Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: 4/30/2004
Publication Date: 5/31/2004
Citation: Alfano, J.R., Buell, C.R., Collmer, A., Shan, L., Tang, X., Schneider, D.J. 2004. Genomic mining for substrates of the type iii secretion system in pseudomonas syringae pv. tomato dc3000: new insights into mechanisms of pathogenesis. In: Iacobellis, N.S., Ullrich, M.S., Collmer, A., Hutcheson, S.W., Mansfield, J.W., Morris, C.E., Murillo, J., Schaad, N.W., Stead, D.E., Surico, G.,editors. Pseudomonas syringae and Related Pathogens: Biology and Genetics. Springer-Verlag. pp.363-371. Interpretive Summary:
Technical Abstract: The draft sequence of the P. syringae pv. Tomato DC3000 genome has being analyzed to identify potential substrates of the type III secretion system (TTSS) by two independent means. First, the genome was searched with a hidden Markov model to identify putative hrpL-dependent promoters (hrp boxes) since HrpL, an ECF-type sigma factor, was previously been shown to regulate many aspects of the TTSS in P. syringae and several other plant pathogens. Second, the potential open reading frames in the draft genome were analyzed for similarity to previously reported TTSS substrates from various P. syringae pathovars. A regular expression was describing the location and character of amino acid residues in the N-terminal portion of these sequences was constructed. This regular expression was then used to identify candidate TTSS substrates, and the resulting collection was refined by imposing constraints on the statistical bias of residue frequencies in the first 50 residues. Several of the candidate genes identified by these procedures have been shown to code for proteins that are translocated into plant cells or secreted in culture media in a TTSS dependent manner.