all strategy I plants in controlling effective iron acquisition system in roots.

  12. Endo-(1,4-β-Glucanase gene families in the grasses: temporal and spatial Co-transcription of orthologous genes1

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    Buchanan Margaret

    2012-12-01

    Full Text Available Abstract Background Endo-(1,4-β-glucanase (cellulase glycosyl hydrolase GH9 enzymes have been implicated in several aspects of cell wall metabolism in higher plants, including cellulose biosynthesis and degradation, modification of other wall polysaccharides that contain contiguous (1,4-β-glucosyl residues, and wall loosening during cell elongation. Results The endo-(1,4-β-glucanase gene families from barley (Hordeum vulgare, maize (Zea mays, sorghum (Sorghum bicolor, rice (Oryza sativa and Brachypodium (Brachypodium distachyon range in size from 23 to 29 members. Phylogenetic analyses show variations in clade structure between the grasses and Arabidopsis, and indicate differential gene loss and gain during evolution. Map positions and comparative studies of gene structures allow orthologous genes in the five species to be identified and synteny between the grasses is found to be high. It is also possible to differentiate between homoeologues resulting from ancient polyploidizations of the maize genome. Transcript analyses using microarray, massively parallel signature sequencing and quantitative PCR data for barley, rice and maize indicate that certain members of the endo-(1,4-β-glucanase gene family are transcribed across a wide range of tissues, while others are specifically transcribed in particular tissues. There are strong correlations between transcript levels of several members of the endo-(1,4-β-glucanase family and the data suggest that evolutionary conservation of transcription exists between orthologues across the grass family. There are also strong correlations between certain members of the endo-(1,4-β-glucanase family and other genes known to be involved in cell wall loosening and cell expansion, such as expansins and xyloglucan endotransglycosylases. Conclusions The identification of these groups of genes will now allow us to test hypotheses regarding their functions and joint participation in wall synthesis, re

  13. Caenorhabditis elegans ortholog of the p24/p22 subunit, DNC-3, is essential for the formation of the dynactin complex by bridging DNC-1/p150Glued and DNC-2/dynamitin

    OpenAIRE

    Terasawa, Masahiro; Toya, Mika; Motegi, Fumio; Mana, Miyeko; Nakamura, Kuniaki; Sugimoto, Asako

    2010-01-01

    Dynactin is a multisubunit protein complex required for the activity of cytoplasmic dynein. In Caenorhabditis elegans, although 10 of the 11 dynactin subunits were identified based on the sequence similarities to their orthologs, the p24/p22 subunit has not been detected in the genome. Here, we demonstrate that DNC-3 (W10G11.20) is the functional counterpart of the p24/p22 subunit in C. elegans. RNAi phenotypes and subcellular localization of DNC-3 in early C. elegans embryos were nearly iden...

  14. Candida albicans AGE3, the ortholog of the S. cerevisiae ARF-GAP-encoding gene GCS1, is required for hyphal growth and drug resistance.

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    Thomas Lettner

    Full Text Available BACKGROUND: Hyphal growth and multidrug resistance of C. albicans are important features for virulence and antifungal therapy of this pathogenic fungus. METHODOLOGY/PRINCIPAL FINDINGS: Here we show by phenotypic complementation analysis that the C. albicans gene AGE3 is the functional ortholog of the yeast ARF-GAP-encoding gene GCS1. The finding that the gene is required for efficient endocytosis points to an important functional role of Age3p in endosomal compartments. Most C. albicans age3Delta mutant cells which grew as cell clusters under yeast growth conditions showed defects in filamentation under different hyphal growth conditions and were almost completely disabled for invasive filamentous growth. Under hyphal growth conditions only a fraction of age3Delta cells shows a wild-type-like polarization pattern of the actin cytoskeleton and lipid rafts. Moreover, age3Delta cells were highly susceptible to several unrelated toxic compounds including antifungal azole drugs. Irrespective of the AGE3 genotype, C-terminal fusions of GFP to the drug efflux pumps Cdr1p and Mdr1p were predominantly localized in the plasma membrane. Moreover, the plasma membranes of wild-type and age3Delta mutant cells contained similar amounts of Cdr1p, Cdr2p and Mdr1p. CONCLUSIONS/SIGNIFICANCE: The results indicate that the defect in sustaining filament elongation is probably caused by the failure of age3Delta cells to polarize the actin cytoskeleton and possibly of inefficient endocytosis. The high susceptibility of age3Delta cells to azoles is not caused by inefficient transport of efflux pumps to the cell membrane. A possible role of a vacuolar defect of age3Delta cells in drug susceptibility is proposed and discussed. In conclusion, our study shows that the ARF-GAP Age3p is required for hyphal growth which is an important virulence factor of C. albicans and essential for detoxification of azole drugs which are routinely used for antifungal therapy. Thus, it

  15. The Orthology Clause in the Next Generation Sequencing Era: Novel Reference Genes Identified by RNA-seq in Humans Improve Normalization of Neonatal Equine Ovary RT-qPCR Data.

    Directory of Open Access Journals (Sweden)

    Dragos Scarlet

    Full Text Available Vertebrate evolution is accompanied by a substantial conservation of transcriptional programs with more than a third of unique orthologous genes showing constrained levels of expression. Moreover, there are genes and exons exhibiting excellent expression stability according to RNA-seq data across a panel of eighteen tissues including the ovary (Human Body Map 2.0.We hypothesized that orthologs of these exons would also be highly uniformly expressed across neonatal ovaries of the horse, which would render them appropriate reference genes (RGs for normalization of reverse transcription quantitative PCR (RT-qPCR data in this context. The expression stability of eleven novel RGs (C1orf43, CHMP2A, EMC7, GPI, PSMB2, PSMB4, RAB7A, REEP5, SNRPD3, VCP and VPS29 was assessed by RT-qPCR in ovaries of seven neonatal fillies and compared to that of the expressed repetitive element ERE-B, two universal (OAZ1 and RPS29 and four traditional RGs (ACTB, GAPDH, UBB and B2M. Expression stability analyzed with the software tool RefFinder top ranked the normalization factor constituted of the genes SNRPD3 and VCP, a gene pair that is not co-expressed according to COEXPRESdb and GeneMANIA. The traditional RGs GAPDH, B2M, ACTB and UBB were only ranked 3rd and 12th to 14th, respectively.The functional diversity of the novel RGs likely facilitates expression studies over a wide range of physiological and pathological contexts related to the neonatal equine ovary. In addition, this study augments the potential for RT-qPCR-based profiling of human samples by introducing seven new human RG assays (C1orf43, CHMP2A, EMC7, GPI, RAB7A, VPS29 and UBB.

  16. Characterization of the expression patterns of LEAFY/FLORICAULA and NEEDLY orthologs in female and male cones of the conifer genera Picea, Podocarpus, and Taxus: implications for current evo-devo hypotheses for gymnosperms.

    Science.gov (United States)

    Vázquez-Lobo, Alejandra; Carlsbecker, Annelie; Vergara-Silva, Francisco; Alvarez-Buylla, Elena R; Piñero, Daniel; Engström, Peter

    2007-01-01

    The identity of genes causally implicated in the development and evolutionary origin of reproductive characters in gymnosperms is largely unknown. Working within the framework of plant evolutionary developmental biology, here we have cloned, sequenced, performed phylogenetic analyses upon and tested the expression patterns of LEAFY/FLORICAULA and NEEDLY orthologs in reproductive structures from selected species of the conifer genera Picea, Podocarpus, and Taxus. Contrary to expectations based on previous assessments, expression of LFY/FLO and NLY in cones of these taxa was found to occur simultaneously in a single reproductive axis, initially overlapping but later in mutually exclusive primordia and/or groups of developing cells in both female and male structures. These observations directly affect the status of the "mostly male theory" for the origin of the angiosperm flower. On the other hand, comparative spatiotemporal patterns of the expression of these genes suggest a complex genetic regulatory network of cone development, as well as a scheme of functional divergence for LFY/FLO with respect to NLY homologs in gymnosperms, both with clear heterochronic aspects. Results presented in this study contribute to the understanding of the molecular-genetic basis of morphological evolution in conifer cones, and may aid in establishing a foundation for gymnosperm-specific, testable evo-devo hypotheses.

  17. Vitis vinifera VvNPR1.1 is the functional ortholog of AtNPR1 and its overexpression in grapevine triggers constitutive activation of PR genes and enhanced resistance to powdery mildew.

    Science.gov (United States)

    Le Henanff, Gaëlle; Farine, Sibylle; Kieffer-Mazet, Flore; Miclot, Anne-Sophie; Heitz, Thierry; Mestre, Pere; Bertsch, Christophe; Chong, Julie

    2011-08-01

    Studying grapevine (Vitis vinifera) innate defense mechanisms is a prerequisite to the development of new protection strategies, based on the stimulation of plant signaling pathways to trigger pathogen resistance. Two transcriptional coactivators (VvNPR1.1 and VvNPR1.2) with similarity to Arabidopsis thaliana NPR1 (Non-Expressor of PR genes 1), a well-characterized and key signaling element of the salicylic acid (SA) pathway, were recently isolated in Vitis vinifera. In this study, functional characterization of VvNPR1.1 and VvNPR1.2, including complementation of the Arabidopsis npr1 mutant, revealed that VvNPR1.1 is a functional ortholog of AtNPR1, whereas VvNPR1.2 likely has a different function. Ectopic overexpression of VvNPR1.1 in the Arabidopsis npr1-2 mutant restored plant growth at a high SA concentration, Pathogenesis Related 1 (PR1) gene expression after treatment with SA or bacterial inoculation, and resistance to virulent Pseudomonas syringae pv. maculicola bacteria. Moreover, stable overexpression of VvNPR1.1-GFP in V. vinifera resulted in constitutive nuclear localization of the fusion protein and enhanced PR gene expression in uninfected plants. Furthermore, grapevine plants overexpressing VvNPR1.1-GFP exhibited an enhanced resistance to powdery mildew infection. This work highlights the importance of the conserved SA/NPR1 signaling pathway for resistance to biotrophic pathogens in V. vinifera.

  18. Proteomic characterization of the small subunit of Chlamydomonas reinhardtii chloroplast ribosome: identification of a novel S1 domain-containing protein and unusually large orthologs of bacterial S2, S3, and S5.

    Science.gov (United States)

    Yamaguchi, Kenichi; Prieto, Susana; Beligni, María Verónica; Haynes, Paul A; McDonald, W Hayes; Yates, John R; Mayfield, Stephen P

    2002-11-01

    To understand how chloroplast mRNAs are translated into functional proteins, a detailed understanding of all of the components of chloroplast translation is needed. To this end, we performed a proteomic analysis of the plastid ribosomal proteins in the small subunit of the chloroplast ribosome from the green alga Chlamydomonas reinhardtii. Twenty proteins were identified, including orthologs of Escherichia coli S1, S2, S3, S4, S5, S6, S7, S9, S10, S12, S13, S14, S15, S16, S17, S18, S19, S20, and S21 and a homolog of spinach plastid-specific ribosomal protein-3 (PSRP-3). In addition, a novel S1 domain-containing protein, PSRP-7, was identified. Among the identified proteins, S2 (57 kD), S3 (76 kD), and S5 (84 kD) are prominently larger than their E. coli or spinach counterparts, containing N-terminal extensions (S2 and S5) or insertion sequence (S3). Structural predictions based on the crystal structure of the bacterial 30S subunit suggest that the additional domains of S2, S3, and S5 are located adjacent to each other on the solvent side near the binding site of the S1 protein. These additional domains may interact with the S1 protein and PSRP-7 to function in aspects of mRNA recognition and translation initiation that are unique to the Chlamydomonas chloroplast.

  19. Caenorhabditis elegans ortholog of the p24/p22 subunit, DNC-3, is essential for the formation of the dynactin complex by bridging DNC-1/p150(Glued) and DNC-2/dynamitin.

    Science.gov (United States)

    Terasawa, Masahiro; Toya, Mika; Motegi, Fumio; Mana, Miyeko; Nakamura, Kuniaki; Sugimoto, Asako

    2010-11-01

    Dynactin is a multisubunit protein complex required for the activity of cytoplasmic dynein. In Caenorhabditis elegans, although 10 of the 11 dynactin subunits were identified based on the sequence similarities to their orthologs, the p24/p22 subunit has not been detected in the genome. Here, we demonstrate that DNC-3 (W10G11.20) is the functional counterpart of the p24/p22 subunit in C. elegans. RNAi phenotypes and subcellular localization of DNC-3 in early C. elegans embryos were nearly identical to those of the known dynactin components. All other dynactin subunits were co-immunoprecipitated with DNC-3, indicating that DNC-3 is a core component of dynactin. Furthermore, the overall secondary structure of DNC-3 resembles to those of the mammalian and yeast p24/p22. We found that DNC-3 is required for the localization of the DNC-1/p150(Glued) and DNC-2/dynamitin, the two components of the projection arm of dynactin, to the nuclear envelope of meiotic nuclei in the adult gonad. Moreover, DNC-3 physically interacted with DNC-1 and DNC-2 and significantly enhanced the binding ability between DNC-1 and DNC-2 in vitro. These results suggest that DNC-3 is essential for the formation of the projection arm subcomplex of dynactin.

  20. GPX5 orthologs of the mouse epididymis-restricted and sperm-bound selenium-independent glutathione peroxidase are not expressed with the same quantitative and spatial characteristics in large domestic animals.

    Science.gov (United States)

    Grignard, Elise; Morin, Joelle; Vernet, Patrick; Drevet, Joel R

    2005-09-01

    We report here on the cloning of cDNAs coding bovine and equine orthologs of mouse epididymis-restricted and sperm-bound glutathione peroxidase 5 (GPX5), a selenium-independent member of the multigenic GPX family in mammals. The complete sequence of bovine GPX5 as well as a partial sequence of the equine GPX5 were characterized, conceptually translated and aligned with other known mammalian GPX5 proteins. Using Northern blotting assays, we show that the level of expression of GPX5 is high in bovine but low in equine and that in both species the regionalization of GPX5 expression in epididymis is not totally identical to what was reported for rodent mouse GPX5. An antibody was produced against GPX5 and used in Western blot assays as well as in immunohistochemistry assays on bovine epididymis sections. It shows that the protein is essentially present in the cytoplasmic compartment of the caput segment 2 epithelium of the bovine epididymis. Unlike in the mouse model, bovine GPX5 seems to be poorly secreted and does not seem to be present on cauda epididymal spermatozoa.

  1. Structures of PHR Domains from Mus musculus Phr1 (Mycbp2) Explain the Loss-of-Function Mutation (Gly1092 → Glu) of the C. elegans Ortholog RPM-1

    Energy Technology Data Exchange (ETDEWEB)

    Sampathkumar, Parthasarathy; Ozyurt, Sinem A.; Miller, Stacy A.; Bain, Kevin T.; Rutter, Marc E.; Gheyi, Tarun; Abrams, Benjamin; Wang, Yingchun; Atwell, Shane; Luz, John G.; Thompson, Devon A.; Wasserman, Stephen R.; Emtage, J. Spencer; Park, Eun Chan; Rongo, Christopher; Jin, Yishi; Klemke, Richard L.; Sauder, J. Michael; Burley, Stephen K. (Rutgers); (UCSC); (Lilly); (UCSD)

    2010-11-15

    PHR [PAM (protein associated with Myc)-HIW (Highwire)-RPM-1 (regulator of presynaptic morphology 1)] proteins are conserved, large multi-domain E3 ubiquitin ligases with modular architecture. PHR proteins presynaptically control synaptic growth and axon guidance and postsynaptically regulate endocytosis of glutamate receptors. Dysfunction of neuronal ubiquitin-mediated proteasomal degradation is implicated in various neurodegenerative diseases. PHR proteins are characterized by the presence of two PHR domains near the N-terminus, which are essential for proper localization and function. Structures of both the first and second PHR domains of Mus musculus (mouse) Phr1 (MYC binding protein 2, Mycbp2) have been determined, revealing a novel {beta} sandwich fold composed of 11 antiparallel {beta}-strands. Conserved loops decorate the apical side of the first PHR domain (MmPHR1), yielding a distinct conserved surface feature. The surface of the second PHR domain (MmPHR2), in contrast, lacks significant conservation. Importantly, the structure of MmPHR1 provides insights into a loss-of-function mutation, Gly1092 {yields} Glu, observed in the Caenorhabditis elegans ortholog RPM-1.

  2. Overexpression of OsKTN80a, a katanin P80 ortholog, caused the repressed cell elongation and stalled cell division mediated by microtubule apparatus defects in primary root in Oryza sativa

    Institute of Scientific and Technical Information of China (English)

    Lei Wan; Xiuwen Wang; Shaoqing Li; Jun Hu; Wenchao Huang; Yingguo Zhu

    2014-01-01

    Katanin, a microtubule-severing enzyme, consists of two subunits:the catalytic subunit P60, and the regulatory subunit P80. In several species, P80 functions in meiotic spindle organization, the flagella biogenesis, the neuronal development, and the male gamete production. However, the P80 function in higher plants remains elusive. In this study, we found that there are three katanin P80 orthologs (OsKTN80a, OsKTN80b, and OsKTN80c) in Oryza sativa L. Overexpression of OsKTN80a caused the retarded root growth of rice seedlings. Further investigation indicates that the retained root growth was caused by the repressed cell elongation in the elongation zone and the stalled cytokinesis in the division zone in the root tip. The in vivo examination suggests that OsKTN80a acts as a microtubule stabilizer. We prove that OsKTN80a, possibly associated with OsKTN60, is involved in root growth via regulating the cell elongation and division.

  3. Expression of the ctenophore Brain Factor 1 forkhead gene ortholog (ctenoBF-1) mRNA is restricted to the presumptive mouth and feeding apparatus: implications for axial organization in the Metazoa

    Science.gov (United States)

    Yamada, Atsuko; Martindale, Mark Q.

    2002-01-01

    Ctenophores are thoroughly modern animals whose ancestors are derived from a separate evolutionary branch than that of other eumetazoans. Their major longitudinal body axis is the oral-aboral axis. An apical sense organ, called the apical organ, is located at the aboral pole and contains a highly innervated statocyst and photodetecting cells. The apical organ integrates sensory information and controls the locomotory apparatus of ctenophores, the eight longitudinal rows of ctene/comb plates. In an effort to understand the developmental and evolutionary organization of axial properties of ctenophores we have isolated a forkhead gene from the Brain Factor 1 (BF-1) family. This gene, ctenoBF-1, is the first full-length nuclear gene reported from ctenophores. This makes ctenophores the most basal metazoan (to date) known to express definitive forkhead class transcription factors. Orthologs of BF-1 in vertebrates, Drosophila, and Caenorhabditis elegans are expressed in anterior neural structures. Surprisingly, in situ hybridizations with ctenoBF-1 antisense riboprobes show that this gene is not expressed in the apical organ of ctenophores. CtenoBF-1 is expressed prior to first cleavage. Transcripts become localized to the aboral pole by the 8-cell stage and are inherited by ectodermal micromeres generated from this region at the 16- and 32-cell stages. Expression in subsets of these cells persists and is seen around the edge of the blastopore (presumptive mouth) and in distinct ectodermal regions along the tentacular poles. Following gastrulation, stomodeal expression begins to fade and intense staining becomes restricted to two distinct domains in each tentacular feeding apparatus. We suggest that the apical organ is not homologous to the brain of bilaterians but that the oral pole of ctenophores corresponds to the anterior pole of bilaterian animals.

  4. Characterization and expression analysis of mcoln1.1 and mcoln1.2, the putative zebrafish co-orthologs of the gene responsible for human mucolipidosis type IV.

    Science.gov (United States)

    Benini, Anna; Bozzato, Andrea; Mantovanelli, Silvia; Calvarini, Laura; Giacopuzzi, Edoardo; Bresciani, Roberto; Moleri, Silvia; Zizioli, Daniela; Beltrame, Monica; Borsani, Giuseppe

    2013-01-01

    Mucolipidosis type IV (MLIV) is an autosomal recessive lysosomal storage disorder caused by mutations in the MCOLN1 gene coding for mucolipin-1 (TRPML1). TRPML1 belongs to a transient receptor potential channels (TRP) subfamily, which in mammals includes two other members: mucolipin-2 (TRPML2) and mucolipin-3 (TRPML3). Bioinformatic analysis of the Danio rerio (zebrafish) genome and trascriptome revealed the presence of five different genes related to human mucolipins: mcoln1.1, mcoln1.2, mcoln2, mcoln3.1 and mcoln3.2. We focused our efforts on the characterization of the two putative zebrafish MCOLN1 co-orthologs. Transient-expression experiments in human HeLa cells demonstrated that fish Mcoln1.1 and Mcoln1.2, similarly to TRPML1, localize to late endosomal/lysosomal compartments. Real-Time PCR (RT-PCR) experiments showed that both genes are maternally expressed and transcribed at different levels during embryogenesis. RT-PCR analysis in different zebrafish tissues displayed ubiquitary expression for mcoln1.1 and a more tissue-specific pattern for mcoln1.2. Spatial and temporal expression studies using whole-mount in situ hybridization confirmed that both genes are maternally expressed and ubiquitously transcribed during gastrulation and early somitogenesis. Notably, in the next developmental stages they are more expressed in neural regions and in retina layers, tissues affected in MLIV. Interestingly, mcoln1.1 is detected, from 10 somite-stage until to 36 hpf, in the yolk syncytial layer (YSL) and in the intermediate cell mass (ICM), the earliest site of hematopoiesis. Overall, the redundancy of mucolipins together with their expression profile support the biological relevance of this class of proteins in zebrafish. The data herein presented indicate that Danio rerio could be a suitable vertebrate model for the study of some aspects of MLIV pathogenesis.

  5. Analysis of genomic DNA of DcACS1, a 1-aminocyclopropane-1-carboxylate synthase gene, expressed in senescing petals of carnation (Dianthus caryophyllus) and its orthologous genes in D. superbus var. longicalycinus.

    Science.gov (United States)

    Harada, Taro; Murakoshi, Yuino; Torii, Yuka; Tanase, Koji; Onozaki, Takashi; Morita, Shigeto; Masumura, Takehiro; Satoh, Shigeru

    2011-04-01

    Carnation (Dianthus caryophyllus) flowers exhibit climacteric ethylene production followed by petal wilting, a senescence symptom. DcACS1, which encodes 1-aminocyclopropane-1-carboxylate synthase (ACS), is a gene involved in this phenomenon. We determined the genomic DNA structure of DcACS1 by genomic PCR. In the genome of 'Light Pink Barbara', we found two distinct nucleotide sequences: one corresponding to the gene previously shown as DcACS1, designated here as DcACS1a, and the other novel one designated as DcACS1b. It was revealed that both DcACS1a and DcACS1b have five exons and four introns. These two genes had almost identical nucleotide sequences in exons, but not in some introns and 3'-UTR. Analysis of transcript accumulation revealed that DcACS1b is expressed in senescing petals as well as DcACS1a. Genomic PCR analysis of 32 carnation cultivars showed that most cultivars have only DcACS1a and some have both DcACS1a and DcACS1b. Moreover, we found two DcACS1 orthologous genes with different nucleotide sequences from D. superbus var. longicalycinus, and designated them as DsuACS1a and DsuACS1b. Petals of D. superbus var. longicalycinus produced ethylene in response to exogenous ethylene, accompanying accumulation of DsuACS1 transcripts. These data suggest that climacteric ethylene production in flowers was genetically established before the cultivation of carnation.

  6. Protein (Cyanobacteria): 104407 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available tein Nos7107_1691 Nostoc sp. PCC 7107 MKGKSLSLIGTALTLAFSANVAVAQSSNSPIAQSSSTSTSSPTEIELSPEGLKILCERFPLNSRCPNGQPLTPTSSGTTTVPETQPSESTTPDST...TAPESTPDSTTVPDTTNPTNTTPAPGGTTLPDSTTPNQITPAPGSTTTPDSTTPGSLTPAPDSTTPGSLTPAPDSTTPGSTTAPDSTIPNQITPAPGSTTAPDSTTPGSVTPAPDSSGTPDSSIQPGSVSPSK ...

  7. Protein (Cyanobacteria): 104415 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available DRAFT_2616 Fischerella sp. JSC-11 MKGKFLTLTGTALTLALTSNIAAAQITKFPELSQQQTETTAKTPEIKLSPEGMKILCQYFPLNSRCQGTSSNTTTPDSTTTPAPDSTTPAPDST...TTPAPDSTTPEDTTPSPDSTSPTQITPAPDSTVPAPDSTTPSPDSTSPTQITPAPDSTVPAPDSTTPSPDSMNPTQMTPGSGTGTGN ...

  8. Protein (Viridiplantae): 302833076 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available PRPSRRCPSPLRPRPPRWRPLAPSPEAGPRQPGCDPGDSTPAAPYLLPPGCDPGDSTPAAPYLLPPGCDPGDSTPAAPYLLPPGCDPGDSTPAAPYLLPPGCDPGDSTPAAPYLLPPGCDPGDST...PAAPYLLPPGCDPGDSTPAAPYLLPPVAHPPMPTAPRGSSPRHPLPGLRRTPWSSFPNQLAAAAAPGRFCR ...

  9. Protein (Viridiplantae): 297788262 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 01:8083 59689:3013 81972:3013 predicted protein, partial Arabidopsis lyrata subsp. lyrata RWYSRNLCETESNFCEERTKHIDST...EVNIFSERWYSTNLCEAESNFCEERTQHLDSTEVNIFSERWYSENLCEAESNFSEERTQHLDSTEVNIFSERWYSKNLCEAESNFCEERTQHLDST...ERWYSRNLCVAESNFCEERTQHLDSTEVNIFSERWYSKNLCEAECNFCEERTQHLDSTEVNIFSERWYSKNLCEAESNFCEERTQHLDST...EVNIFSERWYSKNLCETESYFCEERTQHLDSTEVNIFSERWYSKNLCEAESSFCEEQTQYLDSTEVNIFSERWYSKNLCEAESNFCEERTQHLDSTEVNIFSERWYSKNLCEAESNFCEEQTRHLDSTELNIFSERLYFGKSP ...

  10. Protein (Cyanobacteria): 104409 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available n all4578 Nostoc sp. PCC 7120 MKGKSLTLIGTALTLALTANFAVAQSSKSQIAQSSESSTSSPTEIQLSPEGFEILCKRFPLNSRCEGNSAVTPSGSSNTTVDTQPASSETPATPAPDST...TLPAPSEAPATPAPDSTTLPAPSEAPATPAPDSTTLPAPSEAPATPAPDSTTLPAPSEAPLTPAPDSTTVPAPSEAPVTPLPSSNSPGTVPDSGVPKMPTPGN ...

  11. Protein (Cyanobacteria): 210308 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ike protein Stanieria cyanosphaera PCC 7437 MSEPKAEAKRILETKDNLANVLPTAPEQQKPVSSAQALKERLDWGEPAFTIADARDRDSFNTERILGAVPIDSEETLGRLMNSLSTRRELYIYGDNDEQAQSAVEQFVSAGFENVSRLQGGLAGWKAISGPTEGRVA ...

  12. Protein (Cyanobacteria): 178745 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available rea producens 3L MAGFVVRLHSSKVSSPARCVIRSNDLVAYEDLRVKNLVKNHCLAKSINDAGWYQFRKWLEHFGTKFGRVTVAVNPAYTSQNCSKCGETVKKSLSTRTHVCKCGCKLDRDHNAALNILKRALGTVGHTGTWILDPNASGDLTSTVLGPGQVQQVGSLSEESPRL ...

  13. Protein (Cyanobacteria): 209948 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available nothece sp. ATCC 51472 MSPEAKPPTVNQTSLEQTLPIPPEQQMPVSSPQALKQRLEWGEPALTILDARDNESFLEEHITGAMLLEFVEDSLSSMSDDRDIYVYADGEENAKQAAEKLRNKGFNRVSRIEGGLANWKSIAGPTEGRAA ... ...ZP_08974945.1 1117:3992 1118:3229 43988:1400 860575:1174 Rhodanese-like protein Cya

  14. Protein (Cyanobacteria): 359077 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available M5_04971 Acaryochloris sp. CCMEE 5410 MCVGCYAMPIMTLVSPGPEAPPATAVPLIDSPEAKVMQVQPQVSATQVRADISTMIARLPDSADSVILREEFTAVYQRLEGVTNVDEANTIVGEGMLNIADRLGTNPNADRVIKILYEIQEPEAQKQATHPLLKQSAWGWIS ...

  15. Protein (Cyanobacteria): 329917 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available Synechococcus sp. CC9311 MLGALIGGCSADPTAETPSSRVNAPPLVSPEAKDVSPPPPTALTVLPSVAEVLVSVPEGRTDPFAPFPQRSSSPELGASGELDWKVLGVLSVADQLRALILTKDGSGVVCLGAGGRCPGEAQQLLPMDVEVQSIDIRTGCLTVLQSRRSQRVCIT ...

  16. Protein (Viridiplantae): 159465487 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 84 predicted protein Chlamydomonas reinhardtii MPPIHLLRLLFASALLFATWHVSRADDIASQASITTSDNIPQMKYFFLNEVTGATQLTDPGNTPYEDEQTGELYWLAEDGVTRLAQDPNRLRFAWIETYSPEAKRSFYFNQVTRESTWERPADLAWRRLRAEE ...

  17. Protein (Viridiplantae): 225445899 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available EDICTED: 60S ribosomal protein L7-4 Vitis vinifera MGGEEVKGVVVPESVLKKRKRSEEWALAKKQELECTKKKNATNRTLIYVRAKQYAKE...YDEQQKELIQLKREAKLKGGFYVSPEAKLLFIIRIRGINAMHPKTRKILQLLRLRQIFNGVFLKVNKATMNMLHRVEPYVT

  18. Protein (Viridiplantae): 145341877 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available EVRPKPKLPPAAVATAKPEPSPTPSAEATKEIALYHATLRAAVTDAVGKYAAALFPKEVPKQSIDEAQTKLDALAQDLLTKIIDDDAEIVDEAPMACKSYARAKESIRQGLGTPGAESPAVGASSTRDVARAILATPAIKRAVEPMLKLAVQSVKTMSATNRPVPVPRMDREPEPS ...

  19. Protein (Viridiplantae): 145329615 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 1935 ECA1 gametogenesis related family protein Arabidopsis thaliana MGESIQRVCASILTVMVVMLSLLEDTKGNNDFAMAPISENGLLPNPMACVKDAGKIPDCVEAMKQGYLKDITKECCFILLSLPEDCFGILFPMRLYYRIVLKVTCKLLGIF ...

  20. Protein (Viridiplantae): 297601087 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available SLAGRAPTTGTKRQCSSPPPSADRSEKKAKEDLAMEEPPEALAMEEQQDALATKEQALAMEEEQGAPATKGEQEVLPEMEEEQLVMEEEQESLAMDKMESGMEEQPGIEEEVLPEMEEQLMIEEE...QELSAMDKMESGMEEQPGIEEEVLPEMEEQLMIEEEQELSAMDKMESGMEEQPGIEEEVLPEMEEQLMIEEEQELSAMDKMESGMEEQPGIEEEQPATEEVPAMETPVLEKESVPYFAGPSFNFAPHPSELPFPSLLIHLIHSH ...

  1. Protein (Viridiplantae): 302842199 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ELPSMPASATTAMLGANEASSGSNVAPTVSLDGGGEAAPVSLWTSEGAPTAATASPLRDTSNDPWVMGMQPATTRTGRIAAAPTGSMAAPTGGMAAPTGGMAAPTGGMAAPTGGMAAPTGGMAAPTGGMAAP...TGGMAAPTGGMAAPTGGMAAPTGGMAAPTGGMAAPTGGMAAPTDSMAPGSMTAPHDVGPEPGPVSGNDGIMSPATADTAAADTAPSQQQEAFAPLAAGAPSADLGQGQGQGQARDLGHLQVEDHEQIAKK ...

  2. Protein (Viridiplantae): 350535639 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available :1065 3398:1065 71240:2435 91827:2435 71274:159 91888:159 4069:159 4070:159 424551:159 424574:159 4107:159 49274:159 4081:159 phytoph...thora-inhibited protease 1 Solanum lycopersicum MASNFFLKNITVVLLLFSILSLYPFIVTSRNLKEL

  3. Protein (Cyanobacteria): 55674 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ynechococcus sp. CC9605 MTWLLLAEAGVPEGGLFDLDATLPLMAVQVVLLTFLLNVLFFRPVGKVVEDREGYISTSRADAKQKLAQVERLEADLAEQLKGARQSAQAVIVEAEQEVDRLYREALAQAEAEANRTKEESRRAIEAERESARTQLKGQVDQLSTTIINRLLAA ...

  4. Protein (Cyanobacteria): 29524 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available _0321 Synechocystis sp. PCC 6803 substr. PCC-P MLLITIAFLRFYDQTDFEFLGLVANPRQWSNGFTVAALLATLANFGVEWNRRNRETNRLAQEAQRRVEEGQRRMAQERADESRRAEERERQIARTRIETRCRIAEIQFQLDPSDRNRRLLREALALLAEYGDLFS ...

  5. Protein (Viridiplantae): 357148991 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 024:1950 3398:1950 4447:782 4734:782 38820:782 4479:782 359160:428 147368:988 147385:988 15367:988 15368:988 PREDICTED: putative adag...io-like protein 2-like Brachypodium distachyon MEWDSDSDGGSGDEEEEEEGVGPWGGGGGGGGAGFS

  6. Protein (Cyanobacteria): 38769 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YP_007000628.1 1117:727 1161:4029 1162:4571 1163:534 46234:319 peptidase family S14... ClpP Anabaena sp. 90 MDISHLKAVQAPYSGDSSYRTPPPDLPSLLLKERIVYLGMPLVPSVTELIVAQLLYLQSDDPEKPIKIYINSTGTSGYSGEPIGFE

  7. Protein (Cyanobacteria): 249413 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available bicarbonate transporter protein Leptolyngbya sp. PCC 7376 MEKKRLFFLKNDYFDISHKKVIKVISCLLIGLFFSLTLSNCTQPAAQPLR...IGANLWPGYETLYLARELGYYGDKPIHLVDYPSGTEEVRAYRHNEIEGAGLSIDQAIVLATTQKNIKIVGIMDISHGGDAILGKPGMSNMQDLKGKKVGVESTALGAF

  8. Protein (Viridiplantae): 255083394 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available predicted protein Micromonas sp. RCC299 MKVLRKVKGKSRILIFVAVVALLSLALRKLKQDTKKHREILPWHQGGYEDHHGDLDGGFVPDRGVLGAVGAMRGGGGRDVGGESTSTSKVLDDGGVRDAPGGNRNIDDISHLVDDDDEDVLGVKDEAFAGMRDSREKASR ...

  9. Protein (Cyanobacteria): 215473 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available nin alpha chain Gloeobacter violaceus PCC 7421 MKTVITEVIASADSQGRFLNNTELQAANGRFQRATASMEAARALTSNADSLVKGAVQEVYN...KFPYLTQPGQMGYGDTNQAKCARDISHYLRFITYSLVAGGTGPLDDYIVAGLREVNRTFNLSPSWYIEALKHIKGKVGSQLSGQPLTEANAYIDYCINALS ...

  10. Protein (Cyanobacteria): 118077 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ical protein Microcystis aeruginosa PCC 9432 MNPNRVVIDTNVFISALLNPLGTPKKVINITVSQFTILQSEATYQELATRISKKKFDKYLEKDDRLDFLSSLRNRSLFVDISHETRVCSDLDDNKFLELAVSGMAQYIITGDNALLILNTYQGIPIITPAEFLVIF ...

  11. Protein (Cyanobacteria): 215472 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available nin alpha chain Gloeobacter violaceus PCC 7421 MKTVITEVIASADSQGRFLNNTELQAANGRFQRATASMEAARALTSNADSLVKGAVQEVYN...KFPYLTQPGQMGYGDTNQAKCARDISHYLRFITYSLVAGGTGPLDDYIVAGLREVNRTFNLSPSWYIEALKHIKGKVGSQLSGQPLTEANAYIDYCINALS ...

  12. Protein (Cyanobacteria): 367022 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available RSQGHGYDDHRQNHISEYERHFAKDISHKIAELLSQWESHLILLVAEPQMLGFVRESLMPHLSRNIKLEELAKDLCKLKPLELHEYLAHKNLVPARKAVVL ... ...ein Crocosphaera watsonii WH 8501 MGISRILSESPMNQAVVAVMDGTKARFFTLEEADFPEYQSSPNLIEHQCLTNAAKEMAGKELWANTKTGRNRGS

  13. Protein (Cyanobacteria): 95974 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available rotein Chroococcidiopsis thermalis PCC 7203 MKTTSENRKVFICGSALRGQPDHQNLQSAKFVKTAATQPRYRLHAAGDGWHPAIYEVAEGGISIPGEVYEMTKEQFEYLSANEPPNMYASDIVLEDGEVLTAFLYPKELIEKYNWTDISHLGGWAAYKASSSES ...

  14. Protein (Cyanobacteria): 403639 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available tein ANA_C20730 Anabaena sp. 90 MEIQFREFNPFDAWIWLKFSNVPSQREKQYVEEVFNSWFYLGKLGGFNAENLQIQDTGLDISHMDYDARGYDKSLMALMHNMGEFEYEGEWGRCWFDLGTSDAIALDILINALTQLTEEYVTIEELYIGGENPDWPTEDSESRPSSIYDN ...

  15. Protein (Cyanobacteria): 118035 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ical protein Microcystis aeruginosa PCC 7941 MNPNRVVIDTNVFISALLNPLGTPKKVINITVSQFTILQSEATYQELATRISKKKFDKYLEKDDRLDFLSSLRNRSLFVDISHETRVCSDLDDNKFLELAVSGMAQYIITGDKDLLILNTYQGIPIITPAEFLVIF ...

  16. Protein (Cyanobacteria): 400133 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available protein Cyast_0536 Cyanobacterium stanieri PCC 7202 MQISNRDSWQSNYLLAIASSFLLWTFTLTVCFLVVGFPVVVVLMTVGVLAAIILQSILPASAILLVTGSILGATAVAILVSSLLLTIKGIDPHDVRWLGWLHEKEAKQQILPLYASCPLTCDISHI ...

  17. Protein (Cyanobacteria): 118042 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available tical protein Microcystis aeruginosa PCC 9809 MNPNRVVIDTNVFISALLNPLGTPKKVINIAVSQFTILQSEATYQELATRISKKKFDKYLEKDDRLDFLSSLRNRSLFVDISHETRVCSDLDDNKFLELAVSGMAQYIITGDKDLLILNTYQGIPIITPAEFLAIF ...

  18. Protein (Cyanobacteria): 271076 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available rotein Cyanothece sp. ATCC 51472 MSNLVSKSFLLLVEDSDEDFTAFLRFSQPFLKEHSVKRCRNGEETIQFLERVETAPYSDISRFPTVIILDLNLSGVDGREILIRIQENPQWQKIPTLIFSSSNDPRDINFCYQHGAKSYILKPMDISHLKKTIQMLWEYWFNIVVLPSK ...

  19. Protein (Cyanobacteria): 392493 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 7428_2274 Gloeocapsa sp. PCC 7428 MFDQQPGLGEEALNKVAEIGIASQLDEVENLDVDIKTDPFKLIQGEVDSVTIDGDGLVMQGDLRVEELDMHMSS...VAINPLSVALGKIELTKPTEASVRAVLTEADINRAFNSDYVRQQLQQQQIHVHGQPVTVDAQQVDFRLPGEGKVALNASVMLREGQTHQVAFSAVPRVSASGQTVTLENVEYGDNEELSPELTQALIEETSEILNLSNFDLEGMTLKINNLQIEAGKIILQAEAHVEQIPSG ...

  20. Protein (Viridiplantae): 302854675 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ATCWVSPSATAHVAAAKTHQPASWNPGWWCPSAGGCNGCQCWRASGCHASPLGPDSCDWRHATSWCWTPGAPAHGGCNGCQCWRTSGCHASP...LGPDSCDWRHATSWCWTPGAPAHGGCNGCQCWRTSGCHASPLGPDSCDWRHATSWCWTPGAPAHGGCNGCQCWCTSGCHASPLGPDSCDWRHATSWCWTPGPPAHGGCNGCQCGFRSSNL ...

  1. Protein (Viridiplantae): 302855728 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 3068:1908 hypothetical protein VOLCADRAFT_100778 Volvox carteri f. nagariensis MEAREMEAREMEAREMEAREMEAREMEAREREAREMEAREREAREMEARE...MEAREMEAREMEAREMEAREMEAREMEAREREVREREAREMEAREMEAKEMEAREMEARERECPCDRRLYSYFGQCSGPPKTCSVPR ...

  2. Protein (Viridiplantae): 145341746 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 7:616 pentatrichopeptide repeat (PPR) protein Ostreococcus lucimarinus CCE9901 MDDDAFERLDKQKASRREKRTAVRAVREEAASGGARGGTDARLSFLYEEGVNAN...DAGAVTKCNDVLRRCASMEEVLGLVKEMRDAGLEPVESTYVAVMLVCQNVGSPERAVQVYDAMTEAQVRMTGRTFHLAIELAL

  3. Protein (Viridiplantae): 224118952 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 4:7786 predicted protein Populus trichocarpa MLDRCLGTHRVRQIQRATRHGKITLLCLFMTVVVLRGTIGAGKSGTPEQDFNDLRNHIYASRK...HAEPHRVLTESNQSNNNKNDEGSNANDANNYAAFDINKILVDEGEDEKPDPNKPYFLGPKISDWDEQRAKWLSENPNFSNF

  4. Protein (Cyanobacteria): 493036161 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available PAFIQVKAKFLPTRNLFEFDALLAPPLDKAPKFLKASKADKTAVQQEKRQNKSPQKPSTGRQKPEGKEQQSEGTEQKPSIKRQKPYKKPKVETKEQQPSTDEQKLEAKEPKVETKEQQPSTD...EQKLEAKEPKVETKEQQPSTDEQKPEAKEQKPTTEEQNPEAKKPKPSKVRKRVKAKEQKPEDKTE

  5. Protein (Cyanobacteria): 4242 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available EEQGHPAFIQVKAKFLPTRNLFEFDALLAPPLDKAPKFLKASKADKTAVQQEKRQNKSPQKPSTGRQKPEGKEQQSEGTEQKPSIKRQKPYKKPKVETKEQQPSTDEQKLEAKEPKVETKEQQPSTD...EQKLEAKEPKVETKEQQPSTDEQKPEAKEQKPTTEEQNPEAKKPKPSKVRKRVKAKEQKPEDKTE ...

  6. Protein (Viridiplantae): 225436803 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 478 58024:14478 3398:14478 71240:8172 91827:8172 71275:10399 91834:3545 403667:3545 3602:3545 3603:3545 29760:3545 PREDICTED: classic...al arabinogalactan protein 26-like Vitis vinifera MAAIWSLIAVFMVFITIHSSVAFPYQLKLQTST

  7. Protein (Viridiplantae): 357485501 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 024:5224 3398:5224 71240:4670 91827:4670 71275:7259 91835:5904 72025:5974 3803:5974 3814:5974 163742:8268 3877:8268 3880:8268 Functio...nal candidate resistance protein KR1 Medicago truncatula MSFDALQEEEKYVFFLTLLVASKDINRQRSKKYFMLINGDIMKDQIIVLLEKSLIKISEYGYVALHDLVEDMKKKF ...

  8. Protein (Cyanobacteria): 405210 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available action center protein Psb28 Thermosynechococcus elongatus BP-1 MGAMAEIQFIRGINEEVVPDVRLTRARDGSSGQAMFYFDNPKIVQEGNLEVTGMYMVDEEGEIVTRDVNAKFINGQPVAIEATYTMRSPQEWDRFIRFMDRYAASHGLGFQKSENS ...

  9. Protein (Viridiplantae): 225437740 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available REDICTED: suppressor of disruption of TFIIS-like Vitis vinifera MDAVEGSNRAKYECLLFDMDDTLYPMSSGLNLACRKNIEDYMLQ...58024:7078 3398:7078 71240:7012 91827:7012 71275:300 91834:3147 403667:3147 3602:3147 3603:3147 29760:3147 P

  10. Protein (Cyanobacteria): 434391582 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 96 ... protein of unknown function DUF305 Gloeocapsa sp. PCC 7428 MLLKKRFALNIVAIAATGGFIASCAAVPPTPTPRANTQSTQQMPHHGMNHAMAMDLGPADANYDWRFI...DAMVPHHQGAVEMAQAALEKSQRAEIKELATEIIAVQQREIAQLQQWRQAWYPQASNTPVAYNPQTGETVPMSQQQMHSMMMHGDLGAADAEFDRRFIDAMIPHHEGAVIMAQDALNKSQRPEIRKLAQEIINSQEAEIKQMQAWRQAWYQQ

  11. Protein (Cyanobacteria): 52247 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available tein Cha6605_1849 Chamaesiphon minutus PCC 6605 MNFKVKLLAPIALLLGGIGFGSLAIANLTNQRSNSTIAQNSGGMNHGGMNHGSMKKGGMMNHNMDVGPADANYDLRFID...SMIPHHQGALVMAQEVLQKSKRPELIKLAKGIITEQKKEIAQMQQWRKQWYPKASATPIMWHAAMNHEMAMTAEHKQSMMMSMSLGKADAGFDRRFIDAMIPHHQGAVTMGQDLLKKSQRPEMKKLAQNIITSQQAEIAQMTQWQKQWSASK ...

  12. Protein (Cyanobacteria): 505000144 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available tein of unknown function DUF305 Gloeocapsa sp. PCC 7428 MLLKKRFALNIVAIAATGGFIASCAAVPPTPTPRANTQSTQQMPHHGMNHAMAMDLGPADANYDWRFID...AMVPHHQGAVEMAQAALEKSQRAEIKELATEIIAVQQREIAQLQQWRQAWYPQASNTPVAYNPQTGETVPMSQQQMHSMMMHGDLGAADAEFDRRFIDAMIPHHEGAVIMAQDALNKSQRPEIRKLAQEIINSQEAEIKQMQAWRQAWYQQ

  13. Protein (Cyanobacteria): 504981950 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available hetical protein Synechococcus sp. PCC 7502 MKLTPYLFLTITVTAIIGTSVWQSSAQMNKMMNHNMDEMSMELGAADANLDLRFIDAMIPHHQGA...VQMAKEALKKSKRPEIQKLATAIIKAQQEEIAQLQKWRKLWYPNMSSTPMAWHGEMGHMMTMSASQQKAMMMSMDLGAGDAKFDLRFIDAMIPHHEGALTMAQEALSKSKRPEIQKLAKAIITSQKAEIIEMQKWRKAWY

  14. Protein (Cyanobacteria): 52198 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 02412 Synechococcus sp. PCC 7502 MKLTPYLFLTITVTAIIGTSVWQSSAQMNKMMNHNMDEMSMELGAADANLDLRFIDAMIPHHQGAVQMAKEALKK...SKRPEIQKLATAIIKAQQEEIAQLQKWRKLWYPNMSSTPMAWHGEMGHMMTMSASQQKAMMMSMDLGAGDAKFDLRFIDAMIPHHEGALTMAQEALSKSKRPEIQKLAKAIITSQKAEIIEMQKWRKAWY ...

  15. Protein (Cyanobacteria): 428222362 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ... hypothetical protein Syn7502_02412 Synechococcus sp. PCC 7502 MKLTPYLFLTITVTAIIGTSVWQSSAQMNKMMNHNMDEMSMELGAADANLDLRFID...AMIPHHQGAVQMAKEALKKSKRPEIQKLATAIIKAQQEEIAQLQKWRKLWYPNMSSTPMAWHGEMGHMMTMSASQQKAMMMSMDLGAGDAKFDLRFIDAMIPHHEGALTMAQEALSKSKRPEIQKLAKAIITSQKAEIIEMQKWRKAWY

  16. Protein (Viridiplantae): 356497027 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 29 3398:129 71240:142 91827:142 71275:664 91835:684 72025:699 3803:699 3814:699 163735:470 3846:470 3847:470 PREDICTED: EPIDERMAL PAT...TERNING FACTOR-like protein 2-like Glycine max MGRDHHLVVCGQRLSFLSISLCFLIISSWTQMGLVT

  17. Protein (Viridiplantae): 356511992 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 29 3398:129 71240:142 91827:142 71275:664 91835:684 72025:699 3803:699 3814:699 163735:470 3846:470 3847:470 PREDICTED: EPIDERMAL PAT...TERNING FACTOR-like protein 2-like Glycine max MGFDHYVICGQRLGFVGICLLFLIISSLIQKGLVIE

  18. Protein (Viridiplantae): 356515647 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 29 3398:129 71240:142 91827:142 71275:664 91835:684 72025:699 3803:699 3814:699 163735:470 3846:470 3847:470 PREDICTED: EPIDERMAL PAT...TERNING FACTOR-like protein 2-like Glycine max MRIMVAKPRIGSRPPKCEKRCSSCGHCEAVQVPVVPQIFQTHRRRHYSSERATKAVTYSSRGDDLSNYKPMSWKCKCGDYLFNP ...

  19. Protein (Viridiplantae): 356512687 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 29 3398:129 71240:142 91827:142 71275:664 91835:684 72025:699 3803:699 3814:699 163735:470 3846:470 3847:470 PREDICTED: EPIDERMAL PAT...TERNING FACTOR-like protein 1-like Glycine max MASLNSYHYYTTTSLLIILLLHDLLSLSLVSASNHP

  20. Protein (Cyanobacteria): 441113 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YP_007045238.1 1117:25511 1118:7874 167375:491 59930:654 292564:654 polyprenyl p-hydroxybenzoate/phenylacryl...ic acid decarboxylase Cyanobium gracile PCC 6307 MAPSSLPVVLAVSGASAQPLAERALQLLLEDDLP

  1. Protein (Cyanobacteria): 441159 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available -hydroxybenzoate/phenylacrylic acid decarboxylase Pleurocapsa sp. PCC 7327 MTSNQLPAIGSKTRPLILGISGASGLIYAVRAI...YP_007083232.1 1117:25511 52604:2774 44474:2781 54308:2781 118163:2781 polyprenyl p

  2. Protein (Cyanobacteria): 441174 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YP_007054066.1 1117:25511 1161:4031 1185:4005 373984:1204 373994:1204 polyprenyl p-hydroxybenzoate/phenylacr...ylic acid decarboxylase Rivularia sp. PCC 7116 MSNNARPLILGVSGASGLIYAVRALKFLLAADYAIE

  3. Protein (Cyanobacteria): 66863 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ITQSSESFQQTTNQFMEAAQAFERSQFPQTLSSATTNLANTQRNFSQSATSLSSSVQSVDLAMIELQNYSKRLIKFGEQMNQTNQTSQEIIEAHRINQQSLGEMTQQLQNATQGFQLAMNTLDILQRRMVTRTESLEEIQSELTKLVIAIERYTESVRTGLDKLGDRLTQNTMYSTVQNPQP ...

  4. Protein (Viridiplantae): 357448693 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 163742:14047 3877:14047 3880:14047 hypothetical protein MTR_2g032590 Medicago truncatula MAMIELKKVLVIMFMIIIMLVVVQLCDTTQSKIVDESCAIERFACRAECLITCAGFDNCLEGCFEHCLMCSRNAYADIDCLIHVDDLQQY ...

  5. Protein (Viridiplantae): 255073445 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available NEEFELEFVDPAVWRDQPSTKNLYWYAQGEAKTKVEAFLDRAEQFLKDEAEHLELDYEVMRKEFAVGILPQSSTVYENLEEISIGAMIELSDAEVPYCAFNGGNDVFVDVGNKNIGLQTLMNYLGFEGHQTLHVGDRFTSTGNDSRVRDACSILWVASPDETTFFMRLLYRDIVNARVL ...

  6. Protein (Viridiplantae): 168015283 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available NLDLKDQVTSEKAPEHEEHHHTLSNVEEGMKKIHIDEGEKHVEEKEKKKDKEGGEEGAEKKEKKEKKKDEEGGEKKEKKEKKKDKDVTEEGGEKKEKKEKKKKDKEGEEGGEKKEKKDKKKKDKEGEEEG...EKKDKELTVEGGETKEKKDKKKKDKDGEGGGEKKEKKEKKKKDKEGDEAGGEKKEKKDKKKKDKDGEEGGEKKEKTDKKKKDKEGEEGGEKKEKTDKKKKDKDGEEG...GEKKEKTDKKKKDKDGEEEGGEKKEKDKKKDKEGAEEGGEKKEKKDKKKDKEGAEEGGEKKEKKEKKDKEGAEEG...GEKKEKKEKKDKEGAEEGGEKKEKKEKKDKEGAEEGGEKKEKKEKKDKEGAEEGGEKKEKKEKKDKAADEKDGTEKKEKKEKKEKDPEAKEKKSKEKVADE ...

  7. Protein (Cyanobacteria): 188336 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available SSAPNLEVIPSSLEEVSEIESALNIANMANLSNEELEELEQQEKLIRDKKGQISLARKEGIEIGREEGIGIGREEGIGIGREEGIGIGREEGIGIGREEG...IGIGREEGIGIGREEGIGIGREEGIGIGREEGIGIGREEGIGIGREEGMRILVKRQIRRKFGEVPPEVQTQIEQLSLEKLDILGDEIFDLAIIADLENWLANNG ...

  8. Protein (Cyanobacteria): 188337 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available SSAPNLEVIPSSLEEVSEIESALNIANMANLSNEELEELEQQEKLIRDKKGQISLARKEGIEIGREEGIGIGREEGIGIGREEGIGIGKEEGIGIGREEG...IGIGREEGIGIGKEEGIGIGREEGIGIGREEGIGIGREEGIGIGREEGMRILVKRQIRRKFGEVPPEVQTQIEQLSLEKLDILGDEIFDLAIIADLENWLANNG ...

  9. Protein (Cyanobacteria): 318030 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available VSIGGGIDIPVNLINLSMDVGITVGETVSSEVSMSVNVPAGKKAIATFTPQFFKSTGTMEVCKEFRLGNGEFDVSCEEYETTMIFPVTKDLDGKQILVGEYDYEVIGESDNPDSPPKEEGNPKEEGNPKEEGEEGEEGEEGEEGEEGEEGEEGEEGEEGEEGEEGEEGEEGGQNQVIT ...

  10. Protein (Viridiplantae): 162462135 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 5 58024:6055 3398:6055 4447:3637 4734:3637 38820:3637 4479:3637 147370:2432 147369:2432 147429:2432 4575:1217 4577:1217 physical impe...dance induced protein2 Zea mays MQPGDANAEVSPEMLRRIKRAKRVSQISEKVATGILSGVVKVTGYFTSSLA

  11. Protein (Cyanobacteria): 321324 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available Synechococcus sp. JA-3-3Ab MNGQDRLDRVEQLLAQAAEQTAANSREIQELRQAIRESHAELSEQNAARSREIEQLRQAIRESHAELSEQNAARSREIEQLRQAIR...ESHAELSEQNAARSREIEQLRQAIRESHAELSEQNAARSREIEQLRQAIRESHAELSEQNAARSREIEQLRQAIRESHAELSEQNAARSREIEQLRQAIRESHAELSEQNAARSREIEQLRQAIR...ESHAELSEQNAARSREIEQLRQAIRESYEQNVAQAQGLRDLQEVVRETRSDLAHLAEWAEEVTQALITLTALQQEHERAIQAINQRQIENDQRFNVLLEEVRYLIRRQGLDGSSSPPSG ...

  12. Protein (Cyanobacteria): 52216 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available DUF305 Gloeocapsa sp. PCC 7428 MLLKKRFALNIVAIAATGGFIASCAAVPPTPTPRANTQSTQQMPHHGMNHAMAMDLGPADANYDWRFIDAMVPHHQG...AVEMAQAALEKSQRAEIKELATEIIAVQQREIAQLQQWRQAWYPQASNTPVAYNPQTGETVPMSQQQMHSMMMHGDLGAADAEFDRRFIDAMIPHHEGAVIMAQDALNKSQRPEIRKLAQEIINSQEAEIKQMQAWRQAWYQQ ...

  13. Protein (Cyanobacteria): 106637 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ZP_05038898.1 1117:2038 1118:2503 1129:1219 91464:2931 Redoxin superfamily Synechoc...occus sp. PCC 7335 MVKTASTMLPLGTPAPSFKLEDVISKKTISLDTFKGKKGLLLMFICQHCPFVKHVEDQLGKIGQDYADKGIGILAISSNSIETHPQDSP

  14. Protein (Cyanobacteria): 373777 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 110_32280 Cyanothece sp. CCY0110 MRYLIPTILSFWIGAIITLLIGVITKAIFDYTLLWFDFILLGGILASTMLTAYLLYFDNPVASQLNAVSKIMVDHGFNYSDWCKVEKQIKERNLIDAIVALPHSDSSKLQNNRAQITLLLSQNYSDFQFTLTFPTKVALLRLKRKT ...

  15. Protein (Viridiplantae): 302830920 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 058 3068:3058 hypothetical protein VOLCADRAFT_87241 Volvox carteri f. nagariensis MPNPLAEMELLGFWGLKLVATVTDCHMSDSGRVMTAFVFKVVSYRNEAAST...LAEMELLGFWGLKLVATVTDCHMSDSGRVMTAFVFKVVSYRNEAASTMLTPEPLPESLEYLQAQVERALDERRELERVMWA...AREGRGGPSMLSCKQLETIELSTMGEAAELEVKRALEAITVVQYSMPNPLAEMELLGFWGLKLVATVTDCHMSDSGRVMTAFVFKVVSYRNEAASTMLTPEPLPESLEYLQAQVERALDERRELERVMWAAREGRGGPSMLSCKQLETIELSTMGEAAELEVKRALEEMFH ...

  16. Protein (Viridiplantae): 242088443 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available AYLGNRVFEELLRMSQEEFGFTSDGRITLPCDASTMEYAMCLLRRSVSSETKRRKEEVIMTSAKMMARLAKNWQRMTSLGR...KRLTRGAAKESDECCSSVAVKGHCVVYTADERRFEVPLAYLGNRVFEELLRMSQEEFGFTSDGRITLPCDASTMEYAMCLLRRSVSSEVEKAFLSTMESPCIYASCVAPSAGVIQQVAVCSF ...

  17. Protein (Viridiplantae): 293336073 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ncharacterized protein LOC100382321 Zea mays MKMHEVEEPPAEITRDAHPAHALRLVATDDGAPFRCDGCKEPGSGQGRRYRCGHGCDFDLHVAC...EHRCVACDAAAAAAGKRFWAYRWAYGGTHGYLHVACMKKIAFQSWEQAYQASVVGGGLVEASVPTMTAVLHRKRTDEITGGVKIIDTGIRGQYLSSSTWGT ...

  18. Protein (Viridiplantae): 255084319 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available cted protein, partial Micromonas sp. RCC299 MPGAERLLALLRRHEVPTALATSTPAKYLSAKLASHPNLLEHVACVCTGDQFPLGKPDPSIFLLAAERLGVEDPSCCLVVEDTPLGCQAAKAAGMRVLAVPSIQNHDLYTGHADELCRSLYDVDPTRWGLPAF ...

  19. Protein (Cyanobacteria): 112951 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 2_0885 Synechococcus sp. PCC 6312 MRVYLDTSVFNRPFDDQSQAKIFLETQAVILIFQAIESQQIELVFSDVLEYESSRNPKQEQAIFVLTYSQFAIHKVTLTQSIIDRAKTLQEIGVKELDALHVACAEAANCSYMLTCDKRLINRCKNLIISVINPVDFILEFDNEN ...

  20. Protein (Cyanobacteria): 112977 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available protein CWATWH0003_4198 Crocosphaera watsonii WH 0003 MEALACQNIFLQAEAEDINLVWSFMHQDETLLCPFDQRKQEVLKLSRLCTIRIAPSREIYQLAQSFQQMQGLSSKDAVHVACGDYIKANFFLTCDDNLIKKSNKLNLAMYIMNPIDYIRQEEI ...

  1. Protein (Viridiplantae): 242067819 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ypothetical protein SORBIDRAFT_05g006210 Sorghum bicolor MRMPEFEELPAEITRDAHPAHALKLVTTTDGAPPFRCDGCKEPGNGQGRRYRCGEHGCDFDLHVAC...MEMSAFLGGHLQAQLCWEAAAVDADHRCIVCDGAGGKKKFWAYRWGFGGTHAYLHVACMKRIAFQSWEQAYRASVGGGLVEASVPTMAAVMQKKRTDEYTGGVKIIDTVRSSLS ...

  2. Protein (Viridiplantae): 302765477 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ARIFVLNRYKFLNDVLRDPMKYGFLPDITHVACCGGGDEFNASVVCGGQLPCKNPQEHVYFDFVHFTDRFNKQEIQAFSLTEEYIISNHYKQTSLLDVCVNLLTAKLS...NRSVSSIMETVPDTVKLLVSEGIRTVSVLNVPQPACTPDYRLRHPAEDLDEFGCVRAIGEVVKRHNSMLEAALLALYNKPHSSVRIFVLNRYKFLNDVLRDPMKYGSSKFKVVLKLSPSFSPYQCMEISVTGFDRDITHVACCGGGIQRECSVWGTDSLRKPSGARLLRLPSLHRPF ...

  3. Protein (Cyanobacteria): 36660 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 02_2092 Cyanothece sp. PCC 8802 MNLPSFLWLWKIAAWSMGLSLTCYAILGLSGGWIFYRRQQGANRPQWLRPFHYTMGGIMVGLVLLLLIIGLIGTIGHYGSLGHSVHLVAGLLTVILVLISAMSATQMSPQRPWVRSLHITTNIILFFAFAFVGLTGWSVVQKYLP ...

  4. Protein (Viridiplantae): 297847396 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 59689:9698 81972:9698 indigoidine synthase A family protein Arabidopsis lyrata subsp. lyrata MASSSAHSRISNLQ...8024:13549 3398:13549 71240:8145 91827:8145 71275:10370 91836:7597 3699:7597 3700:7597 980083:7597 3701:7597

  5. Protein (Cyanobacteria): 282109 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available QQQVCVSRLNQISAIAPGGHWLAFISSSQVLQFLKLPNLERVKTSINCSIDSQLVTLDSRHGMIINSAEEKKPKTQFTLLTRRGNLWRFFSLSISLHSLVSNSHLPDQIFALEVSEKILGILINLKPLKVTRI...PLEIKPDFILGQPWGFLLASRQGKVILLGIRGEKLGGFQVEEEITAMAFYDQFRLLMATDYQSEKRLYFINLEEKLANKIYLNSNSNTLS ...

  6. Protein (Viridiplantae): 308807106 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available RRIGSTWTETQILTVPADLELEAERFELTTTHAFVRARAYSDPRRRQRMIIVYKVLSNGTWVYDTRIPLEVTNFWSEGSFI...HKLTPSNASQFEDFGVYVKLSGETAFIGSTGSKSSIHVFRRIGSTWTETQILTVPADVDLTSSQRFELTATRAFIHGRDAQRRWQRMIIVYKVLSNGTWVYDTRIPLE

  7. Protein (Viridiplantae): 145354220 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available WYRVGDGGEFDDKESWRVGDGGEFDDKESFFRTVHAGACMRAARIMGSGCLKFAREHVAPWDEWTCAIAAYYGNLDCLKYAHENGCPWNENTCIAAAWNGHLDCLKYAHEHGYPWNERTCASA...AWKGHLDCLKYAHEQGCDWDAWTCDNAADGGHLECLKYAHERGCDWDERTCASAAWEGHLDCLKYAHENGCDWNETMCASA

  8. Protein (Viridiplantae): 356565205 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LKQVQGVSFPRDVIAEECIPASVNNRKTGISNMIDMERRKETGTVGCSFGENRESNHADSITCSVGSCSITSRNSCKLQFPVSAGPFDDVDSSFSDAESVCQRSDEEGDCSPPTQEELAAEIHRLELHAYRCTIEALHASGPLSWEQEALMTNLRLSLHISNDEHLMELRNLISSENSIPLR ...

  9. Protein (Cyanobacteria): 329974 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available tein Arthrospira sp. PCC 8005 MSIVHPLPNSEFVLLGYLATVPHLRNIKIGSRFLEYIINVVQQDDKSLILEVEHPDFGENRELKQRRVAFYRRLGAKIFQDIIYIFPALDGTTTTEMMLMIIGEKHHDKLPQTLVQQLIRDLYSEVYNCNPDDSIFNWIADIKHDINLVS ...

  10. Protein (Cyanobacteria): 105494 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available S1096/IS1165 family protein Acaryochloris sp. CCMEE 5410 MQRGENRESEDQELLEPLVQQHPDLATLVDLAHTFLELLRQRQAKDFDDWLMKALTCPIQPLKKFAAGLMDDYAAVKASMMMEVSHGLVEGLNNKLKMLKRQMFGRAGLTLLAKRFIMAA ...

  11. Protein (Viridiplantae): 357137776 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ctomannan galactosyltransferase 1-like Brachypodium distachyon MARALGDALLFSAGAAVATV...024:2964 3398:2964 4447:4420 4734:4420 38820:4420 4479:4420 359160:2412 147368:2211 147385:2211 15367:2211 15368:2211 PREDICTED: gala

  12. Protein (Viridiplantae): 357152031 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ctomannan galactosyltransferase 1-like Brachypodium distachyon MASESAPFCLSGTGGGKGAA...024:2964 3398:2964 4447:4420 4734:4420 38820:4420 4479:4420 359160:2412 147368:2211 147385:2211 15367:2211 15368:2211 PREDICTED: gala

  13. Protein (Cyanobacteria): 176221 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available tion initiation inhibitor, yjgF family Rivularia sp. PCC 7116 MQITRTFSGASWESTVGYCRAIKAGNHIYVSGTTAVAEDGSVFAPG...NAYAQAKRCFEIVKQALQNLNADIHNVTRTRMYVTDISLWAEFGKAHQEFFAENPPASTMLEVNSLIDSAMLIEVEVDAVCLD ...

  14. Protein (Cyanobacteria): 58236 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 2)-isopentenylpyrophosphate transferase Prochlorococcus marinus str. MIT 9211 MSSSKPLIIVLLGPTASGKTALGIEIAEHLGLEIHNV...HLIGKFGKELPLLNTIGYAEASQMIDGKLPLNDAIFQTNKRTKQFAKRQKTWFRGQHNPKWLNEKNPLSEALSLIHNVIR ...

  15. Protein (Cyanobacteria): 32394 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available Cd cation transporter Rivularia sp. PCC 7116 MTQLSSSIDVPQLTRLKVEHHHHHHGDCTHTHGVIDPEIASSALGIWAVKWSLVGLLLTAIVQAAVFWLSGSVALLADIIHNVGDAMTAVPLGVAFLISRRKPTPFIPSMQELLELVWDLQMPMNLLGAMKS ...

  16. Protein (Viridiplantae): 638121 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available l Physcomitrella patens MSGFSSLTSLPNELVNLSSLEELVLSDCLSLTSLPNELANLSSLTILDLSGCSSLTSLPNELANLSSLTILDLSGCSSLTSLSNELANL...SSLTTLDLSGCSSLISLPNELTNLSFLEELVLSGCSSLTSLPNELVNLSSLKMLDLNGCSNLISLPNELANLSFLTILDLSGCFSLISLPNELANL...SSLEVLVLSGCSSLTSLPNELANLSSLKALYLIGCSSLTSLPNELANLSSLEELVLSGCSSLTSLSNELANLSSLRRLNLSGCFSLISLPNELANL...YSLKFLVLSGCSSLTSLPNELVNLSSLEELIMSGFSSLTTLPNELTNLSSLEELVLSGCSSLISLPNELTNLSSLKMLDLNGCSSLISLPNELTNLSSLTRLDLNGCSSLKSLPNELANL...SYLTRLNLSGCSCLTSLPNELANLSFLTRLDLSGCSSLTSLPNELTNLSFLTTLDLSGCSSLTSLPNELANLSSLKMLDLNGCSSLIILPNELANLSFLTRLNLSGCLSLISLPNELANLSSL

  17. Protein (Cyanobacteria): 648530234 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available NQDDLTPEARHTVQVLLEEAETEECDRATEILTQKNEISLSNNEIVDVTPLASLQNIEELVLWRNEIVDVTSLANLQNLTRLTLDNNEIVDVTPVANLQNLEKLSLAFNEVVDVTPLANL...QSLTTLWLDNNEIVDVSPLANLQSLTALHLSYNEIVDITPVANLQSLTRLLLVANEIVDVSPLANLQNL...EALYLNENEIEDVTPLASLQSLTTLYLRENNIEDVTPLANLQNLQALVLSRNEIADITPLTNLQNLKWLQLSGNDLESPTCPIQPETACNFE

  18. Protein (Viridiplantae): 638146 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available l Physcomitrella patens MSKEWTNITSLKTLDMSGCSSLTSLPNELANLFSLEELYLNGCSSLINLPNELVNLSYLRKLDLSYCSSLTILPNKLANISSLQ...SLYLNSCSRLISLPNELTNLYTLEALHLSDCLSLTHLPNECTNLSSLKELVLSGCSSLISFPNELANLSFLTRLNLSGCSSLKSLPNELANL...SSLKAFYLSGCSSLTSLPNELANLSSLIILDLSGCSTLTSLPNKLKNLFSLTRLDLSGCSSLASLPNELANLSSLTSLNLSHCSRLTSLPNELANLSSLTILNLSCCSSLTSLPNEFANLSSLTILDLSGCS

  19. Protein (Cyanobacteria): 497311047 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available eptide repeat protein Pseudanabaena biceps MANQEHITQLQQGVSCWNTWRSQEHRLQIDLVEANLAYAEVSKANFSGADLSLANLGGSNLVGANLREANLTLANL...SGSNLSLATFQDVTLCMTNLSGTNLSLANLSTVNLSLANLSGANLSGAVLRNANLMGVNLSGADLTNADLTDANLSGANLNGANLSHAQLCDTELSGANLSGANLTRANLSGAVLRKTNFNGARLKEADLSNTDLHAVKLDGAILENVKH

  20. Protein (Viridiplantae): 638142 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available l Physcomitrella patens SLPNELANLSSLIKFSLRGCSSLTRLPNEFVNLSSLTILNLSSCLSLKSLPNELTNLSSLISLNLSDCSSLTSMLSELINHSPL...SLTSLPNELTNHTSLTTLILSGCSSLTSLPNELANLTSLTILILSGCSSLTSLVNELANLSSLTRFSLRGCSSLKSLPNELTNLSSLRILDLSCCSCSGLTSLPNELV...NLSSLTILILHGCSSLISLPNELAKLSSLTILNLSGCLNLTSLPNELANLSSLVVLDLSDCSSLTSLPNELANLSSLTSLNLSGFSSLTSFPKELANLSSLTTL

  1. Protein (Viridiplantae): 638155 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available l Physcomitrella patens LANLSYLKKLDLRYCSSSISLPNELKNLSSLTILDLSGCSSLKSLPNELINLSSLEELDLNGYSSLTCLPNELVNLFSLTRLNLRGCSSLTSLSNELANL...SLPNELAKLSSLTSLDLSDCSSLTSLPNELVNLSFLTRLHLSGCSSLTSLPNELANLSSLTILDLSGCSSLTSLPNELANLFF ...04260:603 ... 3214:603 ... 114656:603 ... 3215:603 3216:603 ... 3217:603 ... 3218:603 ... predicted protein, partia

  2. Protein (Viridiplantae): 638143 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available l Physcomitrella patens LPNELLNLSSLKRLSLRGYSSLTSLPNELANLSSLKELYLRDCSSLRSLPNELANLSSLTTLDLNGCSSLTSLPNDLVNLSSLKRLFLKGCSNLTSLSNELANL...SSLEELNLRNCLSLASLPNELANLSSLITLDLSGCSSLVSLPNELANLSSLKRLSLRGCSSLTSSSNKLANL...SSLTTLDLSGCSSLTSLPNVLANLSSLEELNLSNCSSLARLPNELTNLSSLTVLYLSGCLSLTSLPNELANLSSVNELYFRDCSSLISFLPNELVNL

  3. Protein (Viridiplantae): 638125 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available l Physcomitrella patens SLISLPNDLANLSSLTRLDLSDCSSLTSLSNDLTNLSSLTRLDFSGCSSLTSLTNDLTNLSSLTRLDFSGCSSLTSLTNDLTNL...GCLYLTSLTNDLINLASLIKLHLSGCCSRLLSLPNDLKNLSFLTTLNFSGSSSLISLPNDLANLSSLTTLYFSSCSRLITLRNDFVNLFSLRSLYLSGCLNLTSLPNDLANL...SSSTTLYFSSCSRLISLTNDLANLSSWTSLYFSGFSRLISLTNDLKNLSSWKTLNFSGSSSLISLPNDLANLSSLTTLYFSSCSRLTTFLPKNLRNLSTLRRLG...LKGCSSLACLPNKLPNLFSLIELNLSGCSSLIQLPNDLVNLSFLRTLNLHHCSSLTSLPNELANLSSLTTLDLSDCSSLISLPKELANLSSFTTLNLYHCLSLISLSNELANLSSLIMLNLSGCSSLIKL

  4. Protein (Cyanobacteria): 246091 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available PPDQKYTIEILLREAKTENCQTASNYLTNLQELSLVNNQIVDLTPLANLTNLIELRLRQNQIVNVNALANLTNLTHLDLQTNQIIDITSLANLTNLEVLLLSDNKIKDITPLANFTNLRTLSLMDNQIVDVSPLANLNNLEVLFLSDNKIKDLRLFGTWYGSIGEHKSTQSLSGKRFN ...

  5. Protein (Viridiplantae): 638120 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available l Physcomitrella patens TNLNSLKTLNMSGCSSLISFPNELENLSSLKNIYLKNCSNLTRLPNKLTNLSVLEELDLSGCSSLTSLPNELANLSSLTRLDLS...GCSSLIILLNELANISSLKKLYLNNCSNLTRLPNKLTKLFSLEGIFLHHCSSLTSLPNELAHLSSLIELDLGGCLSLTSLPNELANL...SSLKKLNLSGCSSLISLPNELANISSLDELYLNGCLSLISLPNELANLSSLKKLYLNNCFSLTRLPNKLAYLSSLIELDLGGCSSLTSLPNELANLSSLKRL...KELANFSSLTRLKHNLSGCSNLISLPNELENLSSLEDLNLSGCSSLTSLPNELANLSSFERLYLSSCSSLTSLPNELANLSSLERLYLSGCSSLTSLPNGLENLSSLKVLYFNGYSSLTSLPNKLANLSSLKKFYLNNCSSLTSLPNKFTN

  6. Protein (Cyanobacteria): 300206 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ynechococcus sp. WH 5701 MPVIRFVREGRDVECYPGENLREVALREGLELYGLKGQLGNCGGCGQCITCFVDVVAEASPGALTPRTAVEDRKLRRRPDGWRLACQALVQRSLVVLTRPQAGLADREALLAAARAEPLGAGPTAWPAAEEPSEAEPADLESTATAGEAAEEGSIGG ...

  7. Protein (Cyanobacteria): 435157 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ein S16P Trichodesmium erythraeum IMS101 MIKLRLKRYGKKRESSYRIVAMNSDSRRDGRPLEELGFYNPRTDETRLDVPGITRRLEQGAQPTDTVRDILKKANVLELSRTGVNTQANVSVSHAESTEAITNAEPIQATANTESNEVSDSESTATATIRESEEQPPISES ...

  8. Protein (Cyanobacteria): 433741 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available omal protein L22 Prochlorococcus marinus str. NATL1A MTTSSTKTTAQAHGRYIRGSASKVRRVLDQIRGRTYRDALIMLEFMPYRSTEPITKVLRSAVANAENNLGLDPSSLMISTATADMGPPMKRYRPRAQGRAFAIKKQTCHISISVSATQSTNSEDSD ...

  9. Protein (Viridiplantae): 224127650 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available SKVAENSFIVVMLSKSKVSSGGPSTATAAPPNVSSGGPSTATAAPPTLVSAQPTSSLPSNVTQPSSTSQAAVPAAAFSDAD...redicted protein, partial Populus trichocarpa MKVFVKTLKGTNFEIEVKPEDTVVVEVKKNIENVQGADVYPAAQQMLIYQGKVLKDDTTLDE

  10. Protein (Viridiplantae): 224069842 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available SLLASEKGFTEWELDVLSRQHTCFNIHSSATTLGSLSKLVQSLPRMIIMDEIGKQVKFSLEAAKLARVNASLGFYDASAVSSRQARSLAEDAFFHPSIMSVSYYSFEHCFAVYSPFFLPVSMHVLLAALREWRRYKQEKAKYLLWKAKEKVAS ... ...LLLQLPNGEISKTNAFISPMWGGVMVWNPQSCSRDSDSELLVRHIMSPEDLQKVFEVFVGQFRQLFGLKSGSLHVGAMGTY

  11. Protein (Viridiplantae): 225431386 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 0:2998 PREDICTED: uncharacterized protein LOC100266100 Vitis vinifera MAAASLLCLCDTNLIHSSRKESPWHPKLFPGVGHKILD...LSVTRKRNRTHPGRQKGNLSHKFSVSATTEGSAKSNKSEETIPSWARPDSSEPPPWAQDEGMGNESEKSFEIPFYVYLLTSAVTAIAAIGSIFEYANKRPVFGVLSSDSIFYAPLLGFFVFTGIPTSAFLWFKSVQTANKEAEEQDKRDGYF ...

  12. Protein (Viridiplantae): 225458145 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available CTED: lon protease 2 Vitis vinifera MALPQLIPSPPSSSLSRKLFLNPNCRFFSPSSSVIPVPSLARHRHHRRRKENSLRCSASSFSEKHHTGSPKS...DDVVELPLFPLPLVLFPGAILPLQIFEFRYRMMMHTLLQTDLRFGVIYSDATTGTADVGCVGEVVKHERLVDDRFFLICKG

  13. Protein (Viridiplantae): 225460235 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available S-box transcription factor 26 Vitis vinifera MARGKIQMKRIENPVHRQVTFCKRRAGLLKKAKELSVLCDAEIGIFIFSAHGKLYELATKGTM...QGLIEKYMKSSCGSQDDQAKEAQLLDTKEEINMLKHEIELLQKGLRYMLGGGAGTMTLDELHIFEKHLEIWIYNIRSAKMEIMFQEIQLLKNKEGILKAANNYLQEMIDDQTGITNIAPMINPYPLTTQNEIFQT ...

  14. Protein (Viridiplantae): 359487731 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 1 PREDICTED: uncharacterized protein LOC100261344 Vitis vinifera MESTAGPSHIHGTKKKEPKPVGPQPQVLAVAPLNSMPYIGPDM...RRFSCDIKPDGNILIKGVTTTGEKIVCRNFQIFKMQTQNLCPPGHFSISFQLPGPVDDQQISGGFGINGIFEGIVKKR ...

  15. Protein (Viridiplantae): 359478760 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available DICTED: ataxin-7-like protein 3-like Vitis vinifera MSAPNEDTMSSQLSSHFFGDLLDSIIVDVASECHRIARLGLDRNLEEEEEELRLSA...QARVRVADPSNSGEANSKYVVDIFGQSHPAIASEIFECMNCGRSIMAGRFAPHLEKCMGKGRKARLKATRSSTAAQNRYSRGSPVSSYSPYSNSTSTSRLSNGTPGVGGEEYSNGTLEEP ...

  16. Protein (Viridiplantae): 359497758 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ED: DEAD-box ATP-dependent RNA helicase 38-like, partial Vitis vinifera DGFKDDSLRIMKDIERSGAQCQVLLFSATFNDTVKN...FVTRIVKDYNQMFVKKEELSLQSVKQYKVKCPDELSKILVIKDKIFELGQKLGQTIIFVRTKNSAGMLHKALVDFGYEVTT

  17. Protein (Viridiplantae): 359474329 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available DP-glucuronate 4-epimerase 3-like Vitis vinifera MVTLGHVSPSGSLSLILKVIVFPNNILQISKSADPQPAIVWASSSSVYGLNSKVPFSEK...DRTDRPASLYAATKKAGEAIAHTYNHIYGLSITGLRFFTVYGPWGRPDMAYFFFTRDILTGKPITIFEGPDHGSVARDFTY

  18. Protein (Viridiplantae): 359477512 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available :3146 PREDICTED: photosystem I reaction center subunit II, chloroplastic isoform 3 Vitis vinifera MAMATQASLF...TPTLSGDRVTVPWKSSSSLSFTTPKLPKSSVAPRTTIRAMAEEAPTKEAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWDSPKEQIFE

  19. Protein (Viridiplantae): 359482710 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available finger protein ALFIN-LIKE 5 Vitis vinifera MDGGANYNPRTVEEVFRDFKGRRAGMIKALTTDVDEFYQQCDPEKENLCLYGFPNELWEVNLPA...EEVPPELPEPALGINFARDGMQEKDWLSLVAVHSDAWLLAVAFYFGARFGFDKADRKRLFNMINDLPTIFEVVTGTAKKQV

  20. Protein (Viridiplantae): 225460885 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 0:4156 PREDICTED: GDP-L-galactose phosphorylase 1 Vitis vinifera MNTLRIKRVPTVVSNYQKEDSDDGARQVGGCGRNCLKQCCIQG...PTEFRVDKVLQPFDGNKFNFTKVGQEEVLFQFEPSNDEEPEFIPNAPIDVENSTSVVAINVSPIEYGHVLLIPRIFECLPQRIDRESFLLALDMAVEAGNPYFRLGYN...SLGAFATINHLHFQAYYLATPFPIEKAPTRKITTAGNGVKIFELLKYPVRGLVFEGGDTLQDLANTVADSCICLQDNNIPFNVLIADAGKRIFLFAQCYAEKQALGEV...NQELLDTQVNPAVWEVSGHIVLKRKEDYEGASEQNAWRLLAEVSLSEERFQEVNALIFEAIACGDDEKGNLTEDMIEEPDVTPPSHEDAGAINNSSYPAAMVAGKQECLVQQ ...

  1. Protein (Cyanobacteria): 236183 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YP_007091121.1 1117:4513 52604:3961 54298:1743 54299:1743 251229:1743 Cell wall assembly/cell prolife...ration coordinating protein, KNR4 Chroococcidiopsis thermalis PCC 7203 MEEIWQRIDLWLQVNAPQIFE

  2. Protein (Viridiplantae): 225433762 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 3 PREDICTED: vesicle transport protein GOT1A Vitis vinifera MAYEMTEQKRVGLGLIGFGIFFTFLGVILFFDRGLLALGNIFWLTGVA...LLIGWRSTWNLFSNRANYKGSISFLLGLFLIFVRWPIVGIIFEIYGYIVLFGGFWPSVKVFLYQIPVVGWILRFF ...

  3. Protein (Viridiplantae): 225451265 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available PREDICTED: uncharacterized protein LOC100264176 Vitis vinifera MAGIWCSSTVSSTLHLRVTVASKIAVYLFWEYVNFFWFRQHLQK...RVHGIRCCSTTPDNKEKTPQLLRIAVGGVTELLRLVSFGQNRLDSMSYKQGDELLVSCIDDVLLILKSDYENAYFVTGIFTSAIYDEDCIFE

  4. Protein (Viridiplantae): 225432682 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available uncharacterized protein LOC100261343 Vitis vinifera MSSIIWKNFNLCLSKLKCFPTTLPSSPPSKHDHNRHPSSSSSSSISSTSSVLIKN...FNSLYDLTSDSTSKSLTRTTDDFLSTSEDSVDSESPPDFATVFASQRFFFSSPGRSNSIFEASESPPESDSIVNGGVAVHT

  5. Protein (Viridiplantae): 359489981 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 0:6257 PREDICTED: uncharacterized protein LOC100853468 Vitis vinifera MNFSTLSSLWCPIQKLIDGSKISDPVQLKEEHGANFQE...IFDTKSVLRRGISPEIINLGLSLVKETYVLYLGSIKHWVLMVILSSLLLKKLLNITDPDIFEAMRSSFFPLCKGKLGYVYAAAEH ...

  6. Protein (Viridiplantae): 359476919 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ICTED: putative acyl-CoA synthetase YngI-like Vitis vinifera MFRGNTVMSGYLKDEKATEEAFRGGWFRSGDLAVKHPDGYIEMKDRL...KDIIISGGENISTVEVETVLYNHPAILEAAVVARPDNHWGQTPCAFVKLKEGFDVDAQEILKFCRDHLPHYMAPKTVIFEDLPRTSTGKIQKFILREKAKALGSLS ...

  7. Protein (Viridiplantae): 225446505 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 4127 PREDICTED: OPA3-like protein Vitis vinifera MILPVVKLGTLALKTMCKPIAARLKKDAGLHPKFRQFIINIAQANHQFTTTMQRRIYGH...ATNVEIRPLNEEKAVQAAADLVGELFVFTVAGAAVIFEVQRSSRSEARKEELRKQELQALKQRDEDLVREVEQLKHKLEELEQLAKGQGLSGLFNFKHAHVTEDGKALPN ...

  8. Protein (Viridiplantae): 225463823 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available S-box protein SVP Vitis vinifera MARQKIQIKKIDNTAARQVTFSKRRRGLFKKAQELSILCDAEIALIVFSAAGKLFEYSSSSVSQVIGRHNQHPQT...PGKPEPPSLELQLENSTCAALSKEIAQQTQRLRQMKGEELQVLKIEELTELEELLEAGLCNVVEEKEERIRTEISDLQRKGDLLQEENERLRKEMENIFEAQPLL ...

  9. Protein (Viridiplantae): 225433644 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ED: 30S ribosomal protein S1 homolog Vitis vinifera MIFSGASGSVTGLSILSKLFCWDSSSNTNSSASLLINPSKISSFYRRSPLRRSPFH...PSHSCKEPHKTIQEIAKGLIGSLISVKVILADEEKRKLIFSEKEAAWLKFSKQINIGDIFEAMVGSVEDYGAFVHLRFPDGLYHLTGLVHVSEVSWDLVQDVRDVLNE...GDEVRVKIVKVDRVKSRITLSIKQLEEDPLLETLDKVIPQDGSTGPDSLRTSDSYDIEPLPGLETIFEELLQEEGISDVRISRQGFEKRVVSQDLQLWLSNAPAVDKQFTLLARAGRQVQEIQLTTSLDQEGIKKALQRVLERVP ...

  10. Protein (Cyanobacteria): 129219 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available NP_486566.1 1117:2513 1161:199 1162:281 1177:524 103690:2260 luciferase-alpha subun...it Nostoc sp. PCC 7120 MKTGLFCNYENHHQDSRRAIFEQVALVRQAEKLGFDEAWVTEHHFNEVNLSSSILLLMAHLAGVTSTIKLGTAAVLLPFHNPIRV

  11. Protein (Viridiplantae): 359482708 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available finger protein ALFIN-LIKE 5 isoform 2 Vitis vinifera MDGGANYNPRTVEEVFRDFKGRRAGMIKALTTDVDEFYQQCDPEKENLCLYGFP...NELWEVNLPAEEVPPELPEPALGINFARDGMQEKDWLSLVAVHSDAWLLAVAFYFGARFGFDKADRKRLFNMINDLPTIFE

  12. Protein (Viridiplantae): 225434239 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 0:3294 PREDICTED: uncharacterized protein LOC100250911 Vitis vinifera MEKDEGRGRRLSIKDSQRRPPWLHKLRENCFRRVKEER...RMFYEDIRMNQTHRDGCNGTTEEEDEDYLDPAIFENLRLEDDKGCKEIWCPICKKGKLRQNNHLIYCTLCELGLERGDQVNLDCLQVRLGEAYSEHLDRGCRFTPQFHVYTQFSLTALYIQCEACKIFELIL ...

  13. Protein (Viridiplantae): 225466049 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available adenylate kinase Vitis vinifera MWRRVTSLSPFISSSKPSIRNQASYGGKIWELFTTEILTPAKAGISSDEKTPFITFVVGGPGSGKGTQCAKIVET...FVLFFHCPEEEMVKRLLSRNEGRVDDNIDTIKKRLEVFTALHLPVIKYYSEKGKLYKINAVGTVDEIFEQVRPVFAVCEATK ...

  14. Protein (Viridiplantae): 225436273 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available : probable glutathione S-transferase Vitis vinifera MAEELKLFRTWSSVFALRIVWALKIKGVEYETIFEDLSNKSPSLLQYNPVHKKVPV...ELKGKRFFGGERIGFVDLALGWLANMISIFEEVAGLKMVDEDKFPLLAAWMQEFADSPIIKDNWPPRDKMIAKFQALRDAKLAAAASK ...

  15. Protein (Viridiplantae): 224365627 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available otein L5 (mitochondrion) Vitis vinifera MFPLHFHYEDVSRQDPLLKPNHANVMEVPGSCEIRVIPKRPSSFIIQNGKLAMEIPRGQRFIQTQRGS...TGKSFRSNQFLGSNKDKGYVSDLARQSTLRGHGMSNFSVRISIVMSLLDSPVEIRENSIQFSMETEFCEFSPELEDHFEIFEHIRGFNVTIVTSANTQDETLPPWSGFFQKDEGQ ...

  16. Protein (Viridiplantae): 225465298 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available finger protein Alfin1 Vitis vinifera MEGLPPHPVPRTVEEVFSDYRGRRAGLIKALTTEVEKFYQQCDPEKENLCLYGLPNETWEVNLPVEEVPP...ELPEPALGINFARDGMQEKDWLSLVAVHSDSWLLAVAFYFGARFGFGKSERKRLFQMINELPTIFEVVTGVKQQRDMSGNH

  17. Protein (Viridiplantae): 359489173 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available : LOW QUALITY PROTEIN: probable glutathione S-transferase-like Vitis vinifera MAESVPELYQNIVSEEVKLLRTXSSLFALRIVWAPKIKGIEYETIFE...FGDDKVVTSIFQGFFLKEGKEKKKAMVEAMKHLQFLEDKLKGKRLFGGERIGFVDLALGWLANFISIFEEVVGLKIVDEDKFPLLSEWMKEFSDSPIIKDNWPPQDKMIAKFHALYDATIAAAAASK ...

  18. Protein (Viridiplantae): 225466235 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available : probable glutathione S-transferase Vitis vinifera MSKEEVVLLDFWASPFCGRVKIALAEKGVEYENREEDVLGSKSELLLNSNPIHKKV...PVLLHNGKPVCESTVIVNYIDEAWPSPPLLPTCPYERARARFWGDFIDKKIFEGGAKIWGSKGEALEVGKKDFIEILKQLE

  19. Protein (Viridiplantae): 225443566 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 4127 PREDICTED: OPA3-like protein Vitis vinifera MVLPLVKLGTLALKTLSKPIASRLKQQAGLHPQFRQFIVNMAQANHRMTTTMQRRIYGH...ATDVEIRPLNEEKAVQAAVDLIGELFVFTVAGVAVIFEVQRSSRSEARKEEIRKQELEELRQRDENLAREVELLKHKLGEIEQLAKGRGLGGIFKLKPAQTEIEKSTAV ...

  20. Protein (Viridiplantae): 359490272 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available TED: LOW QUALITY PROTEIN: chalcone synthase-like Vitis vinifera MASVEEIRRHAQRPCGLPTILAIGTTLLDNCFPQAEFPDFFFRA...TKSDYLTQLKENFKLICKSLILYEKIIKENPNIGTSLDTLFGDGVAALIVGSDLDTLIERPLFQLISADQIFIPDSENAIEGHVCEMALVVNLAKNVLNLIFE

  1. Protein (Viridiplantae): 225456077 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available DICTED: uncharacterized protein LOC100252476 Vitis vinifera MGSSSAAPSNLLSTSFTCVTSNSTHTFLRPSKLSCITKTTLPPKISHT...KSPGRTWMLIFTAQKQLKGGSYFPLTAVQRFDAAGKRIENGVYLGPIGCLTFEGRFSWKKRILAFIFECIRIKVGPFNPLEISLGQKDDREPGTKDPFFIWFYIDEEIAVARGRSGGTAFWCRCSRVMSS ...

  2. Protein (Viridiplantae): 225435046 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available PREDICTED: probable histone H2B.1-like isoform 1 Vitis vinifera MAPKAEKKPAEKKPAEEKKSTVAEKAPAEKKPKAGKKLPKEGG...AGPGDKKKKRTKKSVETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS ...

  3. Protein (Viridiplantae): 359477514 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available :3146 PREDICTED: photosystem I reaction center subunit II, chloroplastic isoform 4 Vitis vinifera MAMATQASLF...TPTLSGDRVTVPWKSSSSLSFTTPKLPKSSVAPRTTIRAMAEEAPTKEAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWDSPKEQIFE

  4. Protein (Viridiplantae): 359494577 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ICTED: LOW QUALITY PROTEIN: medium-chain-fatty-acid--CoA ligase-like Vitis vinifera MNELHFGVPMARAALCTLNIHHDS...MFHCNGWRLTWGVAAXGCINVFLRNVTVKGIFESIAQHKATHMGATPTILNMIINTPVSVLFKMKELGFGISHSYGLIVTYGPGSVCTWKPEXDLLPPKKQAKIKAWQ...GLHHLGMEEIDIKDLITMKSVPPDAKAVGEVMFRDNTVMNGYLKKSTXEALENGWFRSKDLGVKHHDGYIELKDHSKDIIISRGENISTIKVDALFFSHPTIFEAVVVGKPDDYXVETPCAFVKSKEGCNANANEIIKFFRDKLPHYMPVRLKRVACFAYFCPPTN ...

  5. Protein (Cyanobacteria): 129244 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YP_320978.1 1117:2513 1161:199 1162:280 1163:3227 1172:914 240292:914 luciferase-li...ke protein Anabaena variabilis ATCC 29413 MKTGLFCNYENHHQDSRRAIFEQVALVRQAEKLGFDEAWVTEHHFNEVNLSSSILLLMAHLAGVTS

  6. Protein (Viridiplantae): 225454876 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 0:4837 PREDICTED: uncharacterized protein LOC100247606 Vitis vinifera MTTSLPWHPLFSSKPQTLRRFAAPVRHRLPMPVRAFRR...SDFDGFAKRMASGDAWRDAWRSANDGFELLIFEAKKTAERINRQYAVSRRFSEAVGSAGDWAREVDREFEIGRRWRTVTLD

  7. Protein (Cyanobacteria): 236178 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ZP_08491474.1 1117:4513 1150:509 44471:3713 119532:1019 756067:1019 KNR4-like cell ...ATDEEIDRAEVFLGVEFPEDFKLSYRVHNGQDEESYSLFPNLEFLSLQSAIKISEKWQDCSDDNFRCDRDDIFEGIWNGWWNPNWIPFTMEGNGACECVDLAPAAGGNVGQVIIVEWQEATRGLIAPSFRVYLETFADALERGDYRFSEDGYGLVDLVDFEILDRAVGNG ...

  8. Protein (Viridiplantae): 225427284 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ED: phosphatase YqaB Vitis vinifera MTVSSGENSADSKYSLSGLAPLEAVLFDIDGTLCDSDPLHYYAFRELLLQIDYNGGVPITEEFFIEKIAGKH...AVVVGSECDRAKPFPDPYLKALEVLQVSKDHTFIFEDSVSGIKAGVAAEMPVVGLTTRNPESLLMEAKPVFLIRDYDDPKLWAALAELDQKGAPGATAAA ...

  9. Protein (Viridiplantae): 359480834 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available S-box transcription factor 18-like Vitis vinifera MGRVKLQIKRIENNTNRQVTFSKRRNGLIKKAYELSVLCDIDIALIMFSHSGRLSHFS...GKRRVEDVLTRYINLPDHERGGIVHNREYLISTLKKLKTENDIALQLANPVAVNSNVEELNQEINNLQHQLQIAEEQLRIFEPDPLAFTSTGELESCEKNLLEALNRVTERKVNPAINPSLISSS ...

  10. Protein (Cyanobacteria): 205319 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ZP_16391152.1 1117:3878 1118:2761 1125:273 1126:871 1160282:1406 Linear gramicidin ...ne racemase (ATP-hydrolyzing) ; ATP-dependent tryptophan adenylase ; ATP-dependent glycine adenylase ; Linear

  11. Protein (Cyanobacteria): 205430 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ZP_18822011.1 1117:3878 1118:2761 1125:273 1126:871 1160286:203 Linear gramicidin s...e racemase (ATP-hydrolyzing) ; ATP-dependent tryptophan adenylase ; ATP-dependent glycine adenylase ; Linear

  12. Protein (Cyanobacteria): 205526 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ZP_10227544.1 1117:3878 1118:2761 1125:273 1160279:878 Linear gramicidin synthase s...e (ATP-hydrolyzing) ; ATP-dependent tryptophan adenylase ; ATP-dependent glycine adenylase ; Linear gramicid

  13. Protein (Viridiplantae): 308803609 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LKGRCLESFATTDVGVFPSQPGKVVVVLAGRYAGKKAVIVKNVDDGNSAHPYGHALVCGLSTIPRKVRNDLHRCARTAPFGCTEILTARSVAFENAQVTKKMDEKKQAKRSKCKTFIKNINYSHLMPTRYTLDVNFKDVVTSDVLDNATKKVAAQKEAKKLLEERFKTGKSRWFFTRLAF ...

  14. Protein (Cyanobacteria): 329090 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available data, contig C315 Microcystis aeruginosa PCC 7941 MKTLSRLNSKESALTVLVIVSQIFLVNHRVIAQSIPRISIPGLATPVIPVITPNVAIPTVNVTTTTNNIPATSLRSQPIIPT...VNVTTTNNIPATSLRSQPIIPTVNVTTTNNIPSTSLINSPTPVIPTVNVTFDNKGVPTAVPELKPLTFSVTGSEDNPSSFLSV

  15. Protein (Cyanobacteria): 329089 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available SIPRISIPGLATPVIPVTTPNVAIPTVNVTTTNNIPATSLRSQPIIPTVNVTTTNNIPATSLRSQPVIPTAVTPTVNVTTTNNIPATSLRSQPIIPTVNVTTTNNIPSTSLINSPTPVIPTV...g data, contig C315 Microcystis aeruginosa PCC 9432 MLFTIQTSDSVIPLSTIKNEANKMKTLSRLNSKESALTVLVIVSQIFLVNHRVIAQ

  16. Protein (Viridiplantae): 242044854 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available QRAAWARTPPLPRRTSAPSSLKRATREESSSEQMAAAAAECSSHSNDGGGSSNKRRKAAAGVVCPFALLKPDGLDGGATLADINARILMRPARPVRHPVGEFACAPRVSADQPGISGKAVASFTRLHTSGRGTITIIRTRG ... ...GEPLKAQQQQQQASAFNSSCVTHEQADYCTPTTDSFVHYDDDGDDPLSSIFSAGPAPALAAERAVFHQQLPAAEAAEEPLPSSSSSNCRGDPPAAGGVDLQVQVQGQG

  17. Protein (Viridiplantae): 359478107 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available SIPAEIPDPKAKEPDDWDEEEDGLWRRPKIPNPAYKGPWKRKKIKNPNYKGKWKTPWIDNPEFEDDPDLYVLKPIKYIGIEVWQVKAGSVFDNILICDDPEYARQVVEDVWGKNREAEKEAFEEAEKVRRAREEKEAERTREESEKRKAARDSRYGARKRRRRHDPDDDLDDYHDEL ...

  18. Protein (Viridiplantae): 302792799 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available WPDLIMGVVVGEGVMMPCSTVTERGAPVFLSCGYLAGVVVAPQLGRYHKGGVRTSKGREVELAPIAKVLEELGKSKYKSYLEGETDMIMVLKSRQQMLVEFAPISWKLPEQEWKDNHPLEEFAEAAKSVKGRPLIPGKAPRGKLRTREESKAIKERKELEARQVLAARKQMVRTVYGGDE ...

  19. Protein (Viridiplantae): 302765955 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available WPDLIMGVVVGEGVMMPCSTVTERGAPVFLSCGYLAGVVVAPQLGRYHKGGVRTSKGREVELAPIAKVLEELGKSKYKSYLEGETDMIMVLKSRQQMLVEFAPISWKLPEQEWKDNHPLEEFAEAAKSVKGRPLIPGKAPRGKLRTREESKAIKERKELEARQVLAARKQMVRTVYGGDE ...

  20. Protein (Viridiplantae): 357480979 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 163742:17721 3877:17721 3880:17721 hypothetical protein MTR_5g006880 Medicago truncatula MSTPAQPAGENTEPISAHVLMRSSRVTGQSGNGFFGRIDSGGEFKHHPEKFQKQSKTREESRSESQYINQQKLATESWDLRRKRKGK ...

  1. Protein (Cyanobacteria): 336109 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available protein Cri9333_1007 Crinalium epipsammum PCC 9333 MADPQELSAQFLTREESIKVDAALLTSQDKFVTRLALYALKSLKQIAQETGAPIENITPQQLSAWIEKDETFKQEIENDATFEDFFTRLVISSLNPLKQVSQAANLPIEDLTVEQVIAWFEKQAKLK ...

  2. Protein (Cyanobacteria): 140596 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available hetical protein Npun_R5805 Nostoc punctiforme PCC 73102 MQPAQAGFVCAAAISNHQVIFEPLSLTVEPFILSVEPLSLRVEPLSLRVEPFSLSIEPLSLTVEPFILNVEP...LSLRVEPFSLSIEPFILNVEPFILNVEPLSLTTLSKVLLLYKKCYNFLVAVTLLIKSCLNRLSKYC ...

  3. Protein (Viridiplantae): 303279957 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 64608:4267 predicted protein, partial Micromonas pusilla CCMP1545 TQSTVDPGMESIVEPCMESIVEPGMESIVEPCMESIVEPGMVSAVEPGIESIVEPGIEPCMESIVEP...GMESIVEPCMESIVEPGMVSAVEPGIESIVEPGIEHQSGTTQSTVEPGMESIVEPCMESIVEPGMESIVEPCMESIVEPGMVSAVEPGMESIVEP...GIESTVDPGMESTVDPGMESIVEPGMESTVEPGMESTVDPGTESIVEPGMESIVEPGMESIMEPGMESTVEPGMESTVESIA ...

  4. Protein (Cyanobacteria): 325995 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available o7428_4138 Gloeocapsa sp. PCC 7428 MSRFTHTLILRWGAGALFALALAPLLAETAAATVRTSTPELGSANSEALYAQRKGAKGVKGQPTTPPKGVEPPPPKGVEPPPPKGVEPPPPKGVEPPPPKGVEPPPPKGVEPPPPKGVEPPPPKGVEPPPPKGVEPPPLPPTL ...

  5. Protein (Cyanobacteria): 104326 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available RSHEIGVVEGDRITQVYQFDGELFWQTSGLAEGLDYLPAPSQPGSSLEANDPLEGVRQEIREALSNQRPLNGNGIIENPDSFSRPAPPAEVVPKPATVEP...GNLTGDLDSSVSTDTSPESVDSLNAVPTTEDSTLPTTDIENPTVDSPDTIAPDAVTPAPINIIDITPAAEEPPIEILSPTDQIEIIVPVMDPGVPVEPPVPVEP...PVEPPAPIEPPVPIEPPVPIEPPTPVEPPVEPPAPVEPPVPVEPPVEPPAPVEPPVPVEPPVEPPVPVEPPVEPPVEPPVPVEPPVPVEPPVPVEPPVEPPGPVEPPVEP...PVPVELPVEPPGPVEPPTPVEPPVEPPGPVEPPTPVEPPVPVEPPVPSGPGEQMSNGVVNPSP ...

  6. Protein (Cyanobacteria): 189042 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available n MAE_13150 Microcystis aeruginosa NIES-843 MFELSDLKQTRVYQEALAEGEKQGLERGLQEGLERGLERGLERGLERGLERGLERGLERGLERGLERGLERGLQEGKRLVVENLLRVRFGELDPEIQAIISRILQLSPEEFTPLLLHCSKQELLKRFPPEKSRGN ...

  7. Protein (Cyanobacteria): 493214371 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available P)H-quinone oxidoreductase subunit 4 Nodularia spumigena MKIFPSLKKFVVYSLVLLVSVCSLLFTAPTAIAAVDVSTQYIAFDTSTGSIDEAVASYRSLKGKVAKQQSLSIDE...IKQALGVINDKINTLVQEKKDLLAADSNASTDNLDSSIASYRSLKGKVAKQQSLSIDEIKQALGVINAKINSLT

  8. Protein (Cyanobacteria): 465666 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available (P)H-quinone oxidoreductase subunit 4 Nodularia spumigena CCY9414 MKIFPSLKKFVVYSLVLLVSVCSLLFTAPTAIAAVDVSTQYIAFDTSTGSIDE...AVASYRSLKGKVAKQQSLSIDEIKQALGVINDKINTLVQEKKDLLAADSNASTDNLDSSIASYRSLKGKVAKQQSLSIDEIKQALGVINAKINSLT ...

  9. Protein (Viridiplantae): 302816282 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 3:2934 3244:2934 3245:2934 3246:2934 88036:2934 hypothetical protein SELMODRAFT_19757, partial Selaginella moellendorffii KGNKDGLECAVCLCKYEEREILRLLPKCKHAFHVDCVDTWLGSHSTCPLCRSHV ...

  10. Protein (Cyanobacteria): 340172 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available al protein PMT0535 Prochlorococcus marinus str. MIT 9313 MLLLLTLFIPYGFLEVEIASAGPVEWKEVPATEAGQQWWDIGSLHYDKDGNLSVLSRFTPALREGEKQQNGSLYLMHVDCDQKLFRDTSVNGLHRFRAEWKPSDGDELIDAVIDEVCTAEVT ...

  11. Protein (Cyanobacteria): 201747 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available VRLVIFRFGIVLGDGGALAKMIPPFKMFAGGPIGEGKQWFSWIHIDDLVNLLVRAIEDSNISGTFNATAPYPVTMNQLCDTLGKVMNRPSWLPVPSFALELLLGDGAKVVLEGQKVLPEKTSEEIGYNFQYSELQPALKDIVK ... ...own function DUF1731 Cyanobacterium stanieri PCC 7202 MKIAITGATGFVGKELVKKLAVNHQIVVLTRNVDKARSIFPNNLQSNLEYVSYT...PKQSGDWQKQLSGCDGVVNLAGAPIGERWNPSYKQEIFDSRQLGTRNIVEGIKSSAQKPSFLINASAIGFYGTSETATYTEISPAGDDFLAKVCVAWEEEAQKVKEAD

  12. Protein (Cyanobacteria): 79536 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available olling factor protein Microcystis sp. T1-4 MSAKDRFHGAVRKGLEKEGWIITDDPLRIEVGDVEMYVDLGAEQLIAAEKDNEKIAVEIKSFIGKSSISEFHTAIGQFFNYRVALEEKEPKRQLYLAVPLDIYYSFFELRFIQTVVKRFQIYLIIYDPIGEVIVEWKN ...

  13. Protein (Viridiplantae): 303289765 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 564608:6779 predicted protein Micromonas pusilla CCMP1545 MSTAREDDVARGAEGAPRADVAVPDRATEAKGGEALPAPTPEDGAGTRVVRVGSGVAVPIGEERGPVVVNADGSLSSIANWDEMTDREREATRRRIAKRNNARLEALKAAGGDEREGKRDDAS ...

  14. Protein (Viridiplantae): 302846531 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available DMVAVKLINGSIVDGRALQRDMESFHAELSILSRLRHKNIVRVYGGCLRPPCIFLVMQLMQQSLDSVIHHGQRHLTLRRALQLARDVAAGLSYLHPTIVHRDLKPANILIDESGTAKISDFGLARYKYKAYLSTRTPDQGSVAYMAPGTYITVVFVWKCFVQQRGLTDVTACPLINRLR ...

  15. Protein (Cyanobacteria): 370048 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available e-dependent formaldehyde-activating GFA Stanieria cyanosphaera PCC 7437 MMLAVGKQPKEKKTILLFNDKIKAMSEEKKSVIYQGGCHCGAVRFQVVVDRWEVEDCNCSI...CRKKGFLHLIVPPSNFTLLKGEKFLTTYTFNTGTAKHTFCSICGIHSFYYPRSHPGWIDINIRCLDENVISQFLVKSFDGINWEENVHKIQNN ...

  16. Protein (Cyanobacteria): 369984 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available endent formaldehyde-activating GFA Nostoc sp. PCC 7107 MAINIPEPMIYEGGCHCGAVRFRVVVKQHKVDDCNCSICRKKGFLHLIIPKEQ...FTLLQGENELTTYKFNTGVAQHKFCSICGIHSFYIPRSHPDCIDVNVRCLDGDVIANFEVIPFDGMNWEANIHKLIN ...

  17. Protein (Viridiplantae): 226491436 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available rized protein LOC100275991 Zea mays MSATLCFMGVARESLSLDAPVAAPKLGRERRSALASANSGPQCWRWRRGLAMRCQTGSTAAPFLRTEEAPAAASGARNAQAGFTIVMKFDGSSLASVERMREVAGLILSAGERTRLPLDRTEGKIHTTADRVRRKMAITEPI ...

  18. Protein (Cyanobacteria): 107937 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available hetical protein Npun_R4090 Nostoc punctiforme PCC 73102 MLNNLYQFLSPRQWGISLAGLGLLLGLGFIGKQTQVVPITDSSLSSAQVQKT...KTSENSLLSQLRKVREQRSQLRASAGERGIFVHQSGKTLPTTTALVPDSQGATKGAEGLPKVNFPVKDGVYLYGQSPKSNQLGQGYIIFQKQQDKITGALYMPQSEFN

  19. Protein (Viridiplantae): 115452239 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 89 39947:5189 Os03g0277500 Oryza sativa Japonica Group MASEGAVSPAFAYTVVYVKDVAKSAAFYSAAFGYTVRRLDQSHKWAELESGTT...TIAFTPLHQRETDALTGAVQLPDSAGERGPVEICFDYADVDAAYRRAVDSGAVPVSPPEQKSWGQKVGYVRDIDGIIVRMGSHVRA ...

  20. Protein (Viridiplantae): 224149464 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available RHCGRVRNRASGGEAVSATISKAAATQFSGRLPSQQDYRVNRDYYRVKKDCARIENQSSAGERDDYRVIRHCGRVRNRASG...GEAVSATISKAAATQFSGRLPSTDYRVNRDYYRVKKDCARIENQSSAGERVLSTISKAAATLFSVTLTESTGNVRRDKSRHQLGKQFCWGSCFGDNFQGGSDSVFGDD

  1. Protein (Viridiplantae): 308801933 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available STARAEVPVDARVALERFAESAEEIERALAPLLEAEASAVRRRLRPLERAETHLSIARAIATLFEMYLRTLGVDPSKHAVRKELERVETYEGKIEETRRRVGDGSRGASAGERNAAPSVEDAAKAMERGEGEPGDLLRAALAEKKGDDGDGDDAGGGKPRRARSRGEDVGQAKEVSDGFV ...

  2. Protein (Cyanobacteria): 147427 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available e Synechococcus sp. RS9916 MAKRAVCAPRVLCLGEALVDRLGPLGGDPATATPAECDDRLGGAPANVACALARLGTPVAFLGRLGDDAIGSSFQELLRNRGVDLRGLQTDMQRPSRVVLVRRDAN...GERVFQGFAGERGQDFADQGLDHRQLALAWPALAPSARWLLVGTIPLATPASTDALLWAIEQVDHSGLRLALDVNWRPTFWDP

  3. Protein (Viridiplantae): 303289991 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available CAECEHEWKAGVCSRTRSDAAAECMRCRGCSARGISFRVWCDANGERGKSLLEEYVDTDRGPMDVTRASGYKALWKCATCEHEWRTKICNRTTANNPTGCPKCPGFVARSNKFQVWCDANGER...AYKALWKCATCEHEWRAKVGSRTNSRRPCGCPKCANHLPLSKTNNFQAWCDANGERGKTLLEEYIDPDRGPTRVTNGSTYKALWKCATCEHEWRTTLNCRTLSGRPTGCPANCRKKRKRHSPATTC ...

  4. Protein (Cyanobacteria): 12658 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available in Cyagr_1452 Cyanobium gracile PCC 6307 MTSSPLRPLLGCLALLLAVPVAGAAPARAQMTQEQAFQRGRAANLARMRAEVINGGLGVYRPALCMYERSGGSCLVRADAEGFLFRFYGGVPGWVQLGLPPSVETEILVAPDGRSVLSISYNGVPRSQPAPAGPPQAQPGL ...

  5. Protein (Viridiplantae): 15222222 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available NP_177075.1 33090:559 35493:1107 131221:1107 3193:1107 58023:823 78536:1104 58024:1...104 3398:1104 71240:676 91827:676 71275:2291 91836:500 3699:500 3700:500 980083:500 3701:500 3702:525 cystei

  6. Protein (Cyanobacteria): 138867 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ynechocystis sp. PCC 6803 MFKKLGEVEKIKFKNWCVDKNNLMVKEKWFGKEVKEDRRMVWFGVGIELGKNEKFKGLEIDNSLKKRCLEFYGENFNSLLLIKYGDGSKLNLHKDRDCFDKKVVIVNSGICVFEYDGERKILEDGKIYEIDGKKSHGVVKVVGERYSLSIRKVL ...

  7. Protein (Viridiplantae): 302828520 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available EDLVARMAPPAAATAAADRSGSPRNSGICIAQEGLKKETAAATSPTMTTPGGAMAAAEVGPLGPPAAVHPWSAAAAATAAG...KTMPPSAGRAVQQQPSSSPNATCQPAVATAPAAPAAATAVAATAAEDLGADPASCLSRMAQSPSKGGPDLLEKMRIAEDLLTRRDKLTPEMVQMVIKQLAALCQSVSV

  8. Protein (Cyanobacteria): 275082 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available SKVYVVTNLCENKTQRLQQPQGIWTIGRDGNSGICIADKYLSDRHAAIQYIEDQGFYLFDFNSANGSFVNGEPVYQPIKLKDGDRIRLGTITFDFFVNHLCRTLPTVAIELLMQLVPRMDSNSVKILNSQHEQQKHRTQNLNDSLEAARESGLIEEMGHEHSSFSAEEKSDILDRLFSKQKL ...

  9. Protein (Cyanobacteria): 138866 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ynechocystis sp. PCC 6803 MFKKLGEVEKIKFKNWCVDKNNLMVKEKWFGKEVKEDRRMVWFGVGIELGKNEKFKGLEIDNSLKKRCLEFYGENFNSLLLIKYGDGSKLNLHKDRDCFDKKVVIVNSGICVFEYDGERKILEDGKIYEIDGKKSHGVVKVVGERYSLSIRKVL ...

  10. Protein (Cyanobacteria): 275068 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available TVYLMTNLCDNQTQSLRQSQQIWTIGRNQNSGICIADNYMSRRHAAIQYIDDQGFYFIDFNSTNGSFVNGDRALEPIKLEDGDRIRLGNMTFDFFVNYTCRVLPTVAMELLMQLVHRKNDNQVEILSFRRDKQKYIPEKVDENLEIFRNSRLLENLEHYYDNFSSEQKSEILDRFFSRQIP ...

  11. Protein (Cyanobacteria): 365552 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 407_0073 Geitlerinema sp. PCC 7407 MDANLFEYRPLSCPVCHRGLGHPARPLGEQFARVFWDQMEDGRSPHQGLLTCQHCRQRVVVSWSGHYVRDPFILQKLAMGRSLRRQSRPLARILRDVGLARHSPLWAIVGGLVLLGLTFSMAEGPLLPEVPKPESWGTLAPPS ...

  12. Protein (Cyanobacteria): 17320 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available se Stanieria cyanosphaera PCC 7437 MARSKITEKLLAAKQAKGITFEDLEKIVGRDETWIASVIYRQASADLEEATKIVTALGLSESMAEPLTIPPLKGSLEPTIPTDPLIYRFYEIMQVYGMPLKAVIHEKFGDGIMSAIDFTLEVEKVEDPKGDRVQVSMCGKFLPYKKW ...

  13. Protein (Cyanobacteria): 88129 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available Synechococcus sp. JA-2-3B'a(2-13) MQSMAESRDPDTPPQDRRRLIREVAGWLAMLGVLIPGLQRFYMGHQRWGWGYLVAGLMVFVPSIPLQILSYGVRALCLLEGLWILTMSNADFDFRFNRELIELEWTSVEGREARDPEQQLESLLKQGLITRAEYEERRRQIRKIS ...

  14. Protein (Cyanobacteria): 80770 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available n DUF29 Gloeocapsa sp. PCC 7428 MTDNTLYSKDFIAWAEQQALLLEAEEFQRLDLTNLIEEVRDMSRREIKAAQSQLVRLIKHLLKLRVQPDYPDKKNWLISIKDARVELDESMAESTVLKNKLLSPETLARCYAKAVVQASNETDLSLSDFPNELPYSIEQLLNPEFFGE ...

  15. Protein (Cyanobacteria): 113139 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available l regulator, AbrB family Cyanobacterium aponinum PCC 10605 MGESNPTPLEGKELLQKVKELSDIPRRQRAKECGYYTIGKNGKERVNLT...AFYDAVLAAKGVPLDPERTKDGRGREATFRVSVHKNGQIVIGSSYTEKMGLKPGDEFEIKLGYKHIHLRQLDEDEA ...

  16. Protein (Cyanobacteria): 132521 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available l protein LYNGBM3L_25960 Moorea producens 3L METMSTEAIASVINVYFANMAAMNPGGWVEIFAEDAVIYDPVGKPPINVSEDSEKFFALLSSFFNSFDISQEQIFIAGNGAAVKWRMQVSAKNGREATAEGISVFEINDDGKIQKVLSYWNEAEMMGKLKG ...

  17. Protein (Cyanobacteria): 104373 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available APDRVCPTPDIFIPTPEAVKPAPDIVCPIPTPEVVKPAPDIVCPIPTPEVVNPAPDIVCPTPDIFIPTPEAVKPAPDRVCPTPDIFIPTPEAVKPAPDIVCPIPTPEVVKPAPDIVCPI...PTPEVVNPAPDRVCPTPDIFIPTPEVVKPAPDIVCPTPDIFIPTPEAVKPIPDIVCPIPTPEVVKPAPDIVCPI...PTPEAVKPAPEVVNPAPDIVCPIPDMDFAIPTPEAVKPIPEVVKPAPDIVCPIPTPEVVKPTPDMVCPIPTPEVVKPTPEAVKPTPEVVKPAPDIVCPIPDMDFAIPTPDIICPI...PTPEVVKPTPEAVKPTPEVVKPAPDIVCPIPDMDFAIPTPDIICPIPTPEVVKPTPEAVKPTPEVVKPAPDIVCPIPDMDFAIPTPDIVCPIPTPEVVKPTPEVVKPIPDIVCPI...PDMDFAIPTPEVVKPAPEAVKPTPDIVCPIPTPEVVKPTPEVVKPTPEVVKPAPDMVCPIPTPEVVKPTPEVVKPAPEVVKPTPEVVKPAPEVVKPTPEVVKPAPEVVKPTPEVVKPTPEAVKPTPEAH ...

  18. Protein (Cyanobacteria): 493030435 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available enoviral fiber protein (repeat/shaft region) Coleofasciculus chthonoplastes MSLNPPLQLSLNPPLQLSLNLALQLSLNPPLQLSLNLALQLSLNPPLQLSLNLALQLSLNLALQLSLNPPLQLSLNLALQLSLNPPLQLSLNLASTIVPKPGFYNCP

  19. Protein (Cyanobacteria): 102007 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ein CwatDRAFT_0848 Crocosphaera watsonii WH 8501 MYRKEEQPLPPPEKFELPFEGKLSPNNCWVIMAELIPWDDFEEEYAKLFSAEKGAPAKLFRMALGTLIIKEKLGTSDRETIEQIRENPYLQYFIGLNCYQQEPPLESSMLVHFRKRIDGGLINKINKKIVKEK ...

  20. Protein (Cyanobacteria): 102009 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ein CwatDRAFT_6339 Crocosphaera watsonii WH 8501 MYRKEEQPLPPPEKFELPFEGKLSPNNRWVIMAELIPWDDFEEEYAKLFSAEKGAPAKLFRMALGTLIIKEKLGTSDRETIEQIRENPYLQYFIGLNCYQQEPPLESSMLVHFRKRIDGELINKINKK ...

  1. Protein (Cyanobacteria): 102010 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ein CwatDRAFT_4626 Crocosphaera watsonii WH 8501 MYRKEEQPLPPPEKFELPFEGKLSPNNRWVIMAELIPWDDFEEEYAKLFSAEKGAPAKLFRMALGTLIIKEKLGTSDRETIEQIRENPYLQYFIGLNCYQQEPPLESSMLVHFRKRIDGELINKINKK ...

  2. Protein (Cyanobacteria): 102011 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ein CwatDRAFT_2230 Crocosphaera watsonii WH 8501 MYRKEEQPLPPPEKFELPFEGKLSPNNRWVIMAELIPWDDFEEEYAKLFSAEKGAPAKLFRMALGTLIIKEKLGTSDRETIEQIRENPYLQYFIGLNCYQQEPPLESSMLVHFRKRIDGELINKINKK ...

  3. Protein (Cyanobacteria): 102012 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ein CwatDRAFT_0413 Crocosphaera watsonii WH 8501 MYRKEEQPLPPPEKFELPFEGKLSPNNRWVIMAELIPWDDFEEEYAKLFSAEKGAPAKLFRMALGTLIIKEKLGTSDRETIEQIRENPYLQYFIGLNCYQQEPPLESSMLVHFRKRIDGELINKINKK ...

  4. Protein (Cyanobacteria): 351301 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available tein Cal7507_2524 Calothrix sp. PCC 7507 MTADNIQSAESFESIVVVEISSQTDAIVETEMADETDEVKRETKALIAALKKRAQSEAESAGTISRETYLNIVRQARETIEGKKILQGDRLEYTWAVVQDEAEKNWYLLMKEVTEFSGRVQKAVKAGWEAFNEPHSQR ...

  5. Protein (Cyanobacteria): 351272 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available Glo7428_2381 Gloeocapsa sp. PCC 7428 MTTEPNNTDTSVEVQIIPQTTQISPQTNDLVEAEMAGESDDLKNETKALIDALKKRAQAEAQSAGTLTREAYLNAVRRARETIEGNQLIERDRIEYSFSLIQKEAEKNWNSVVKEVAELGDRLADAAKAAWEVLTAPRPR ...

  6. Protein (Cyanobacteria): 102016 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ein CwatDRAFT_1291 Crocosphaera watsonii WH 8501 MYRKEEQPLPPPEKFELPFEGKLSPNNRWVIMAELIPWDDFEEESAKLFSAEKGAPAKLFRMALGTLIIKEKLGTSDRETIEQIRENPYLQYFIGLNCYQQEPPLESSMLVHFRKRIDGELINKINKK ...

  7. Protein (Cyanobacteria): 102015 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ein CwatDRAFT_2409 Crocosphaera watsonii WH 8501 MYRKEEQPLPPPEKFELPFEGKLSPNNRWVIMAELIPWDDFEEESAKLFSAEKGAPAKLFRMALGTLIIKEKLGTSDRETIEQIRENPYLQYFIGLNCYQQEPPLESSMLVHFRKRIDGELINKINKK ...

  8. Protein (Cyanobacteria): 351302 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available protein Riv7116_5767 Rivularia sp. PCC 7116 MTDKNVQPEVTVEISPQTSEMVESQMPGETKEVKDETAALIEAIKRRAQVEAQSAGTLTRETYLNAVRQARETIEQNQLIERARIENAFEMVQNEATKNFESIVTEVQELGDRLQAAAQAAWDVLTAPRPKP ...

  9. Protein (Cyanobacteria): 422972 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available chococcus sp. WH 7805 MSADTALVAAINRLRKERNAVILAHYYQEPAIQDIADFIGDSLELSRKAASTDADVIVFCGVHFMAETAKILSPEKTVVLPDLDAG...CSLADDCPADEFARFRAEHPDHLVVSYINCTAAVKAQSDLICTSSNAVDLVNQLPADRPILFAPDQNLGRWVQRQSGRDLTLWPGRCIVHETFSEEAVLRLKLENPKAEVIAHPECQENLLDLADFIG

  10. Protein (Cyanobacteria): 422977 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available rotein Synechococcus sp. RS9917 MTADSPASTAATAVPADLPAAIEALRQERHAVILAHYYQEPEIQDVADFIGDSLELSRKAAATDADVIVFCGVHFM...IVHETFSEEAVLKLQLQHPEAEVIAHPECLEPLLDLADFIGSTSKLLHHAEASPAPSFIVLTEPGILHQMEQRLPQKTFLSVPGIDGCSCNSCPYMRLNTLEKLWRCLHSGQPEIQMEEDLRLRALAPIQKMLELSL ...

  11. Protein (Cyanobacteria): 422976 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ococcus sp. CC9311 MKETPDDLVRAINQLRSERNAVVLAHYYQEPEIQDIADFIGDSLELSRKAASTDADVIVFCGVHFMAETAKILSPEKIVLLPDTEAGCS...LADDCPADQFKAFRANHPEHFVVSYINCTAAVKAQSDLICTSSNAVDLVNQLPSNQPILFAPDQNLGRWVQQQSGRELTLWPGRCIVHETFSEEALLKLKLKHPDAEVIAHPECMENLLDLADFIG

  12. Protein (Cyanobacteria): 423030 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ynthetase Rivularia sp. PCC 7116 MFTTALRRPETTQLGALPLDLFAAIENLKKELNAVVLAHYYQEPDIQDIADFIGDSLQLSRAAADTNADVIVFAG...QGSCIVHETFSEKKIVQLKIAHPEAEVIAHPECETTVLQHADFIGSTAALLKYCQQNGSDEFIVATEPGIIHQMQKQAPNKKFIPAPPTNNCNCNECPFMRLNTLEKLYFAMKNRTPEITMSEETRVKALRPMQRMLEMSV ...

  13. Protein (Cyanobacteria): 422967 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available thetase complex, A subunit Cyanobium gracile PCC 6307 MHEKGHRLVFTQTLTHTPQPSPEACPPGAELPAAIETLKDERNAIILAHYYQDDAIQDCADFIG...QLPADRPILFAPDQNLGRWVARQSGRELTLWPGSCIVHETFSEQALLRLRQEHPEAEVIAHPECQQHLLDLADFIGSTSKL

  14. Protein (Cyanobacteria): 423034 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available e synthetase Prochlorococcus marinus str. NATL2A MNWKLITTVSYYKTDISVSNKSKNLIDEINFLRKKRNAIILAHYYQEPAIQDIADFIGD...PDRNLGRWVERQSGRKLTLWPGRCLVHETFNEESLIKLKIKNPTAEVLAHPECQENLLDLADFIGSTSKLLNYSQNSKKDK

  15. Protein (Cyanobacteria): 423038 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available e synthetase Prochlorococcus marinus str. MIT 9312 MISEIKERCKKANAIILAHYYQAPEIQEIADFIGDSLDLSRKAANNDADIIIFCGVH...SCIVHESFSEEALLKLKYQNPGSKVIAHPECSQNLLLLSDFIGSTSKLLDFVSKDSSKTYMVLTEPGIIHQMKKKEPNKIFIEVPDIEGCKCNECPYMKLNTLEKILDCLKNNSPSIELDPEILRRAYVPIKRMLDMSN ...

  16. Protein (Cyanobacteria): 422982 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available nechococcus sp. RCC307 MFAATQSAAPRLDQVERIAQLRQQRHAVILAHYYQEDAIQDIADFIGDSLELSRKAANTDAEVIVFCGVHFMAETAKILSPQKTV...LKAAHPDAAVIAHPECEQHLLDLADFIGSTSKLLNYSQSSEASGFIVLTEPGILHQMRKAVPNKEFYAVPGLDGCSCNACPHMRLNTLDKLEQCLETLEPAIELDEDLRLRALKPIERMLELSR ... ...VLPDLNAGCSLADACPADGFAQFKAEHPDHVVISYINCSAAIKAQSDLICTSSNAVAMVQSVPSDQPILFAPDQNLGRWVSRQAGRELTLWPGSCMVHETFSEEALLG

  17. Protein (Cyanobacteria): 423039 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available nate synthetase Prochlorococcus marinus str. MIT 9215 MISEIKEHCKKANAIILAHYYQAPEIQEIADFIGDSLDLSRKAANNDADIIIFC...WPGSCIVHESFSEEALLKLKYQNPGSKVIAHPECSQNLLILSDFIGSTSKLLDFVSKDTSKTYMVLTEPGIIHQMKKKEPNKIFIEVPDIEGCKCNECPYMKLNTLEKILDCLKNNSPSIELDPEIIRRAYIPIKRMLDMSI ...

  18. Protein (Cyanobacteria): 422979 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available otein Synechococcus sp. WH 5701 MVFAALEAPTNPRDLPAAIDELRRARKAVILAHYYQSPEIQDVADFIGDSLELSRKAAGTDAEVIVFCGVHFMAET...ETFSEQALLRLKLEHPQAEVIAHPECLPNLLDLADFIGSTSQLLARAASSEAHSFLVLTEPGILHQMRLKLPHKTFHEVPGQDGCSCNACPYMRLNTLEKLWRCLDTMSPAIELDEELRVRALAPIQRMLELSR ...

  19. Protein (Cyanobacteria): 423043 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available quinolinate synthetase Prochlorococcus marinus subsp. pastoris str. CCMP1986 MISEIKELCLKANAIILAHYYQAPEIQDIADFIG...KIIFAPDKNLGRWVQKNSGRKLKLWPGSCIVHETFSEEALLKLKYKHPDAKVIAHPECSQNLLVLSDFIGSTSKLLDFVSN

  20. Protein (Cyanobacteria): 422966 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available mplex, A subunit Cyanobium sp. PCC 7001 MVFAAAQTTQARAPEHSTWGTAPPPPSQLPAAIDALRRERNAVILAHYYQDDAIQDIADFIGDSLELA...GRWVQNQSGRELTLWPGSCQVHETFSEQALLQLKLEHPEAEVLAHPECQQHLLDLADFIGSTSKLLARAAESAAPAFIVLT

  1. Protein (Cyanobacteria): 422980 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available echococcus sp. CB0205 MVFAAAQNTASGCPAHRDLPEAIAALKRQRNAVILAHYYQEPEIQDIADFIGDSLELSRKAAATDAEVIVFCGVHFMAEVAKILSP...GLLQLKLDHPKAEVLAHPECQQHLLDHADFIGSTSALLRRSEASAAQEFIVLTEPGILHQMRKAVPGKAFFEVPGADGCSCNACPYMRLNTLEKLWQCLESMEPRIEMDEAMRLRALAPIQKMLEMSR ...

  2. Protein (Cyanobacteria): 423033 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available inate synthetase Prochlorococcus marinus str. NATL1A MNWKLITTVSYYKTDISVSNKNKNLIDEINFLRKKRNAIILAHYYQEPAIQDIADFIG...ILFSPDRNLGRWVERQSGRKLTLWPGRCLVHETFNEESLIKLKIKNPTAEVLAHPECQENLLDLADFIGSTSKLLNYSQNS

  3. Protein (Cyanobacteria): 423041 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available inate synthetase Prochlorococcus marinus str. MIT 9301 MISEIKERCGKANAIILAHYYQAPEIQEIADFIGDSLDLSRKAANNDADIIIF...LWPGSCIVHESFSEEALLKLKYQNPGSKVIAHPECSQNLLTLSDFIGSTSKLLDFVSKDPSKTYMVLTEPGIIHQMKKKEPNKIFIEVPDVEGCKCNECPYMKLNTLEKILDCLKNNSPSIELDPEIIRRAYVPIKRMLDMSN ...

  4. Protein (Cyanobacteria): 423042 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available inate synthetase Prochlorococcus marinus str. MIT 9515 MISEIKERCLETNAIILAHYYQAPEIQDIADFIGDSLDLSRKAANNNADIIIF...LWPGSCIVHETFSEEALLKLRYKYPEAKVIAHPECSQNLLVLSDFIGSTSKLLEFIRDDHSNTYMVLTEPGIIHQMKKKEPNKKFIEVPDIDGCKCNECPYMKLNTLDKILDCLKNNSPSIELEPEIIKKAYKPIKRMLDMSS ...

  5. Protein (Cyanobacteria): 422971 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available echococcus sp. WH 7803 MSADPALVAAINRLRKERNAVILAHYYQEPAIQDIADFIGDSLELSRKAASTAADVIVFCGVHFMAETAKILSPEKTVVLPDLDA...GCSLADDCAADEFARFRAEHPDHLVVSYINCTAAVKAQSDLICTSSNAVDLVNQLPADRPILFAPDQNLGRWVQRQSGRELTLWPGRCIVHETFSEEAVLRLKLENPQAEVIAHPECLENLLDLADFIG

  6. Protein (Cyanobacteria): 422970 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available ococcus sp. WH 8102 MSADTALVAAINRLRQERNAVILAHYYQEPEIQDIADFIGDSLELSRKAASTDADVIAFCGVHFMAETAKILSPQKTVVLPDLDAGCS...LADDCPAEDFAAFRQKHPDHLVVSYINCTAAVKAQSDLICTSSNAVDLVRQLPADRPVLFAPDQNLGRWVQQQSGRELTLWPGRCIVHETFSEEAVLQLKLEHPDAEVIAHPECQENLLDLADFIG

  7. Protein (Cyanobacteria): 422981 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available echococcus sp. CB0101 MVFAAAQNTTGGCPPHAELPAAIAELKRQRKAVILAHYYQEPDIQDIADFIGDSLELSRKAAATDAEVIVFCGVHFMAEVAKILSP...ALLQLKLEHPGAEVLAHPECQQHLLDHADFIGSTSALLRRSEASEASSFIVLTEPGILHQMRKAVPDKQFFEVPGADGCSCNACPYMRLNTLEKLWQCLTDMAPAIELDEAMRQRALEPIQKMLEMSR ...

  8. Protein (Cyanobacteria): 423037 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available inate synthetase Prochlorococcus marinus str. AS9601 MISEIKERCKKANAIILAHYYQAPEIQEIADFIGDSLDLSKKAANNDADIIIFCG...PGSCIVHESFSEEALLKLKYQNPGSKVIAHPECSQNLLILSDFIGSTSKLLDFVSKDPSKTYMVLTEPGIIHQMKKKEPNKIFIEVPDVEGCKCNECPYMKLNTLEKILDCLKNNSPSIELDPEIIRRAYVPIKRMLDMSN ...

  9. Protein (Cyanobacteria): 422962 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available te synthetase complex, A subunit Chamaesiphon minutus PCC 6605 MFVTARPTANLDRIPVDVVAAIQELKQSLNAVILAHYYQDSEIQDVADFIG...EQGIIFAPDRNLGRYVMQQAEREMVLWQGSCMVHETFSEKKLVQLKVNYPNVEIIAHPECEEAVLQHADFIGSTSALLKYI

  10. Protein (Cyanobacteria): 422978 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available echococcus sp. RS9916 MPRLWPILPQMVQMTVDFTPSTALSAAPTPAELPAAIDALRRKKNAVILAHYYQEPEVQDIADFIGDSLELSRKAANTDADVIVFC...WPGRCIVHETFSEEALLKLQLKHPDAEVIAHPECIQPLLDLADFIGSTSKLLNYAETSNSNTFIVLTEPGIIHQMQRRLPHKEFLDVPGTDGCSCNACPYMRLNTLEKLWHCLSTGAPAIEMDETMRQRALKPIEAMLAMSR ...

  11. Protein (Cyanobacteria): 423040 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available nate synthetase complex, A subunit Prochlorococcus marinus str. MIT 9202 MISEIKERCKKANAIILAHYYQAPEIQEIADFIGD...PDQNLGRWVQKNSGRDIKLWPGSCIVHESFSEEALLKLKYQNPGSKVIAHPECSQNLLILSDFIGSTSKLLDFVSKDSSKT

  12. Protein (Viridiplantae): 224125882 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available DGSYEEEGQNNIKGNIWGKASTRFICSIFSLPVPPGNPNRPKEDPTTFSGRSMPEYLEQGRIQKLLLFGLEGSGTSTIFKQGKFLYGNKFTPKELQDIKLMIQSNMYRYLSILLEGRERFEEEALLEKSTATI...NSEECASGKREVEPGENCIYSINQRFKHFSDWLLDIMATGDLDAFFPAATREYAPI

  13. Protein (Viridiplantae): 302857788 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 5109 3068:5109 hypothetical protein VOLCADRAFT_39472, partial Volvox carteri f. nagariensis PSGNPFGEPPSGNPLRGTPSGNPFGNPPPSG...NPLREPPPPLRGTPSGTPPFGEPPSGNPFREPLRGTLFGNPFGEPLRGTPSGNLFGEPFREPLRGTPSGNPFGEPLRGTPSGNPFGEPLRGTP ...

  14. Protein (Viridiplantae): 356520860 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 24:441 3398:441 71240:3539 91827:3539 71275:632 91835:271 72025:690 3803:690 3814:690 163735:1365 3846:1365 3847:1365 PREDICTED: grav...es disease carrier protein-like Glycine max MAKQRQEDGKKGVVDLMPLFAKELLAGGVAGGFAKTVVA

  15. Protein (Cyanobacteria): 189930 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available HARHRNATRAAIKAMGLSLFGPDDCASASITAVAPPESAPAEEIRAIMKKQYDIILAGGQSQLAGKIFRIGHLGFVCDRDILTAVSAIESALQQLGHNSFTPGAGTKAAIEVFSA ... ...ASGSQKGYMIPPGLGFVAVGPKAWEAYKTADLPKYYLDLGAAKKAIAKNSTPFTTAVNMVMALQVSLQMMQEEGLEQIFAR

  16. Protein (Viridiplantae): 297815124 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 01:8747 59689:7110 81972:7110 predicted protein Arabidopsis lyrata subsp. lyrata MANTKDKFDELEKGMGLVKDVVHKMQTGLGDKLCMIVLWKRQTQAYCSYGTPTTGAPPTSSAGLEYGVGVALLSTNVGPPLRWICASASPLWICSFQMGN ...

  17. Protein (Viridiplantae): 308804025 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available unnamed protein product Ostreococcus tauri MACAGRGVLRLGALEGGSDVVFAATVRRDLNGTLAPLRGQREDVAIVVGDDAARLETNAARVTQSLRTRRAHAHVTPASGLGESSSSSSSTDFRTPSPRGPPPSCVVWSLSTLPCRSFRRDTCACASACASASA ...

  18. Protein (Viridiplantae): 302825229 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available SSHVWAIAFQEATQEIVLKAGTTTRIKVLEAGTKRKKKKISPTVHFSGYGRDECQTNDVARPTMCTYSTLRLVFGRLQIPLVPGLLFESLWFQAFSSNPSGSRPSQSL...KVLEAGTKRKKKKISPTVHFSGYSRDECQTNDVARPTMCTYSTLRLVFGRLQIPLVPGLLFESLWFQAFSSNPSGSRPSQSLVAGDSVDAERGILLVYEGCNKELEAL...RKKMFEARESDHICEEIGEEKAARIIKQLVKTNRLIGGAWAREHEERASIIACRKSTSELQSAVREDLKLPPVLKAGTTTRIKVLEAGTKRKKKKISPTVHFSGYSRDECQTNDVARPTMC

  19. Protein (Viridiplantae): 224086357 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 4:195 predicted protein Populus trichocarpa MATTLKSLSSFVILLIVNSLFFTGTTEARPFNIMKSGNSAASRGTESFFDGLSLGGIKEGPSPGAGHEFTNSGTL...GGIKEEGPSPSAGHGFTSSGTLGGIKEGPSPGAGHGFTNSGTLGGIKEGPSPGVGHGFTNSGTLEGIKKEGPSPTNSGTL...GGIKEGPSPGAGHGFTNSETLGGIKEGPSPGVGHEFTNSGTLGGIKEGPSPGVGHGFTNSGTLEGIKKEGPSPTNSGTLGGIKEGPSPGAGHGFTNSE...TLGGIKEGPSPGGIKEGSSPGVGHAFTNSGTLGGIKEGPSPGAGHAFTNSGTLGGIKEGPSPGAGHGFTNSGTLGGIKEGSSPGVGHGFTNSGTLGGIKEGPSPCCGNKYTTGTKH ...

  20. Protein (Viridiplantae): 302857651 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available :8553 3068:8553 hypothetical protein VOLCADRAFT_39527, partial Volvox carteri f. nagariensis PLGTLWEPFGNPLGTLWEPFGNPLGTLWEPFGNPLGTL...WEPFGNPLGTLWEPFGNPLGTLWEPFGNPLGTLWEPFGNPLGTLWEPFGNPLGTLWEPFGNPLGTLWEPFGNPLGTLWEPFGNPLGTLWEPFGNPLGTLWEPFGNPLGTLWEPFGNPLGTLWEPFGNP ...

  1. Protein (Cyanobacteria): 308843 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available protein P9303_25041 Prochlorococcus marinus str. MIT 9303 MPATGDIFENYGNIWVKNAILDNNGTLHNNDGGTLHNFESGTLNIIGREGFGVGKLKNNSGGKLNNSGTL...NNSWYLINDGGMLNNNGTLNNIDYPHSQITNKSGKLNNNGTLNNNGTLNNAYCDLKSSTLNNNGILNNFESSWLVNNNGTLNNSGTLNNSGTL...INRDYATLNNSGMLNNIDGGSLIYKASIDNYGPPAAGTLNNKDGGTLNNNTGCNLTINISTLNNNDGGTLNNSGMLNINDGGTLHNSGMLHNNDGGTL...HNSGTLHNSGIIDNSDNRLKEKGFINNGTYTGDGQIKGSWTDHGHVKPGRSAGGMLVDGHYYKKGGSKEIELGGTYHGDGDRTAT...EHDWIEITGNLELAGKLDVSLIDGFKLSAGNSFVITKVGGDLDGQYEGLDEGDSVGRFASDNGGTLELFITYKGGDSNDIALYTQSLSGVLPESLREPRIIGSDADDS

  2. Protein (Cyanobacteria): 308845 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available protein P9303_19271 Prochlorococcus marinus str. MIT 9303 MGKQVSPNPNYTGPIEPADGDYNSVSYQNYGTLLINNGISFSNDGVLWNYGGKVNNNGDWLNNGTL...NNGGALTNNYTLYNHIGGTLYNYDNGTLINAGTLNNEGTLNNKSTLNFSQGSKFVNANGTLNNSGTINSYIEDLYFGAGGTINFQRGSNFV...NYSTITTKAGVTLTNDNTLTNNVTLNNNSGGTLNNEGTLSNAGTLSNGGTLNNGGKLNNEGTLNNEGTLNNEGTLTLINRLSPIVTISSKFVNTNGTL...NNSGTINSYIEDLYFGAGGTINFQRGSNFVNYATITTKAGVTLTNDNTLTNNDTLNNNSGGSLNNNGILNNNKRGTLNNDGTLNNGGMLKNVAMLNNNSGSILNNNNGGTL

  3. Protein (Viridiplantae): 302816203 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available moellendorffii MKVEVEEICLVPPEINKPGKALLSPLAHFAWEVQYRTRFLFFERPSVKEGACFDALIVRLKAGLRKALGAFYLVGGRLVVREDDLMEVDCNGDGIMFIRASSDTPLSSSSRYQISIFPSPGKNSFPFALQATRFSCGGLCISIKFNHQVMDGTSAWHFWKSWAEVCR ...

  4. Protein (Viridiplantae): 303272475 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available HDTTVSSLAVVEKRPLDLDSIQTWVNNLIVNKGTDLYRMKGVLNIANCPVRFMFQAVHMIFNGEFDEPWGKDEPRESKFVFIGKNLDHKELRKGFEACIMTPELAENKRRSIRFQIGEKVQCNTPDGWQTGTVVAHQYREDDFPPGMTVPYQVEIDGGGLVYAPYDDDDFIRASRKSPKRE ...

  5. Protein (Viridiplantae): 226500320 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 8024:3888 3398:3888 4447:4517 4734:4517 38820:4517 4479:4517 147370:3616 147369:3616 147429:3616 4575:4771 4577:4771 ischemia/reperfu...sion inducible protein Zea mays MKACAKAAGERLPLVCAPSTRQPLARSFVKVRRLPSQHETKSQVSCSVRVS

  6. Protein (Viridiplantae): 297829390 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 24:2811 3398:2811 71240:2716 91827:2716 71275:2448 91836:4490 3699:4490 3700:4490 980083:4490 3701:4490 59689:3736 81972:3736 alphavi...rus core protein family Arabidopsis lyrata subsp. lyrata MAAMAAKLQLSAKSDQSSVRLPRVIN

  7. Protein (Cyanobacteria): 359728 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available othetical protein N9414_10847 Nodularia spumigena CCY9414 MNKKTILSLLSTPMLVSSILSMGAMANQAQAANPETENTDKLTCVQNYHILRPVCARASVLAQIPEYEPANELAGENQDSLLAFNIEESDMAVDLFNCDCPQCINSLRQMRGIAPLVY ...

  8. Protein (Viridiplantae): 357521107 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 7 58024:8377 3398:8377 71240:7000 91827:7000 71275:1375 91835:4837 72025:7275 3803:7275 3814:7275 163742:587 3877:587 3880:587 Alumin...um activated malate transporter Medicago truncatula MAPKLAKSGSFRYTLAEKKERLLSMKGGDHI

  9. Protein (Viridiplantae): 224124826 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 94:2255 predicted protein Populus trichocarpa MQLLDLEEDGSASLFIEKSAAKTASLPISASAAKTASLPISASAAKTAWLPIKKWAAKTVSL...PISVSVVKAASLPSPESAAKTASLLISASAAKTASLPSPESAAKTASLPSPESAAKTASLPISASVDKTASMPSPESAAKTASLPSSESAAKTASLPISA...SAAKTASLPSPESAAKTASLPISASADKTASMPSPESAAKTASLPSPESAAKTASLPISASAAKTASLPSPESAAKTASLPISASADKT...ASMPSPESAAKTASLPSPESAAKTASLPISASAAKTASLPSPESAAKTASLPSPESAANTASLPISASAAKTASLPISASAAKTASLPISASAAKTAFIIISLSLNIYIYFPLGVYK ...

  10. Protein (Cyanobacteria): 245993 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available EVLLEIAGTSDCKQANENLSSRTEFDLKVNQITDISPLSGLTNLIGLSLWGNQIKDVTPLSELTNLTELNLYNNQIKDVTPLSELTNLTELNLYNNQIKDVTPLSGLINLTRLILFSNQITDITPLSGLT...NLTELSLDNNQIIDVTPLSGLANLTELNLYNNQITEVSLSGLTNLTELYLSNNQITEVNLSGLT...NLRRLYLSTNQIIDISPLSGLTNLTELDLKYNQIKDVSPLSGLTNLTELDLKYNQIKDVSPLSGLTNLTGLYLSSNQIKDISPLSGLTNLTLLYLSDNKIKDI...SPLSGLINLTGLDLGSNKIKDISPLSGLINLTGLDLSSNKIKDISPLSGLTNLTWFSLDNNQITEVSLSGLTNLTELYLRNNQITDVSSLSELTNLTRLVLNNNQITDVSPLSGLT...NLTVLNLSNNQITDVSLSGLTNLTVLNLSNNQITDVSPLSGLTNLTGLNLISNQITDVSILSGLTNLTVLILSNNQIKDVSPLSGLTNLRRLYLGDNPIPQQTCPVSPPDVCEF ...

  11. Protein (Viridiplantae): 357494101 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available AQTMQQRPQNYNLMGVNNFNQERYHMNNSVDATALSMTNFPFSANDSRSFMTVARYGRALPLGSGLTSIPQQHRALPLGSGLTSSHQQHQAMPLGSGLT...SSAQQHMRALPLGSGLTSSPQQHQALPLGSGLTSSHQQHRALPLGSGLTSSHQQHMRALPLGSGLTSSPQQHQALPLGSGITSSHQQHRA...LPLGSGITSIPQQHMRQQHRALPLGLGLTSSPQQHRALPLGSGLTSSHQQHRALPLGSGLTSSHQQHRALPLGSGLTSSSQQHMSSSNVDGSQASANWSQNPSRPIFQ

  12. Protein (Cyanobacteria): 245992 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available SLRKTVEVLLEEAGTSDCSQADEILSSLNYLVLGYNQIKDVSPLSGLTNLTVLNLWNNQITDISSLSGLTSLTELYLNNNQITDISPLSGLTNLTVLNLNNNQITDISPLSGLT...SLTGLILGGNQIKDVSPLSGLTNLTVLNLNNNQITDISPLSGLTSLTVLILYSNQITDISSLSGLTSLTVLILSDNQITDISPLSGLT...NLDALYLNNNQITDISPLSGLTNLDALYLNNNQITDISPLSGLTNLDALYLNNNQITDISPLSGLTNLDALYLNSNQITDISLLSGLTNLDALYL...NSNQITDISPLLELTNLNYLILDNNQITDISPLSGLTNLTILILDNNQITDISPLSGLTNLGGLILNSNQITDVSPLSGLTNLTVLNLNSNQITDVSPLSGLTNLRRLHLKDNPIPQPICPISPTGFCEL ...

  13. Protein (Cyanobacteria): 134587 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available l part of Q1F5C4_9CHLR Addiction module toxin Microcystis aeruginosa PCC 9717 MSYSVEYESEALADLEKLDPEIRKRIVNKIEWLAQNFEQITPQSLTGDWTGFYKLRVGNYRIIYQIDLSEKIIMIDVVGHRRQIYD ... ...ZP_18821255.1 1117:2626 1118:2173 1125:176 1126:413 1160286:34 Similar to C-termina

  14. Protein (Cyanobacteria): 134586 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available l part of Q1F5C4_9CHLR Addiction module toxin (fragment) Microcystis aeruginosa PCC 9717 MSYSVTFEPESITDLDLITDFIRLRILNKIKWLAINFEQITPLPLTREWSGFYKLRVGD ... ...ZP_18821384.1 1117:2626 1118:2173 1125:176 1126:413 1160286:34 Similar to C-termina

  15. Protein (Cyanobacteria): 134592 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available al part of Q1F5C4_9CHLR Addiction module toxin Microcystis aeruginosa PCC 9806 MSYSVTFEPESITDLDLITDFIRLRILNKIKWLAINFEQITPLPLTREWSGFYKLRVGDYRVIYEFDRESRIIIIVRVGHRSEVYD ... ...ZP_16388989.1 1117:2626 1118:2173 1125:176 1126:413 1160282:370 Similar to C-termin

  16. Protein (Cyanobacteria): 134591 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available al part of Q1F5C4_9CHLR Addiction module toxin Microcystis aeruginosa PCC 9807 MSYSVTFEPESITDLDLITDFIRLRILNKIKWLAINFEQITPLPLTREWSGFYKLRVGDYRVIYEFDRESRIIIIIRVGHRSEVYD ... ...ZP_18834483.1 1117:2626 1118:2173 1125:176 1126:413 1160283:595 Similar to C-termin

  17. Protein (Cyanobacteria): 134597 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available al part of Q1F5C4_9CHLR Addiction module toxin Microcystis aeruginosa PCC 9443 MSYSVTFEPESITDLDLITDFIRLRILNKIKWLAINFEQITPLPLTREWSGFYKLRVGDYRVIYEFDRESRIIIIIRVGHRSEVYD ... ...ZP_18825798.1 1117:2626 1118:2173 1125:176 1126:413 1160281:573 Similar to C-termin

  18. Protein (Cyanobacteria): 198885 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available GSGKSTLMNILGCLDRPTAGDYIFEDRNLSSLNDDELAYIRNQRIGFIFQQFNLLPRSTAIENVILPMVYANIPKQKRREYAEEALVKVGLAERIFNRPNQLSGGQQQRVAIARALVNQPALVLADEPTGALDTQTSQEVMDLLSELNQQGITIVIVTHEEDIAAQTKRIIRVQDGLIVS ...

  19. Protein (Viridiplantae): 302815259 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available lendorffii PFTLHNESGRQEVILRRSYNSEDIAVTCLFRVSPYDEPEEEEESEEDEPDTPVSQEEIHMVVTIAKGGDGPSLEISCTCSQGEIEIEKISYLDDESSKDDELAYTGPVFGELDENLQKQFTKYLEARGINEELCNFLVNYMPEKERQEYIRWLEKIEKFVKKEAK ...

  20. Protein (Viridiplantae): 357129296 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available PAASRRRDRQNPAGPNGDDSASGLSPSSSKKARRLLSCQTTTTNSRTQSTSSRSFDATSTQQEAPFRDSLPRYVRAPAVFRCVRVTPVDDGGGGGGVDELAYQASVTINGHMFRGFLYDQGRGNVSVDESSSHAAAVRSISDLHLGTAVSASSAVPPGVYDAVGSAQLILGGLSYGNTIN ...