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Systems level analyses establish CodY as a multifaceted metabolic regulator integrating metabolism, motility and virulence in Listeria monocytogenes [ChIP-Seq]

ABSTRACT: To gain knowledge on L. monocytogenes differential CodY activity, we set on analyzing CodY’s regulon in L. monocytogenes in both rich and minimal growth conditions using genome wide sequencing techniques. Remarkably, we identified for the first time a global regulatory role for CodY when BCAAs are limited, that are similar to those within the mammalian niche. Furthermore, our data establish CodY as a central regulator that integrates metabolism, motility, stress responses and virulence in L. monocytogenes.

ORGANISM(S): Listeria monocytogenes

PROVIDER: GSE76821 | GEO | 2016/07/03

SECONDARY ACCESSION(S): PRJNA308650

REPOSITORIES: GEO

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Systems level analyses establish CodY as a multifaceted metabolic regulator integrating metabolism, motility and virulence in Listeria monocytogenes

Project description:To gain knowledge on L. monocytogenes differential CodY activity, we set on analyzing CodY’s regulon in L. monocytogenes in both rich and minimal growth conditions using genome-wide sequencing techniques. Remarkably, we identified for the first time a global regulatory role for CodY when BCAAs are limited, that are similar to those within the mammalian niche. Furthermore, our data establish CodY as a central regulator that integrates metabolism, motility, stress responses and virulence in L. monocytogenes.

2016-06-08 | GSE76159 | GEO

Systems level analyses establish CodY as a multifaceted metabolic regulator integrating metabolism, motility and virulence in Listeria monocytogenes [ChIP-Seq]

Project description:To gain knowledge on L. monocytogenes differential CodY activity, we set on analyzing CodYâ??s regulon in L. monocytogenes in both rich and minimal growth conditions using genome wide sequencing techniques. Remarkably, we identified for the first time a global regulatory role for CodY when BCAAs are limited, that are similar to those within the mammalian niche. Furthermore, our data establish CodY as a central regulator that integrates metabolism, motility, stress responses and virulence in L. monocytogenes. Examination of CodY regulon in rich and minimal conditions.

2016-07-03 | E-GEOD-76821 | biostudies-arrayexpress

Elucidating the CodY regulon in Staphylococcus aureus USA300 lineage using ChIPexo

Project description:CodY is a conserved broad acting transcriptional factor that regulates the expression of genes related to amino acid metabolism and virulence in Staphylococcus aureus. CodY target genes have been studied by using in vitro DNA affinity purification and deep sequencing (IDAP-Seq). In this study we performed the first in vivo determination of CodY target genes using a novel CodY monoclonal antibody in established ChIP-exo protocols. Our results showed, 1) The same 165 CodY target genes in both strains; 2) That the differential binding intensity for the same target genes under the same conditions were due to sequence differences in the same CodY binding site in the two strains; 3) Based on transcriptomic data, a CodY regulon comprising 72 target genes that revealed that CodY is mainly involved in amino acid transport and metabolism, inorganic ion transport and metabolism, and cellular transcription and translation; and 4) CodY systematically regulated central metabolic flux to generate branched-chain amino acids (BCAAs) by mapping the CodY regulon onto a genome-scale metabolic model of S. aureus. Our study performed the first system-level analysis of CodY in two closely related dominant USA300 TCH1516 and LAC strains, thus expanding the size of the known CodY regulon, and giving new insights into the similarities and differences of CodY regulatory roles between closely related strains.

2022-08-29 | GSE163312 | GEO

Elucidation of the CodY target genes in Staphylococcus aureus USA300 using ChIPexo

Project description:CodY is a highly conserved global transcriptional factor that regulates the expression of dozens of genes related to metabolism and virulence in Staphylococcus aureus. The S. aureus CodY regulon has been studied in vitro. However, in vivo CodY DNA-binding activity and the identity of the corresponding target genes remain unknown due to lack of a ChIP-grade monoclonal antibody. Using a novel CodY monoclonal antibody that we developed in established ChIP-exo protocols, we report in vivo target genes of CodY in two S. aureus USA300 clinical strains (TCH1516 and LAC). The total number of CodY-binding sites exceeded 110, but their location varied between the two strains. The majority of the identified binding sites were located within the promoter regions. Based on the sequences of the CodY-binding sites, a model of CodY interaction with DNA is proposed. Furthermore, S. aureus CodY protein is highly conserved across a G+C Gram-positive species, including Bacillus subtilis and Listeria monocytogenes, and thus this study paves the way for exploration of the differential binding of CodY among a range of gram-positive species, including pathogenic ones

2021-08-17 | GSE159856 | GEO

Systems Level Analyses Reveal Multiple Regulatory Activities of CodY Controlling Metabolism, Motility and Virulence in Listeria monocytogenes.

Project description:Bacteria sense and respond to many environmental cues, rewiring their regulatory network to facilitate adaptation to new conditions/niches. Global transcription factors that co-regulate multiple pathways simultaneously are essential to this regulatory rewiring. CodY is one such global regulator, controlling expression of both metabolic and virulence genes in Gram-positive bacteria. Branch chained amino acids (BCAAs) serve as a ligand for CodY and modulate its activity. Classically, CodY was considered to function primarily as a repressor under rich growth conditions. However, our previous studies of the bacterial pathogen Listeria monocytogenes revealed that CodY is active also when the bacteria are starved for BCAAs. Under these conditions, CodY loses the ability to repress genes (e.g., metabolic genes) and functions as a direct activator of the master virulence regulator gene, prfA. This observation raised the possibility that CodY possesses multiple functions that allow it to coordinate gene expression across a wide spectrum of metabolic growth conditions, and thus better adapt bacteria to the mammalian niche. To gain a deeper understanding of CodY's regulatory repertoire and identify direct target genes, we performed a genome wide analysis of the CodY regulon and DNA binding under both rich and minimal growth conditions, using RNA-Seq and ChIP-Seq techniques. We demonstrate here that CodY is indeed active (i.e., binds DNA) under both conditions, serving as a repressor and activator of different genes. Further, we identified new genes and pathways that are directly regulated by CodY (e.g., sigB, arg, his, actA, glpF, gadG, gdhA, poxB, glnR and fla genes), integrating metabolism, stress responses, motility and virulence in L. monocytogenes. This study establishes CodY as a multifaceted factor regulating L. monocytogenes physiology in a highly versatile manner.

| S-EPMC4760761 | biostudies-literature

Genome-wide identification of Listeria monocytogenes CodY-binding sites.

Project description:CodY is a global transcriptional regulator that controls, directly or indirectly, the expression of dozens of genes and operons in Listeria monocytogenes. We used in vitro DNA affinity purification combined with massively parallel sequencing (IDAP-Seq) to identify genome-wide L. monocytogenes chromosomal DNA regions that CodY binds in vitro. The total number of CodY-binding regions exceeded 2,000, but they varied significantly in their strengths of binding at different CodY concentrations. The 388 strongest CodY-binding regions were chosen for further analysis. A strand-specific analysis of the data allowed pinpointing CodY-binding sites at close to single-nucleotide resolution. Gel shift and DNase I footprinting assays confirmed the presence and locations of several CodY-binding sites. Surprisingly, most of the sites were located within genes' coding regions. The binding site within the beginning of the coding sequence of the prfA gene, which encodes the master regulator of virulence genes, has been previously implicated in regulation of prfA, but this site was weaker in vitro than hundreds of other sites. The L. monocytogenes CodY protein was functionally similar to Bacillus subtilis CodY when expressed in B. subtilis cells. Based on the sequences of the CodY-binding sites, a model of CodY interaction with DNA is proposed.

| S-EPMC7176553 | biostudies-literature

Surface Proteins of Listeria monocytogenes

Project description:Listeria monocytogenes cells (strain LI0521) were digested with trypsin for the identification of surface proteins. The supernatant was filter-sterilized and subjected to identification by LC-MS/MS. Concurrently secreted or shed proteins were identified by isolating filter-sterilized supernatants following incubation of L. monocytogenes cells in buffer without trypsin. This was followed by trypsin digest of the sterilized supernatant and identification by LC-MS/MS.

2013-08-27 | PXD000035 | Pride

Listeria monocytogenes

Project description:Systems level analyses establish CodY as a multifaceted metabolic regulator integrating metabolism, motility and virulence in Listeria monocytogenes [ChIP-Seq]

| PRJNA308650 | ENA

CtsR Regulon in Listeria monocytogenes

Project description:The foodborne pathogen Listeria monocytogenes uses a number of transcriptional regulators, including the negative regulator CtsR, to control gene expression under different environmental conditions and in response to stress. Gene expression patterns of DctsR log phase cells were compared to both wt and ictsR-mcsA log phase cells grown with 0.5mM IPTG to identify CtsR-dependent genes.We identified 62 CtsR-dependent genes that showed significant expression ratios (adj. P < 0.05), with ≥ 1.5-fold differential expression either between ΔctsR and wt or between ΔctsR and ictsR-mcsA. Keywords: Listeria monocytogenes, CtsR regulon, log phase

2007-10-14 | GSE7514 | GEO

HrcA Regulon in Listeria monocytogenes

Project description:The foodborne pathogen Listeria monocytogenes uses a number of transcriptional regulators, including the negative regulator HrcA, to control gene expression under different environmental conditions and in response to stress. Gene expression patterns of DhrcA stationary phase cells were compared to wt to identify hrcA-dependent genes. We identified 61 HrcA-dependent genes that showed significant expression ratios (adj. P < 0.05), with ≥ 1.5-fold differential expression between ΔhrcA and wt. Combined with microarray analysis, Hidden Markov Model searches show HrcA directly repress at least 8 genes. Keywords: Listeria monocytogenes, HrcA regulon, stationary phase

2007-11-03 | GSE7517 | GEO

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