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

PLoS Pathogens
Sebastian SchulzSusanne Häussler

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 mo...Continue Reading

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Datasets Mentioned

BETA
GSE54997
GSE54998
GSE54999
SRP037770
SRP037771

Methods Mentioned

BETA
immunoprecipitation
PCR
ChIP-seq
Illumina sequencing
ChIPs
chip
RNA-seq
transcription profiling

Software Mentioned

utils
R package DESeq
stampy
MEME
Tiling Analysis Software
R
EA
mcf script
FIMO
fastq

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