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

Derrick E. Fouts, Robert B. Abramovitch, James R. Alfano, Angela M. Baldo, C. Robin Buell, Samuel Cartinhour, Arun K. Chatterjee, Mark D'Ascenzo, Michelle L. Gwinn, Sondra G. Lazarowitz, Nai Chun Lin, Gregory B. Martin, Amos H. Rehm, David J. Schneider, Karin Van Dijk, Xiaoyan Tang, Alan Collmer

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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 HrpL-responsive 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 virulence-implicated 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 HrpL-dependent 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, AvrP-phD (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), Nε-(indole-3-acetyl)-L-lysine synthetase (laaL), 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.

Original languageEnglish (US)
Pages (from-to)2275-2280
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume99
Issue number4
DOIs
StatePublished - Feb 19 2002

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Pseudomonas syringae
Sigma Factor
Lycopersicon esculentum
Virulence
Genes
Regulon
Ligases
Proteins
Virulence Factors
Arabidopsis
Mutagenesis
Lysine
RNA

ASJC Scopus subject areas

  • General

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Genomewide identification of Pseudomonas syringae pv. tomato DC3000 promoters controlled by the HrpL alternative sigma factor. / Fouts, Derrick E.; Abramovitch, Robert B.; Alfano, James R.; Baldo, Angela M.; Buell, C. Robin; Cartinhour, Samuel; Chatterjee, Arun K.; D'Ascenzo, Mark; Gwinn, Michelle L.; Lazarowitz, Sondra G.; Lin, Nai Chun; Martin, Gregory B.; Rehm, Amos H.; Schneider, David J.; Van Dijk, Karin; Tang, Xiaoyan; Collmer, Alan.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 4, 19.02.2002, p. 2275-2280.

Research output: Contribution to journalArticle

Fouts, DE, Abramovitch, RB, Alfano, JR, Baldo, AM, Buell, CR, Cartinhour, S, Chatterjee, AK, D'Ascenzo, M, Gwinn, ML, Lazarowitz, SG, Lin, NC, Martin, GB, Rehm, AH, Schneider, DJ, Van Dijk, K, Tang, X & Collmer, A 2002, 'Genomewide identification of Pseudomonas syringae pv. tomato DC3000 promoters controlled by the HrpL alternative sigma factor', Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 4, pp. 2275-2280. https://doi.org/10.1073/pnas.032514099
Fouts, Derrick E. ; Abramovitch, Robert B. ; Alfano, James R. ; Baldo, Angela M. ; Buell, C. Robin ; Cartinhour, Samuel ; Chatterjee, Arun K. ; D'Ascenzo, Mark ; Gwinn, Michelle L. ; Lazarowitz, Sondra G. ; Lin, Nai Chun ; Martin, Gregory B. ; Rehm, Amos H. ; Schneider, David J. ; Van Dijk, Karin ; Tang, Xiaoyan ; Collmer, Alan. / Genomewide identification of Pseudomonas syringae pv. tomato DC3000 promoters controlled by the HrpL alternative sigma factor. In: Proceedings of the National Academy of Sciences of the United States of America. 2002 ; Vol. 99, No. 4. pp. 2275-2280.
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AU - Fouts, Derrick E.

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AU - Baldo, Angela M.

AU - Buell, C. Robin

AU - Cartinhour, Samuel

AU - Chatterjee, Arun K.

AU - D'Ascenzo, Mark

AU - Gwinn, Michelle L.

AU - Lazarowitz, Sondra G.

AU - Lin, Nai Chun

AU - Martin, Gregory B.

AU - Rehm, Amos H.

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N2 - 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 HrpL-responsive 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 virulence-implicated 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 HrpL-dependent 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, AvrP-phD (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), Nε-(indole-3-acetyl)-L-lysine synthetase (laaL), 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.

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