Search

The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from the Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 million annotations to 11 million proteins in more than 360 000 taxa, this resource has increased 2-fold over the last 2 years and has benefited from a wealth of checks to improve annotation correctness and consistency as well as now supplying a greater information content enabled by GO Consortium annotation format developments. Detailed, manual GO annotations obtained from the curation of peer-reviewed papers are directly contributed by all UniProt curators and supplemented with manual and electronic annotations from 36 model organism and domain-focused scientific resources. The inclusion of high-quality, automatic annotation predictions ensures the UniProt GO annotation dataset supplies functional information to a wide range of proteins, including those from poorly characterized, non-model organism species. UniProt GO annotations are freely available in a range of formats accessible by both file downloads and web-based views. In addition, the introduction of a new, normalized file format in 2010 has made for easier handling of the complete UniProt-GOA data set

We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is ∼32,000, which is smaller than previous estimates. We conducted comparative analyses between rice and Arabidopsis thaliana and found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene.

Dans leur environnement naturel, les plantes sont exposées en permanence à une grande variété de microorganismes dont certains sont pathogènes. Ainsi, les plantes ont développé au cours de l’évolution des mécanismes de défense multiples et complexes, qui leur permettent de résister à la plupart des microbes pathogènes. La résistance peut s’exprimer localement au site d’infection et systémiquement selon la nature des agents infectieux. Par exemple, suite à une infection par un agent pathogène provoquant des nécroses, la résistance se développe dans toute la plante y compris dans les tissus éloignés du site initial d’infection. Cette forme de résistance, appelée résistance systémique acquise (SAR), se caractérise par l’accumulation locale et systémique de l’acide salicylique (SA) qui agirait sur une activation concomitante de gènes associés à une défense contre certains microbes. Le SA semblerait jouer le rôle de régulateur endogène. En outre, deux hormones végétales, l’acide jasmonique (JA) et l’éthylène sont indispensables à l’activation d’une autre série de gènes impliqués dans la protection contre d’autres agents pathogènes. A l’heure actuelle, de nombreux chercheurs s’efforcent de répertorier les gènes associés à la défense induite et caractériser les fonctions de leurs produits. A part une résistance déployée directement contre les agents pathogènes, les plantes ont aussi développé des mécanismes qui contribuent à restreindre localement les nécroses, sans pour autant affecter directement la prolifération microbienne. Ces mécanismes de protection restent cependant peu étudiés. En premier lieu, nous avons analysé l’expression de deux membres de la super-famille des glutathion S-transférases (GST), AtGSTF2 et AtGSTF6, chez des plantes d’Arabidopsis thaliana inoculées avec une souche avirulente de Pseudomonas syringae. Les deux gènes étudiés sont fortement et rapidement induits après inoculation avec un agent pathogène, ceci même avant l’accumulation de gènes de déf, In response to infection by pathogens, plants deploy various and complex defense mechanisms. Resistance can be expressed locally and systemically, depending on the nature of the inducing stimulus. For instance, after infection by a necrotizing pathogen, resistance develops throughout the plants, in tissues distant from the initial site of infection. This form of resistance, called systemic acquired resistance (SAR), is dependent of the local and systemic accumulation of salicylic acid (SA), which is involved in the concomitant activation of genes associated with defense against certain types of microorganisms. SA seems to play the role of an endogenous regulator. Besides SA, the plant hormones jasmonic acid (JA) and ethylene have been shown to be involved in the activation of separate sets of genes, the products of which mediate resistance against other types of pathogens. Much work is in progress to provide a comprehensive overview of the genes associated with defense and the function of their products. Besides restricting the growth of invading microbes, plants also evolved mechanisms to contain the tissue damage. However, such mechanisms have been poorly studied. We have first analyzed the expression of two members of the glutathione S-transferase (GST) multigene family, AtGSTF2 and AtGSTF6 in Arabidopsis thaliana inoculated with an avirulent strain of Pseudomonas syringae. Both GST genes, were expressed early and to a large extent after the inoculation of the pathogen, before the accumulation of the pathogenesis-related gene PR-1. The expression of the pathogen-induced GSTs correlated with the production of ethylene and the accumulation of SA upon pathogen attack, and both genes were strongly induced by application of exogenous SA or ethylene. Moreover expression studies in NahG plants, cpr1, npr1 and etr1 mutants revealed that AtGSTF2 and AtGSTF6 were SA-dependent but not under the control of NPR1. Interestingly, AtGSTF2 expression was also abolished in etr1, i

Dans leur environnement naturel, les plantes sont exposées en permanence à une grande variété de microorganismes dont certains sont pathogènes. Ainsi, les plantes ont développé au cours de l’évolution des mécanismes de défense multiples et complexes, qui leur permettent de résister à la plupart des microbes pathogènes. La résistance peut s’exprimer localement au site d’infection et systémiquement selon la nature des agents infectieux. Par exemple, suite à une infection par un agent pathogène provoquant des nécroses, la résistance se développe dans toute la plante y compris dans les tissus éloignés du site initial d’infection. Cette forme de résistance, appelée résistance systémique acquise (SAR), se caractérise par l’accumulation locale et systémique de l’acide salicylique (SA) qui agirait sur une activation concomitante de gènes associés à une défense contre certains microbes. Le SA semblerait jouer le rôle de régulateur endogène. En outre, deux hormones végétales, l’acide jasmonique (JA) et l’éthylène sont indispensables à l’activation d’une autre série de gènes impliqués dans la protection contre d’autres agents pathogènes. A l’heure actuelle, de nombreux chercheurs s’efforcent de répertorier les gènes associés à la défense induite et caractériser les fonctions de leurs produits. A part une résistance déployée directement contre les agents pathogènes, les plantes ont aussi développé des mécanismes qui contribuent à restreindre localement les nécroses, sans pour autant affecter directement la prolifération microbienne. Ces mécanismes de protection restent cependant peu étudiés. En premier lieu, nous avons analysé l’expression de deux membres de la super-famille des glutathion S-transférases (GST), AtGSTF2 et AtGSTF6, chez des plantes d’Arabidopsis thaliana inoculées avec une souche avirulente de Pseudomonas syringae. Les deux gènes étudiés sont fortement et rapidement induits après inoculation avec un agent pathogène, ceci même avant l’accumulation de gènes de déf, In response to infection by pathogens, plants deploy various and complex defense mechanisms. Resistance can be expressed locally and systemically, depending on the nature of the inducing stimulus. For instance, after infection by a necrotizing pathogen, resistance develops throughout the plants, in tissues distant from the initial site of infection. This form of resistance, called systemic acquired resistance (SAR), is dependent of the local and systemic accumulation of salicylic acid (SA), which is involved in the concomitant activation of genes associated with defense against certain types of microorganisms. SA seems to play the role of an endogenous regulator. Besides SA, the plant hormones jasmonic acid (JA) and ethylene have been shown to be involved in the activation of separate sets of genes, the products of which mediate resistance against other types of pathogens. Much work is in progress to provide a comprehensive overview of the genes associated with defense and the function of their products. Besides restricting the growth of invading microbes, plants also evolved mechanisms to contain the tissue damage. However, such mechanisms have been poorly studied. We have first analyzed the expression of two members of the glutathione S-transferase (GST) multigene family, AtGSTF2 and AtGSTF6 in Arabidopsis thaliana inoculated with an avirulent strain of Pseudomonas syringae. Both GST genes, were expressed early and to a large extent after the inoculation of the pathogen, before the accumulation of the pathogenesis-related gene PR-1. The expression of the pathogen-induced GSTs correlated with the production of ethylene and the accumulation of SA upon pathogen attack, and both genes were strongly induced by application of exogenous SA or ethylene. Moreover expression studies in NahG plants, cpr1, npr1 and etr1 mutants revealed that AtGSTF2 and AtGSTF6 were SA-dependent but not under the control of NPR1. Interestingly, AtGSTF2 expression was also abolished in etr1, i

The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from the Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 million annotations to 11 million proteins in more than 360 000 taxa, this resource has increased 2-fold over the last 2 years and has benefited from a wealth of checks to improve annotation correctness and consistency as well as now supplying a greater information content enabled by GO Consortium annotation format developments. Detailed, manual GO annotations obtained from the curation of peer-reviewed papers are directly contributed by all UniProt curators and supplemented with manual and electronic annotations from 36 model organism and domain-focused scientific resources. The inclusion of high-quality, automatic annotation predictions ensures the UniProt GO annotation dataset supplies functional information to a wide range of proteins, including those from poorly characterized, non-model organism species. UniProt GO annotations are freely available in a range of formats accessible by both file downloads and web-based views. In addition, the introduction of a new, normalized file format in 2010 has made for easier handling of the complete UniProt-GOA data set