Gene Ontology (GO) for Microbe–Host Interactions and Its Use in Ongoing Annotation of Three Pseudomonas syringae Genomes via the Pseudomonas–Plant Interaction (PPI) Web Site

Genome-scale sequencing of plant pathogens is an increasingly important tool for exploring host–pathogen interactions. While comparative structural analyses 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 and compare gene products with similar function (but possibly different structure) across even diverse pathogens is now possible through genome annotation using the 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 developing precisely defined GO terms that describe the biological processes involved in a microbe’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 of prokaryotic (or eukaryotic) pathogens (or mutualists) that attack plant (or animal) hosts promises to offer a new mechanism for viewing the diversity of microbe strategies for overcoming common host challenges (e.g. finding all gene products across diverse microbes that are annotated to GO:0044414, suppression of host defenses). However, because genome annotation and analysis must continue over time to match experimentation and discovery, genome projects must provide portals for continually updating genome sequence and annotation data. The Pseudomonas- Plant Interaction (PPI) web site (http://pseudomonas-syringae.org) exemplifies the “hub model” of web-based information management for small-scale genome projects. This model maximizes access to the most current analytical tools (e.g. the Artemis Genome Viewer) through links to primary off-site resources, while tailoring instructional tutorials, specific information, and organization to the needs of the P. syringae community. The web site also serves as a portal for submission of updated genome sequence or GO annotation data as it becomes available.