|Van Dijk, Karin|
Submitted to: Proceedings of the National Academy of Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/11/2001
Publication Date: 2/19/2002
Citation: FOUTS, D.E., BALDO, A.M., CARTINHOUR, S.W., LAZAROWITZ, S.G., MARTIN, G.B., REHM, A.H., SCHNEIDER, D.J., VAN DIJK, K., TANG, X., COLLMER, A. GENOME-WIDE IDENTIFICATION OF PSEUDOMONAS SYRINGAE PV. TOMATO DC3000 PROMOTERS CONTROLLED BY THE HRPL ALTERNATIVE SIGMA FACTOR. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES. 2002. v. 99(4). p. 2275-2280. Interpretive Summary: Pseudomonas syringae attacks a wide variety of crops. Infection depends on genes under the control of HrpL, a regulator of gene activity. To characterize the genes involved in infection, we obtained a draft genome sequence for P. syringae and used computer-based and gene expression techniques to identify genes controlled by HrpL. Using laboratory methods, ,we first identified 9 new virulence-related genes and then developed a computer model that could recognize genes with similar characteristics. The model was used to identify 12 additional virulence-related genes. We also used laboratory methods to monitor gene activity to identify additional genes controlled by HrpL. These methods together successfully identified a variety of novel genes, including those directly involved in the process of infection and its side-effects in plants. The results expand our understanding of how pathogenesis is controlled step-by-step and dwill enable us to test the precise role these genes play during infection.
Technical Abstract: Pseudomonas syringae depends on genes activated by the HrpL alternative sigma factor to parasitize tomato and Arabidopsis thaliana. To characterize these genes, we developed a draft sequence of syringae and used computational and gene expression techniques to identify virulence-implicated genes downstream of HrpL-responsive promoters. Hrp promoters control genes encoding the Hrp (type III protein secretion) machinery and a few type III effector proteins in syringae. We first identified 9 new virulence-implicated genes in the Hrp regulon by mini-Tn5gus mutagenesis and developed a Hidden Markov Model (HMM) trained with these and other Hrp promoter sequences. The HMM was used to identify promoters upstream of 12 virulence-implicated genes. Microarray and RNA blot analyses also identified HrpL-dependent expression of additional syringae genes. The Hrp regulon encodes candidates for 4 additional type III secretion machinery accessory factors, homologs of the effector proteins HopPsyA, AvrPpiB1 (2 copies), AvrPpiC2, AvrPphD (2 copies), AvrPphE, AvrPphF, and AvrXv3. We also found virulence factors unrelated to the Hrp type III secretion system, including syringomycin synthetase (SyrE), (indole-3-acetyl)-L-lysine synthetase (IaaL), and a regulon controlling coronatine production. Additional candidate effector genes, hopPtoA2, hopPtoB2, and an avrRps4 homolog, were preceded by Hrp promoter-like sequences, but had HMM E-values of relatively low significance and were not detectably activated by HrpL.