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Structure-based analysis of the gene network controlled by the Salmonella RcsB response regulator

ABSTRACT: RcsB is a transcriptional regulator that controls expression of numerous genes in Enterobacteriaceae. RcsB accomplishes this role alone or in combination with auxiliary transcriptional factors independently or dependently of phosphorylation. To understand the mechanisms by which RcsB regulates such a large number of genes, we performed structural and in vitro and in vivo functional studies with different RcsB variants. Our structural data reveal that RcsB binds the promoters of rprA and flhDC genes in a dimeric active conformation, docking the DNA-binding domains into the major groove of the DNA that preform a weak read-out of the target sequence. Interestingly, comparative structural analysis shows that DNA binding may trigger the active conformation in unphosphorylated RcsB. Furthermore, RNAseq analysis performed in strains expressing wild-type or several RcsB variants provided new insights into the contribution of phosphorylation to gene regulation and assign a potential role of RcsB in regulating iron and molybdenum metabolism. Finally, we delimited the RcsB box for homodimeric active RcsB binding with sequence TN(G/A)GAN4TC(T/C)NA that can be found in promoter and intragenic regions to regulate activation or inhibition of gene transcription.

ORGANISM(S): Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

PROVIDER: GSE154668 | GEO | 2020/07/18

REPOSITORIES: GEO

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Gene regulation by the RcsCB two-component system and the auxiliary protein TviA in S. Typhi

2009-12-11 | GSE15752 | GEO

Gene regulation by the RcsCB two-component system and the auxiliary protein TviA in S. Typhi

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2010-05-18 | E-GEOD-15752 | biostudies-arrayexpress

Salmonella typhimurium igaA(T191P) and related

Project description:We have exploited a spontaneously isolated mutant IgaA(T191P) that is near-maximally activated for the Rcs system, to identify a vast set of genes that respond, and report new regulatory properties of this signaling system in Salmonella enterica serovar Typhimurium. Microarray data show that the Rcs system normally functions as a positive regulator of SPI-2 and other genes important for growth of Salmonella in macrophages, although when highly activated, the system completely represses the SPI-1/SPI-2 virulence, flagellar, and fimbrial biogenesis pathways. The auxilliary protein RcsA, which works with RcsB to positively regulate colanic acid and other target genes, not only stimulates but also antagonizes the positive regulation of many genes in the igaA mutant. We show that RcsB represses motility through the 'RcsB box' in the promoter region of the master operon flhDC, and that RcsA is not required for this regulation. Curiously, RcsB selectively stimulates expression of the flagellar Type 3 secretion genes fliPQR; an RcsAB box located downstream of fliR influences this regulation. We show that excess colanic acid impairs swimming and inhibits swarming motility, consistent with the inverse regulation of the two pathways by the Rcs system. The work was published in Journal of Bacteriology: Wang Q, Zhao Y, McClelland M, Harshey RM. The RcsCDB signaling system and swarming motility in Salmonella enterica serovar Typhimurium: dual regulation of flagellar and SPI-2 virulence genes. J Bacteriol. 2007 Sep 28; [Epub ahead of print] PMID: 17905992 [PubMed - as supplied by publisher] Keywords: Comparative genomic hybridization

2008-06-25 | GSE9584 | GEO

Salmonella typhimurium igaA(T191P) and related

2008-06-24 | E-GEOD-9584 | biostudies-arrayexpress

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2020-06-04 | E-MTAB-9170 | biostudies-arrayexpress

RNAseq of mouse embryonic fibroblasts from conditional knock-in mice carrying a phosphorylation-deficient S180A (SA) mutation in exon 5 of the endogenous mouse Trp53 gene locus

2020-08-25 | E-MTAB-9171 | biostudies-arrayexpress

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2022-03-24 | PXD028663 | Pride

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2021-11-25 | PXD023645 | Pride

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2013-09-26 | E-GEOD-48262 | biostudies-arrayexpress

Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis

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