Gene Ontology (GO) for Microbe—HostInteractions and Its Use in Ongoing Annotationof Three Pseudomonas syringae Genomes via thePseudomonas—Plant Interaction (PPI) Web Site

摘要

Genome-scale sequencing of plant pathogens is an increasingly impor-tant tool for exploring host—pathogen interactions. While comparative structuralanalyses of three Pseudomonas syringae pathovars that differ in pathogenicity(P s. pv. tomato DC3000, P s. pv. phaseolicola 1448A, and P s. pv. syringae B728a)offer valuable insights, a second type of analysis based on the ability to find andcompare gene products with similar function (but possibly different structure)across even diverse pathogens is now possible through genome annotation usingthe controlled vocabularies of the Gene Ontology Consortium (GO; http://www.geneontology.org). As members of the Plant-Associated Microbe Gene Ontology(PAMGO) Interest Group (http://pamgo.vbi.vt.edu), we have been developingprecisely defined GO terms that describe the biological processes involved in amicrobe's interactions with its host (e.g. GO:0044409, entry into host; GO:0044002,acquisition of nutrients from host). Using these terms for annotating the genes ofprokaryotic (or eukaryotic) pathogens (or mutualists) that attack plant (or animal)hosts promises to offer a new mechanism for viewing the diversity of microbestrategies for overcoming common host challenges (e.g. finding all gene productsacross diverse microbes that are annotated to GO:0044414, suppression of hostdefenses). However, because genome annotation and analysis must continue overtime to match experimentation and discovery, genome projects must provide portalsfor continually updating genome sequence and annotation data. The Pseudomonas-Plant Interaction (PPI) web site (http://pseudomonas-syringae.org) exemplifiesthe "hub model" of web-based information management for small-scale genomeprojects. This model maximizes access to the most current analytical tools (e.g. theArtemis Genome Viewer) through links to primary off-site resources, while tailor-ing instructional tutorials, specific information, and organization to the needs ofthe P. syringae community. The web site also serves as a portal for submission ofupdated genome sequence or GO annotation data as it becomes available.