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Identification of the regulatory logic controlling Salmonella pathoadaptation by the SsrA-SsrB two-component system.

Tomljenovic-Berube AM, Mulder DT, Whiteside MD, Brinkman FS, Coombes BK - PLoS Genet. (2010)

Bottom Line: To survive in the host environment, Salmonella enterica uses a type III secretion system and effector proteins, which are activated by the SsrA-SsrB two-component system in response to the host environment.Mutational analysis of a representative promoter validated this palindrome as the minimal architecture needed for regulatory input by SsrB.These data provide a high-resolution map of a regulatory network and the underlying logic enabling pathogen adaptation to a host.

View Article: PubMed Central - PubMed

Affiliation: Michael G. DeGroote Institute for Infectious Disease Research and the Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada.

ABSTRACT
Sequence data from the past decade has laid bare the significance of horizontal gene transfer in creating genetic diversity in the bacterial world. Regulatory evolution, in which non-coding DNA is mutated to create new regulatory nodes, also contributes to this diversity to allow niche adaptation and the evolution of pathogenesis. To survive in the host environment, Salmonella enterica uses a type III secretion system and effector proteins, which are activated by the SsrA-SsrB two-component system in response to the host environment. To better understand the phenomenon of regulatory evolution in S. enterica, we defined the SsrB regulon and asked how this transcription factor interacts with the cis-regulatory region of target genes. Using ChIP-on-chip, cDNA hybridization, and comparative genomics analyses, we describe the SsrB-dependent regulon of ancestral and horizontally acquired genes. Further, we used a genetic screen and computational analyses integrating experimental data from S. enterica and sequence data from an orthologous regulatory system in the insect endosymbiont, Sodalis glossinidius, to identify the conserved yet flexible palindrome sequence that defines DNA recognition by SsrB. Mutational analysis of a representative promoter validated this palindrome as the minimal architecture needed for regulatory input by SsrB. These data provide a high-resolution map of a regulatory network and the underlying logic enabling pathogen adaptation to a host.

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The SsrB binding profile at the SPI-2 locus.Plotted are the SsrB ChIP interaction scores (black trace) for all probes within the SPI-2 locus. ChIP-on-chip experiments were performed with S. Typhimurium grown in SPI-2 inducing (LPM) and non-inducing (LB) conditions. ChIP score was calculated as LB (control/experimental)/LPM(control/experimental) where LB scores were used to normalize the data. Regions of SPI-2 footprinted by SsrB are highlighted with vertical pink bars. G+C content across the region is plotted as a green trace. Genes in the SPI-2 genomic island (top) are plotted to scale and are coloured according to function (see key).
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pgen-1000875-g003: The SsrB binding profile at the SPI-2 locus.Plotted are the SsrB ChIP interaction scores (black trace) for all probes within the SPI-2 locus. ChIP-on-chip experiments were performed with S. Typhimurium grown in SPI-2 inducing (LPM) and non-inducing (LB) conditions. ChIP score was calculated as LB (control/experimental)/LPM(control/experimental) where LB scores were used to normalize the data. Regions of SPI-2 footprinted by SsrB are highlighted with vertical pink bars. G+C content across the region is plotted as a green trace. Genes in the SPI-2 genomic island (top) are plotted to scale and are coloured according to function (see key).

Mentions: In order to rigorously evaluate our genome-wide functional genomics data, we compared it against traditional biochemical experiments describing SsrB-DNA interactions at the SPI-2 locus. Previous data reported SsrB footprints upstream of 6 genes in SPI-2: ssrA, ssrB, ssaB, sseA, ssaG, and ssaM[25],[26]. Our ChIP-on-chip data showed discrete SsrB binding at all of these promoters except for the promoter reported to be between ssrA and ssrB[25] (Figure 3). We attempted to verify functional activity at this site, but could not using transcriptional fusions (data not shown). Our data also identified three additional SsrB binding peaks upstream of sseA, within the CDS of ssaJ, and in the IGR upstream of ssaR (Figure 3). Functional interactions were confirmed for sseA and ssaR in subsequent reporter experiments described below.


Identification of the regulatory logic controlling Salmonella pathoadaptation by the SsrA-SsrB two-component system.

Tomljenovic-Berube AM, Mulder DT, Whiteside MD, Brinkman FS, Coombes BK - PLoS Genet. (2010)

The SsrB binding profile at the SPI-2 locus.Plotted are the SsrB ChIP interaction scores (black trace) for all probes within the SPI-2 locus. ChIP-on-chip experiments were performed with S. Typhimurium grown in SPI-2 inducing (LPM) and non-inducing (LB) conditions. ChIP score was calculated as LB (control/experimental)/LPM(control/experimental) where LB scores were used to normalize the data. Regions of SPI-2 footprinted by SsrB are highlighted with vertical pink bars. G+C content across the region is plotted as a green trace. Genes in the SPI-2 genomic island (top) are plotted to scale and are coloured according to function (see key).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2837388&req=5

pgen-1000875-g003: The SsrB binding profile at the SPI-2 locus.Plotted are the SsrB ChIP interaction scores (black trace) for all probes within the SPI-2 locus. ChIP-on-chip experiments were performed with S. Typhimurium grown in SPI-2 inducing (LPM) and non-inducing (LB) conditions. ChIP score was calculated as LB (control/experimental)/LPM(control/experimental) where LB scores were used to normalize the data. Regions of SPI-2 footprinted by SsrB are highlighted with vertical pink bars. G+C content across the region is plotted as a green trace. Genes in the SPI-2 genomic island (top) are plotted to scale and are coloured according to function (see key).
Mentions: In order to rigorously evaluate our genome-wide functional genomics data, we compared it against traditional biochemical experiments describing SsrB-DNA interactions at the SPI-2 locus. Previous data reported SsrB footprints upstream of 6 genes in SPI-2: ssrA, ssrB, ssaB, sseA, ssaG, and ssaM[25],[26]. Our ChIP-on-chip data showed discrete SsrB binding at all of these promoters except for the promoter reported to be between ssrA and ssrB[25] (Figure 3). We attempted to verify functional activity at this site, but could not using transcriptional fusions (data not shown). Our data also identified three additional SsrB binding peaks upstream of sseA, within the CDS of ssaJ, and in the IGR upstream of ssaR (Figure 3). Functional interactions were confirmed for sseA and ssaR in subsequent reporter experiments described below.

Bottom Line: To survive in the host environment, Salmonella enterica uses a type III secretion system and effector proteins, which are activated by the SsrA-SsrB two-component system in response to the host environment.Mutational analysis of a representative promoter validated this palindrome as the minimal architecture needed for regulatory input by SsrB.These data provide a high-resolution map of a regulatory network and the underlying logic enabling pathogen adaptation to a host.

View Article: PubMed Central - PubMed

Affiliation: Michael G. DeGroote Institute for Infectious Disease Research and the Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada.

ABSTRACT
Sequence data from the past decade has laid bare the significance of horizontal gene transfer in creating genetic diversity in the bacterial world. Regulatory evolution, in which non-coding DNA is mutated to create new regulatory nodes, also contributes to this diversity to allow niche adaptation and the evolution of pathogenesis. To survive in the host environment, Salmonella enterica uses a type III secretion system and effector proteins, which are activated by the SsrA-SsrB two-component system in response to the host environment. To better understand the phenomenon of regulatory evolution in S. enterica, we defined the SsrB regulon and asked how this transcription factor interacts with the cis-regulatory region of target genes. Using ChIP-on-chip, cDNA hybridization, and comparative genomics analyses, we describe the SsrB-dependent regulon of ancestral and horizontally acquired genes. Further, we used a genetic screen and computational analyses integrating experimental data from S. enterica and sequence data from an orthologous regulatory system in the insect endosymbiont, Sodalis glossinidius, to identify the conserved yet flexible palindrome sequence that defines DNA recognition by SsrB. Mutational analysis of a representative promoter validated this palindrome as the minimal architecture needed for regulatory input by SsrB. These data provide a high-resolution map of a regulatory network and the underlying logic enabling pathogen adaptation to a host.

Show MeSH
Related in: MedlinePlus