Genomewide identification of Pseudomonas syringae pv.tomato DC3000 promoters controlled by the HrpL alternative sigma factor

Authors

Derrick E. Fouts, Cornell University
Robert B. Abramovitch, Cornell University
James R. Alfano, University of Nebraska-LincolnFollow
Angela M. Baldo, USDA, Agricultural Research Service
C. Robin Buell, Institute of Genomic Research
Samuel Cartinhour, USDA, Agricultural Research Service
Arn K. Chatterjee, University of Missouri, Columbia
Mark D'Ascenzo, Boyce Thompson Institute for Plant Research, Ithaca, NY
Michelle L. Gwinn, The Institute for Genomic Research, Rockville, MD
Sondra G. Lazarowitz, Cornell University
Na-Chun Lin, Cornell University
Gregory B. Martin, Cornell University
Amos H. Rehm, Cornell University
David J. Schneider, Cornell University
Karin V. van Dijk, University of Nebraska - LincolnFollow
Xiaoyan Tang, Kansas State University
Alan Collmer, Cornell UniversityFollow

Document Type

Article

Date of this Version

2-19-2002

Citation

PNAS, February 19, 2002, vol. 99 no. 4, 2275–2280

Comments

US government work

Abstract

The ability of Pseudomonas syringae pv. tomato DC3000 to parasitize tomato and Arabidopsis thaliana depends on genes activated by the HrpL alternative sigma factor. To support various functional genomic analyses of DC3000, and specifically, to identify genes involved in pathogenesis, we developed a draft sequence of DC3000 and used an iterative process involving computational and gene expression techniques to identify virulence-implicated genes downstream of HrpLresponsive promoters. Hypersensitive response and pathogenicity (Hrp) promoters are known to control genes encoding the Hrp (type III protein secretion) machinery and a few type III effector proteins in DC3000. This process involved (i) identification of 9 new virulenceimplicated genes in the Hrp regulon by miniTn5gus mutagenesis, (ii) development of a hidden Markov model (HMM) trained with known and transposon-identified Hrp promoter sequences, (iii) HMM identification of promoters upstream of 12 additional virulence-implicated genes, and (iv) microarray and RNA blot analyses of the HrpLdependent expression of a representative subset of these DC3000 genes. We found that 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, and genes associated with the production or metabolism of virulence factors unrelated to the Hrp type III secretion system, including syringomycin synthetase (SyrE), N-(indole-3-acetyl)-L-lysine synthetase (IaaL), and a subsidiary regulon controlling coronatine production. Additional candidate effector genes, hopPtoA2, hopPtoB2, and an avrRps4 homolog, were preceded by Hrp promoter-like sequences, but these had HMM expectation values of relatively low significance and were not detectably activated by HrpL.