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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 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.

ORGANISM(S): Listeria monocytogenes

SUBMITTER: Lior Lobel

PROVIDER: E-GEOD-76821 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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 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.

2016-07-03 | GSE76821 | GEO

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

Transcriptomic comparison of Listeria monocytogenes and its derivative mutant strain with inactivated lmo0946 gene in exponential phase of growth

Project description:To gain comprehensive knowledge on role of Lmo0946 in physiology of L. monocytogenes, we set on analyzing whole-transcriptome changes induced by inactivation of lmo0946 gene. Remarkably, we identified for the first time a global effect of lmo0946 inactivation on transcriptome of L. monocytogenes with highly induced genes belonging to SOS regulon in absence of any environmental stress.

2023-08-05 | E-MTAB-10809 | biostudies-arrayexpress

Investigating the effect of CodY mutation on the gene expression in Streptococcus suis serotype 2 SC19 strain.

Project description:To investigate the effect of CodY mutation on the gene expression in Streptococcus suis serotype 2 SC19 strain, we have employed whole genome microarray expression profiling as a discovery platform to identify genes regulated by CodY mutation. DNA microarray analysis was performed using an Agilent custom-designed oligonucleotide microarray. Based upon the whole genome sequence of SC19 , specific 60-mer oligonucleotide probes were designed using eArray (https://earray.chem.agilent.com/earray/), to cover all annotated genes. Probes were printed seven times on microarray slides. Three biological replicates of total RNA from two wild type strains and from two codY mutant strains were amplified and labeled with Cy3-CTP using Low Input Quick Amp Labeling Kit, one-color(Agilent technologies, US), following the manufacturer’s instructions. Labeled cRNA was purified using the RNeasy mini kit (Qiagen). After fragmentation, microarray slides were hybridized with 600 ng Cy3-labeled cRNA. Hybridization was performed at 65 °C for 17 h with rotation at 10 rpm. Microarray slides were washed and scanned by an Agilent Microarray Scanner (G2565BA). Those genes with greater than two-fold change ratios were regarded as differentially expressed genes. codY mutation induced gene expression in Streptococcus suis serotype 2 SC19 was detected in two wild type and two codY mutated strain of Streptococcus suis serotype 2.

2015-04-21 | E-GEOD-68068 | biostudies-arrayexpress

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

CodY regulates the activity of the virulence quorum sensor PlcR

Project description:In Gram-positive bacteria, cell-cell communication mainly relies on cytoplasmic sensors of the RNPP family. Activity of these regulators depends on their binding to secreted signaling peptides that are imported into the cell. These quorum sensing regulators control important biological functions in bacteria of the Bacillus cereus group, such as virulence and necrotrophism. The RNPP quorum sensor PlcR, in complex with its cognate signaling peptide PapR, is the main regulator of virulence in B. cereus and Bacillus thuringiensis (Bt). Recent reports have shown that the global stationary phase regulator CodY, involved in adaptation to nutritional limitation, is required for the expression of virulence genes belonging to the PlcR regulon. However, the mechanism underlying this regulation was not described. Using genetics and proteomics approaches, we showed that CodY regulates the expression of the virulence genes through the import of PapR. We report that CodY positively controls the production of the proteins that compose the oligopeptide permease OppABCDF, and of several other Opp-like proteins. It was previously shown that the pore components of this oligopeptide permease, OppBCDF, were required for the import of PapR. However, the role of OppA, the substrate-binding protein (SBP), was not investigated. Here, we demonstrated that OppA is not the only SBP involved in the recognition of PapR, and that several other OppA-like proteins can allow the import of this peptide. Altogether, these data complete our model of quorum sensing during the lifecycle of Bt and indicate that RNPPs integrate environmental conditions, as well as cell density, to coordinate the behavior of the bacteria throughout growth.

2015-12-17 | PXD003311 | Pride

Differential contributions of CodY, SigB and the hibernation promoting factor HPF to interactions of Staphylococcus aureus USA300 with human lung epithelial cells explained by proteome analysis

Project description:The Gram-positive bacterium Staphylococcus aureus is a leading cause of severe pneumonia. Therefore, we recently investigated the fate of S. aureus upon internalization by human lung epithelial cells. This uncovered three major adaptive responses of the bacteria, involving the SigB and CodY regulons and an upregulation of the S. aureus hibernation-promoting factor (SaHPF). To explore the roles of CodY, SigB and SaHPF in the infection of human lung epithelial cells, we employed derivatives of the community-acquired MRSA strain USA300 with transposon mutations in the respective genes. Interestingly, the investigated codY mutant bacteria displayed a ‘small colony variant’-like phenotype that promotes their intracellular survival and localizes the bacteria to the host cell cytoplasm. Furthermore, our results show that CodY, SigB and saHPF contribute differentially to the different steps in the infectious process, including, host cell adhesion, invasion, intracellular survival and cytotoxicity. Notably, codY or sigB mutant bacteria experienced faster intracellular clearance compared to the parental strain, underscoring the importance of these regulators for intracellular persistence. Furthermore, we show an unprecedented role of SaHPF in human lung epithelial cell infection, including parallel effects of saHPF or SigB deficiency in adhesion and invasion. Altogether, our study focuses attention on the CodY-perceived metabolic state of the bacteria and the SigB-perceived stress in bacterial decision taking during infection. Conversely, our observations indicate important roles for the nutritional status and bacterial stress-inducing conditions in the host for the onset and subsequent course of invasive or chronic staphylococcal lung infection.

2024-09-11 | PXD044962 | Pride

The Lactococcus lactis CodY regulon: identification of a conserved cis-regulatory element

Project description:CodY of Lactococcus lactis MG1363 is a transcriptional regulator that represses the expression of several genes encoding proteins of the proteolytic system. DNA microarray analysis, comparing the expression profiles of L. lactis MG1363 and an isogenic strain in which codY was mutated, was used to determine the CodY regulon. In peptide-rich medium and exponentially growing cells, where CodY exerts strong repressing activity, the expression of over 30 genes was significantly increased upon removal of codY. The differentially expressed genes included those predominantly involved in amino acid transport and metabolism. In addition, several genes belonging to other functional categories were derepressed, stressing the pleiotropic role of CodY. Scrutinizing the transcriptome data with bioinformatics tools revealed the presence of a novel overrepresented motif in the upstream regions of several of the genes derepressed in L. lactis MG1363codY. Evidence is presented that this 15-bps cis-sequence, AATTTTCWGAAAATT, serves as a high-affinity binding site for CodY, as shown by electrophoretic mobility shift assays and DNaseI footprinting analyses. The presence of this CodY-box is sufficient to evoke CodY-mediated regulation in vivo. A copy of this motif is also present in the upstream region of codY itself. It is shown that CodY regulates its own synthesis and requires the CodY-box and branched-chain amino acids to interact with its promoter. Keywords: genetic modification

2005-07-22 | GSE2823 | GEO

ChIP-seq for transcriptional regulator CodY of Lactococcus lactis

Project description:CodY is a widely conserved global regulator, regulating nitrogen metabolism, virulence, and stress response in Gram-positive bacteria. Here, we performed ChIP-seq to define the CodY regulon in L. lactis, and found that CodY served either as an activator or as a repressor of hundreds of genes. The genes involved in amino acid biosynthesis and transport, cell wall synthesis, nisin synthesis and immunity, and several transcription regulators were identified regulated by CodY for the first time. Intriguingly, CodY could directly bind to the downstream of codY. This study gives new insights into the function of CodY controlling cell wall synthesis, nisin synthesis and immunity, as well as self-regulation in L. lactis.

2022-01-28 | GSE139902 | GEO

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