GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts

Genomic projects heavily depend on genome annotations and are limited by the current deficiencies in the published predictions of gene structure and function. It follows that, improved annotation will allow better data mining of genomes, and more secure planning and design of experiments. The purpose of the GeneFarm project is to obtain homogeneous, reliable, documented and traceable annotations for Arabidopsis nuclear genes and gene products, and to enter them into an added-value database. This re-annotation project is being performed exhaustively on every member of each gene family. Performing a family-wide annotation makes the task easier and more efficient than a gene-by-gene approach since many features obtained for one gene can be extrapolated to some or all the other genes of a family. A complete annotation procedure based on the most efficient prediction tools available is being used by 16 partner laboratories, each contributing annotated families from its field of expertise. A database, named GeneFarm, and an associated user-friendly interface to query the annotations have been developed. More than 3000 genes distributed over 300 families have been annotated and are available at http://genoplante-info.infobiogen.fr/Genefarm/. Furthermore, collaboration with the Swiss Institute of Bioinformatics is underway to integrate the GeneFarm data into the protein knowledgebase Swiss-Pro

GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts

Genomic projects heavily depend on genome annotations and are limited by the current deficiencies in the published predictions of gene structure and function. It follows that, improved annotation will allow better data mining of genomes, and more secure planning and design of experiments. The purpose of the GeneFarm project is to obtain homogeneous, reliable, documented and traceable annotations for Arabidopsis nuclear genes and gene products, and to enter them into an added-value database. This re-annotation project is being performed exhaustively on every member of each gene family. Performing a family-wide annotation makes the task easier and more efficient than a gene-by-gene approach since many features obtained for one gene can be extrapolated to some or all the other genes of a family. A complete annotation procedure based on the most efficient prediction tools available is being used by 16 partner laboratories, each contributing annotated families from its field of expertise. A database, named GeneFarm, and an associated user-friendly interface to query the annotations have been developed. More than 3000 genes distributed over 300 families have been annotated and are available at http://genoplante-info.infobiogen.fr/Genefarm/. Furthermore, collaboration with the Swiss Institute of Bioinformatics is underway to integrate the GeneFarm data into the protein knowledgebase Swiss-Prot

Procedimiento para la propagación vegetativa y transformación genética de tomate, pimiento y otras dicotiledoneas, mediante Agrobacterium tumefaciens

Referencia OEPM: P9801920.-- Fecha de solicitud: 11/09/1998.-- Titulares: Consejo Superior de Investigaciones Científicas (CSIC), Centre Nationale de la Recherche Scientifique (CNRS).Procedimiento para la propagación vegetativa y transformación genética de tomate, pimiento y otras dicotiledoneas, mediante Agrobacterium tumefaciens. La invención se basa en que, durante la germinación, el endospermo y el embrión poseen los nutrientes y, particularmente, los reguladores del crecimiento, necesarios para el desarrollo de la planta. A medida que avanza la germinación el agotamiento de dichos nutrientes se sustituye por la progresiva producción de los mismos por los cotiledones y la radícula. La eliminación del meristemo primario y los secundarios, conservando un cotiledón y la radícula, priva al explanto de los órganos necesarios para continuar el crecimiento vegetativo. En la zona de corte se forma un callo con células indiferenciadas totipotentes. La aportación de nutrientes y reguladores del crecimiento por parte del cotiledón y de la radícula proporciona los elementos que estimulan la diferenciación de las células del callo para la formación de yemas y tallos. A partir de los mismos se forman las raíces y, finalmente, se obtiene una planta adulta.Peer reviewe

Mechanical Shielding in Plant Nuclei

International audienceBeyond its biochemical nature, the nucleus is also a physical object. There is accumulating evidence that its mechanics plays a key role in gene expression, cytoskeleton organization, and more generally in cell and developmental biology. Building on data mainly obtained from the animal literature, we show how nuclear mechanics may orchestrate development and gene expression. In other words, the nucleus may play the additional role of a mechanical rheostat. Although data from plant systems are still scarce, we pinpoint recent advances and highlight some differences with animal systems. Building on this survey, we propose a list of prospects for future research in plant nuclear mechanotransduction and development

Ribonucleotide Reductase Regulation in Response to Genotoxic Stress in Arabidopsis1[W]

Ribonucleotide reductase (RNR) is an essential enzyme that provides dNTPs for DNA replication and repair. Arabidopsis (Arabidopsis thaliana) encodes three AtRNR2-like catalytic subunit genes (AtTSO2, AtRNR2A, and AtRNR2B). However, it is currently unclear what role, if any, each gene contributes to the DNA damage response, and in particular how each gene is transcriptionally regulated in response to replication blocks and DNA damage. To address this, we investigated transcriptional changes of 17-d-old Arabidopsis plants (which are enriched in S-phase cells over younger seedlings) in response to the replication-blocking agent hydroxyurea (HU) and to the DNA double-strand break inducer bleomycin (BLM). Here we show that AtRNR2A and AtRNR2B are specifically induced by HU but not by BLM. Early AtRNR2A induction is decreased in an atr mutant, and this induction is likely required for the replicative stress checkpoint since rnr2a mutants are hypersensitive to HU, whereas AtRNR2B induction is abolished in the rad9-rad17 double mutant. In contrast, AtTSO2 transcription is only activated in response to double-strand breaks (BLM), and this activation is dependent upon AtE2Fa. Both TSO2 and E2Fa are likely required for the DNA damage response since tso2 and e2fa mutants are hypersensitive to BLM. Interestingly, TSO2 gene expression is increased in atr versus wild type, possibly due to higher ATM expression in atr. On the other hand, a transient ATR-dependent H4 up-regulation was observed in wild type in response to HU and BLM, perhaps linked to a transient S-phase arrest. Our results therefore suggest that individual RNR2-like catalytic subunit genes participate in unique aspects of the cellular response to DNA damage in Arabidopsis

Plant E2F factors in cell cycle, development and DNA damage response

During the past ten years, emerging data revealed the role of E2F factors in various plant physiology aspects. E2F involvement in cell cycle and plant development was particularly investigated and highlighted some plant specificities, espacially in postembryonic development. A major role of E2F is its transcriptional activity governing specific gene induction throughout the cell cycle and also strong induction of DNA repair genes in response to DNA damage, notably in the context of DNA double strand break (DSB) response. More challenging is the implication of E2F in nuclear foci with gamma-H2AX, a marker of DSB, probably independently of its transcriptional activity, in the DNA damage response