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Roadmap to New Virulence Determinants in Pseudomonas syringae: Insights from Comparative Genomics and Genome Organization

June 2008 , Volume 21 , Number  6
Pages  685 - 700

Magdalen Lindeberg,1 Christopher R. Myers,2 Alan Collmer,1 and David J. Schneider1,3

1Department of Plant Pathology, Cornell University, Ithaca, NY 14853, U.S.A.; 2Computational Biology Service Unit, Center for Advanced Computing, Cornell University, Ithaca, NY 14853, U.S.A.; 3U. S. Department of Agriculture Agricultural Research Service, Ithaca, NY 14853, U.S.A.

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Accepted 31 January 2008.

Systematic comparison of the current repertoire of virulence-associated genes for three Pseudomonas syringae strains with complete genome sequences, P. syringae pv. tomato DC3000, P. syringae pv. phaseolicola 1448A, and P. syringae pv. syringae B728a, is prompted by recent advances in virulence factor identification in P. syringae and other bacteria. Among these are genes linked to epiphytic fitness, plant- and insect-active toxins, secretion pathways, and virulence regulators, all reflected in the recently updated DC3000 genome annotation. Distribution of virulence genes in relation to P. syringae genome organization was analyzed to distinguish patterns of conservation among genomes and association between genes and mobile genetic elements. Variable regions were identified on the basis of deviation in sequence composition and gaps in syntenic alignment among the three genomes. Mapping gene location relative to the genome structure revealed strong segregation of the HrpL regulon with variable genome regions (VR), divergent distribution patterns for toxin genes depending on association with plant or insect pathogenesis, and patterns of distribution for other virulence genes that highlight potential sources of strain-to-strain differences in host interaction. Distribution of VR among other sequenced bacterial genomes was analyzed and future plans for characterization of this potential reservoir of virulence genes are discussed.

Additional keywords:Arabidopsis, nonribosomal peptide synthase, pathogenicity island, REP sequence.

The American Phytopathological Society, 2008