Whole-genome expression profiling defines the HrpL regulon of Pseudomonas syringae pv. tomato DC3000, allows de novo reconstruction of the Hrp cis clement, and identifies novel coregulated genes

Adriana O. Ferreira, Christopher R. Myers, Jeffrey S. Gordon, Gregory B. Martin, Monica Vencato, Alan Collmer, Misty D. Wehling, James R. Alfano, Gabriel Moreno-Hagelsieb, Warren F. Lamboy, Genevieve DeClerck, David J. Schneider, Samuel W. Cartinhour

Research output: Contribution to journalArticle

88 Citations (Scopus)

Abstract

Pseudomonas syringae pv. tomato DC3000 is a model pathogen of tomato and Arabidopsis that uses a hypersensitive response and pathogenicity (Hrp) type III secretion system (T3SS) to deliver virulence effector proteins into host cells. Expression of the Hrp system and many effector genes is activated by the HrpL alternative sigma factor. Here, an open reading frame-specific whole-genome microarray was constructed for DC3000 and used to comprehensively identify genes that are differentially expressed in wild-type and ΔhrpL strains. Among the genes whose differential regulation was statistically significant, 119 were upregulated and 76 were downregulated in the wild-type compared with the ΔlirpL strain. Hierarchical clustering revealed a subset of eight genes that were upregulated particularly rapidly. Gibbs sampling of regions upstream of HrpL-activated operons revealed the Hrp promoter as the only identifiable regulatory motif and supported an iterative refinement involving real-time polymerase chain reaction testing of additional HrpL-activated genes and refinements in a hidden Markov model that can be used to predict Hrp promoters in P. syringae strains. This iterative bioinformatic-experimental approach to a comprehensive analysis of the HrpL regulon revealed a mix of genes controlled by HrpL, including those encoding most type III effectors, twin-arginine transport (TAT) substrates, other regulatory proteins, and proteins involved in the synthesis or metabolism of phytohormones, phytotoxins, and myo-inositol. This analysis provides an extensively verified, rohust method for predicting Hrp promoters in P. syringae genomes, and it supports suhsequent identification of effectors and other factors that likely are important to the host-specific virulence of P. syringae.

Original languageEnglish (US)
Pages (from-to)1167-1179
Number of pages13
JournalMolecular Plant-Microbe Interactions
Volume19
Issue number11
DOIs
StatePublished - Nov 1 2006

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Pseudomonas syringae
Pseudomonas syringae pv. tomato
Regulon
regulon
hypersensitive response
Lycopersicon esculentum
Virulence
pathogenicity
Genes
Genome
genome
type III secretion system
genes
promoter regions
virulence
sigma factors
phytotoxins
Sigma Factor
regulatory proteins
operon

Keywords

  • Weight matrix model

ASJC Scopus subject areas

  • Physiology
  • Agronomy and Crop Science

Cite this

Whole-genome expression profiling defines the HrpL regulon of Pseudomonas syringae pv. tomato DC3000, allows de novo reconstruction of the Hrp cis clement, and identifies novel coregulated genes. / Ferreira, Adriana O.; Myers, Christopher R.; Gordon, Jeffrey S.; Martin, Gregory B.; Vencato, Monica; Collmer, Alan; Wehling, Misty D.; Alfano, James R.; Moreno-Hagelsieb, Gabriel; Lamboy, Warren F.; DeClerck, Genevieve; Schneider, David J.; Cartinhour, Samuel W.

In: Molecular Plant-Microbe Interactions, Vol. 19, No. 11, 01.11.2006, p. 1167-1179.

Research output: Contribution to journalArticle

Ferreira, AO, Myers, CR, Gordon, JS, Martin, GB, Vencato, M, Collmer, A, Wehling, MD, Alfano, JR, Moreno-Hagelsieb, G, Lamboy, WF, DeClerck, G, Schneider, DJ & Cartinhour, SW 2006, 'Whole-genome expression profiling defines the HrpL regulon of Pseudomonas syringae pv. tomato DC3000, allows de novo reconstruction of the Hrp cis clement, and identifies novel coregulated genes', Molecular Plant-Microbe Interactions, vol. 19, no. 11, pp. 1167-1179. https://doi.org/10.1094/MPMI-19-1167
Ferreira, Adriana O. ; Myers, Christopher R. ; Gordon, Jeffrey S. ; Martin, Gregory B. ; Vencato, Monica ; Collmer, Alan ; Wehling, Misty D. ; Alfano, James R. ; Moreno-Hagelsieb, Gabriel ; Lamboy, Warren F. ; DeClerck, Genevieve ; Schneider, David J. ; Cartinhour, Samuel W. / Whole-genome expression profiling defines the HrpL regulon of Pseudomonas syringae pv. tomato DC3000, allows de novo reconstruction of the Hrp cis clement, and identifies novel coregulated genes. In: Molecular Plant-Microbe Interactions. 2006 ; Vol. 19, No. 11. pp. 1167-1179.
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abstract = "Pseudomonas syringae pv. tomato DC3000 is a model pathogen of tomato and Arabidopsis that uses a hypersensitive response and pathogenicity (Hrp) type III secretion system (T3SS) to deliver virulence effector proteins into host cells. Expression of the Hrp system and many effector genes is activated by the HrpL alternative sigma factor. Here, an open reading frame-specific whole-genome microarray was constructed for DC3000 and used to comprehensively identify genes that are differentially expressed in wild-type and ΔhrpL strains. Among the genes whose differential regulation was statistically significant, 119 were upregulated and 76 were downregulated in the wild-type compared with the ΔlirpL strain. Hierarchical clustering revealed a subset of eight genes that were upregulated particularly rapidly. Gibbs sampling of regions upstream of HrpL-activated operons revealed the Hrp promoter as the only identifiable regulatory motif and supported an iterative refinement involving real-time polymerase chain reaction testing of additional HrpL-activated genes and refinements in a hidden Markov model that can be used to predict Hrp promoters in P. syringae strains. This iterative bioinformatic-experimental approach to a comprehensive analysis of the HrpL regulon revealed a mix of genes controlled by HrpL, including those encoding most type III effectors, twin-arginine transport (TAT) substrates, other regulatory proteins, and proteins involved in the synthesis or metabolism of phytohormones, phytotoxins, and myo-inositol. This analysis provides an extensively verified, rohust method for predicting Hrp promoters in P. syringae genomes, and it supports suhsequent identification of effectors and other factors that likely are important to the host-specific virulence of P. syringae.",
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AU - Myers, Christopher R.

AU - Gordon, Jeffrey S.

AU - Martin, Gregory B.

AU - Vencato, Monica

AU - Collmer, Alan

AU - Wehling, Misty D.

AU - Alfano, James R.

AU - Moreno-Hagelsieb, Gabriel

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