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Elucidation of sigma factor-associated networks in Pseudomonas aeruginosa reveals a modular architecture with limited and function-specific crosstalk.

Schulz S, Eckweiler D, Bielecka A, Nicolai T, Franke R, Dötsch A, Hornischer K, Bruchmann S, Düvel J, Häussler S - PLoS Pathog. (2015)

Bottom Line: They provide effective mechanisms for simultaneously regulating expression of large numbers of genes in response to challenging conditions, and their presence has been linked to bacterial virulence and pathogenicity.We furthermore elucidated the de novo binding motif of each sigma factor, and validated the RNA- and ChIP-seq results by global motif searches in the proximity of transcriptional start sites (TSS).Our data indicate that the modular structure of sigma factor networks enables P. aeruginosa to function adequately in its environment and at the same time is exploited to build up higher-level functions by specific interconnections that are dominated by a participation of RpoN.

View Article: PubMed Central - PubMed

Affiliation: Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany; Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany.

ABSTRACT
Sigma factors are essential global regulators of transcription initiation in bacteria which confer promoter recognition specificity to the RNA polymerase core enzyme. They provide effective mechanisms for simultaneously regulating expression of large numbers of genes in response to challenging conditions, and their presence has been linked to bacterial virulence and pathogenicity. In this study, we constructed nine his-tagged sigma factor expressing and/or deletion mutant strains in the opportunistic pathogen Pseudomonas aeruginosa. To uncover the direct and indirect sigma factor regulons, we performed mRNA profiling, as well as chromatin immunoprecipitation coupled to high-throughput sequencing. We furthermore elucidated the de novo binding motif of each sigma factor, and validated the RNA- and ChIP-seq results by global motif searches in the proximity of transcriptional start sites (TSS). Our integrated approach revealed a highly modular network architecture which is composed of insulated functional sigma factor modules. Analysis of the interconnectivity of the various sigma factor networks uncovered a limited, but highly function-specific, crosstalk which orchestrates complex cellular processes. Our data indicate that the modular structure of sigma factor networks enables P. aeruginosa to function adequately in its environment and at the same time is exploited to build up higher-level functions by specific interconnections that are dominated by a participation of RpoN.

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Functional profiling of the crosstalk among sigma factors in P. aeruginosa.The PseudoCAP annotation [55] was used to categorize the members of the direct (violet bars) and indirect (light green bars) sigma factor crosstalk. The enrichment of specific gene classes is displayed. The P values of the enriched categories are provided in S10 Table.
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ppat.1004744.g005: Functional profiling of the crosstalk among sigma factors in P. aeruginosa.The PseudoCAP annotation [55] was used to categorize the members of the direct (violet bars) and indirect (light green bars) sigma factor crosstalk. The enrichment of specific gene classes is displayed. The P values of the enriched categories are provided in S10 Table.

Mentions: Direct crosstalk was mainly found to involve genes of the more complex functional categories adaptation/protection, chaperones/heat shock proteins, chemotaxis, motility/attachment, protein secretion and secreted factors (Fig. 5). There was also a preference of sigma factor combinations within the direct crosstalk. Direct crosstalk with RpoN clearly played the most dominant role (S2 Fig.). In total, 183 out of the 401 genes affected by direct crosstalk were found to be activated by RpoN in combination with either AlgU (51 genes), FliA (43 genes), SigX (40 genes), RpoH (26 genes) or RpoS (23 genes).


Elucidation of sigma factor-associated networks in Pseudomonas aeruginosa reveals a modular architecture with limited and function-specific crosstalk.

Schulz S, Eckweiler D, Bielecka A, Nicolai T, Franke R, Dötsch A, Hornischer K, Bruchmann S, Düvel J, Häussler S - PLoS Pathog. (2015)

Functional profiling of the crosstalk among sigma factors in P. aeruginosa.The PseudoCAP annotation [55] was used to categorize the members of the direct (violet bars) and indirect (light green bars) sigma factor crosstalk. The enrichment of specific gene classes is displayed. The P values of the enriched categories are provided in S10 Table.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4362757&req=5

ppat.1004744.g005: Functional profiling of the crosstalk among sigma factors in P. aeruginosa.The PseudoCAP annotation [55] was used to categorize the members of the direct (violet bars) and indirect (light green bars) sigma factor crosstalk. The enrichment of specific gene classes is displayed. The P values of the enriched categories are provided in S10 Table.
Mentions: Direct crosstalk was mainly found to involve genes of the more complex functional categories adaptation/protection, chaperones/heat shock proteins, chemotaxis, motility/attachment, protein secretion and secreted factors (Fig. 5). There was also a preference of sigma factor combinations within the direct crosstalk. Direct crosstalk with RpoN clearly played the most dominant role (S2 Fig.). In total, 183 out of the 401 genes affected by direct crosstalk were found to be activated by RpoN in combination with either AlgU (51 genes), FliA (43 genes), SigX (40 genes), RpoH (26 genes) or RpoS (23 genes).

Bottom Line: They provide effective mechanisms for simultaneously regulating expression of large numbers of genes in response to challenging conditions, and their presence has been linked to bacterial virulence and pathogenicity.We furthermore elucidated the de novo binding motif of each sigma factor, and validated the RNA- and ChIP-seq results by global motif searches in the proximity of transcriptional start sites (TSS).Our data indicate that the modular structure of sigma factor networks enables P. aeruginosa to function adequately in its environment and at the same time is exploited to build up higher-level functions by specific interconnections that are dominated by a participation of RpoN.

View Article: PubMed Central - PubMed

Affiliation: Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany; Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany.

ABSTRACT
Sigma factors are essential global regulators of transcription initiation in bacteria which confer promoter recognition specificity to the RNA polymerase core enzyme. They provide effective mechanisms for simultaneously regulating expression of large numbers of genes in response to challenging conditions, and their presence has been linked to bacterial virulence and pathogenicity. In this study, we constructed nine his-tagged sigma factor expressing and/or deletion mutant strains in the opportunistic pathogen Pseudomonas aeruginosa. To uncover the direct and indirect sigma factor regulons, we performed mRNA profiling, as well as chromatin immunoprecipitation coupled to high-throughput sequencing. We furthermore elucidated the de novo binding motif of each sigma factor, and validated the RNA- and ChIP-seq results by global motif searches in the proximity of transcriptional start sites (TSS). Our integrated approach revealed a highly modular network architecture which is composed of insulated functional sigma factor modules. Analysis of the interconnectivity of the various sigma factor networks uncovered a limited, but highly function-specific, crosstalk which orchestrates complex cellular processes. Our data indicate that the modular structure of sigma factor networks enables P. aeruginosa to function adequately in its environment and at the same time is exploited to build up higher-level functions by specific interconnections that are dominated by a participation of RpoN.

Show MeSH
Related in: MedlinePlus