Interplay of CodY and CcpA in regulating central metabolism and biofilm formation in Staphylococcus aureus
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ABSTRACT:
ORGANISM(S): Staphylococcus aureus
PROVIDER: GSE204884 | GEO | 2022/05/30
REPOSITORIES: GEO
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Project description:Staphylococcus aureus is a medically important pathogen that exhibit high metabolic versatility allowing it to infect various niches within a host. S. aureus utilizes two major transcriptional regulators, CodY and CcpA, to remodel metabolic and virulence gene expression in response to changing environmental conditions. Previous studies revealed that inactivation of either codY or ccpA has a pronounced impact on different aspects of staphylococcal physiology and pathogenesis. To determine the contribution and interplay of these two regulators in modulating central metabolism, virulence, and biofilm development we constructed and characterized codY ccpA double mutant in S. aureus UAMS-1. In line with previous studies, we found that CcpA and CodY control cellular metabolic status by altering carbon flow through the central and overflow metabolic pathways. Our results demonstrate that ccpA inactivation impairs biofilm formation and decreases incorporation of eDNA into the biofilm matrix while disrupting codY resulted in a robust structured biofilm tethered together with eDNA and PIA. Interestingly, inactivation of both codY and ccpA decreases biofilm biomass and neglects eDNA release in the double mutant. Compared to inactivation of codY, the codY ccpA mutant did not overexpress toxins but maintained overexpression of amino acid metabolism pathways. Furthermore, codY ccpA mutant produced higher amounts of PIA, in contrast to the wild-type strain and ccpA mutant. Overall, results of this study suggest that interplay between CodY and CcpA modulates central metabolism to optimize growth on preferred carbon sources while repressing virulence gene expression until nutrient limitation requires scavenging nutrients from the host.
2022-05-25 | ST002187 | MetabolomicsWorkbench
Project description:Staphylococcus aureus is a medically important pathogen with high metabolic versatility allowing it to infect various niches within a host. S. aureus utilizes two major transcriptional regulators, namely, CodY and CcpA, to remodel metabolic and virulence gene expression in response to changing environmental conditions. Previous studies revealed that inactivation of either codY or ccpA has a pronounced impact on different aspects of staphylococcal physiology and pathogenesis. To determine the contribution and interplay of these two regulators in modulating central metabolism, virulence, and biofilm development, we constructed and characterized the codY ccpA double mutant in S. aureus UAMS-1. In line with previous studies, we found that CcpA and CodY control the cellular metabolic status by altering carbon flux through the central and overflow metabolic pathways. Our results demonstrate that ccpA inactivation impairs biofilm formation and decreases incorporation of extracellular DNA (eDNA) into the biofilm matrix, whereas disrupting codY resulted in a robust structured biofilm tethered together with eDNA and polysaccharide intercellular adhesin (PIA). Interestingly, inactivation of both codY and ccpA decreases biofilm biomass and reduces eDNA release in the double mutant. Compared with the inactivation of codY, the codY ccpA mutant did not overexpress toxins but maintained overexpression of amino acid metabolism pathways. Furthermore, the codY ccpA mutant produced large amounts of PIA, in contrast to the wild-type strain and ccpA mutant. Combined, the results of this study suggest that the coordinated action of CodY and CcpA modulate central metabolism, virulence gene expression, and biofilm-associated genes to optimize growth on preferred carbon sources until starvation sets in. IMPORTANCE Staphylococcus aureus is a leading cause of biofilm-associated infections, including infective endocarditis, worldwide. A greater understanding of metabolic forces driving biofilm formation in S. aureus is essential for the identification of novel therapeutic targets and for the development of new strategies to combat this medically important pathogen. This study characterizes the interplay and regulation of central metabolism and biofilm development by two global transcriptional regulators, CodY and CcpA. We found that the lack of CcpA and/or CodY have different impacts on intracellular metabolic status leading to a formation of morphologically altered biofilms. Overall, the results of this study provide new insights into our understanding of metabolism-mediated regulation of biofilm development in S. aureus.
| S-EPMC9295537 | biostudies-literature
Project description:More than 200 direct CodY target genes in Staphylococcus aureus were identified by genome-wide analysis of in vitro DNA binding. This analysis, which was confirmed for some genes by DNase I footprinting assays, revealed that CodY is a direct regulator of numerous transcription units associated with amino acid biosynthesis, transport of macromolecules and virulence. The virulence genes regulated by CodY fell into three groups. One group was dependent on the Agr system for its expression; these genes were indirectly regulated by CodY through its repression of the agr locus. A second group was regulated directly by CodY. The third group, which includes genes for alpha-toxin and capsule synthesis, was regulated by CodY in two ways, i.e., by direct repression and by repression of the agr locus. Since S. aureus CodY was activated in vitro by the branched chain amino acids and GTP, CodY appears to link changes in intracellular metabolite pools with the induction of numerous adaptive responses, including virulence. Affymetrix GeneChips were used to compare the transcript titers of S. aureus strains UAMS-1 (wild type) and corresponding agr- (strain CM18), codY- (strain MS1), and agr- codY- (strain CM19) isogenic mutant strains during exponential and stationary phase growth. At least two biological replicates were assessed for each strain and each growth phase.
2010-04-13 | E-GEOD-20973 | biostudies-arrayexpress
Project description:Interplay of CodY and CcpA in regulating central metabolism and biofilm formation in Staphylococcus aureus
| PRJNA842676 | ENA
Project description:CodY is a conserved regulator in gram-positive organisms described to repress metabolic genes mainly involved in nitrogen metabolism but also to control the expression of virulence genes in pathogens. We constructed codY gene-replacement mutants in three unrelated S. aureus strains (Newman, UAMS-1, RN1HG). codY mutants grew slower in a chemically defined medium compared to the wild type strains. However, only codY mutants were able to grow in medium lacking threonine. Excess of isoleucine resulted in growth inhibition in the wild type but not in the codY mutants indicating a role of isoleucine for CodY dependent repression of metabolic genes. The prototypic CodY-repressed operon ilvDBCleuABCilvA is preceded by a CodY-binding motif and repressed after up-shift with isoleucine and to a lesser extent guanidine. Transcription of the quorum sensing system agr followed a similar expression pattern. The codY dependent repression of agr is in line with the concomitant influence of CodY on typical agr regulated genes such as cap, spa fnbA and coa. However, transcriptional analysis revealed that most of these virulence genes (e.g. cap, fnbA, spa hla) are also regulated by CodY in an agr negative background. Microarray analysis revealed the large majority of codY-repressed genes are involved in amino-acid transport and metabolism, genes showing codY dependent activation were mainly involved in nucleotide transport and metabolism or virulence. In summary, CodY in S. aureus not only acts as repressor for genes involved in nitrogen metabolism but also contributes to virulence gene regulation by supporting as well as substituting agr function.
2008-11-07 | GSE12340 | GEO
Project description:CodY is a conserved regulator in gram-positive organisms described to repress metabolic genes mainly involved in nitrogen metabolism but also to control the expression of virulence genes in pathogens. We constructed codY gene-replacement mutants in three unrelated S. aureus strains (Newman, UAMS-1, RN1HG). codY mutants grew slower in a chemically defined medium compared to the wild type strains. However, only codY mutants were able to grow in medium lacking threonine. Excess of isoleucine resulted in growth inhibition in the wild type but not in the codY mutants indicating a role of isoleucine for CodY dependent repression of metabolic genes. The prototypic CodY-repressed operon ilvDBCleuABCilvA is preceded by a CodY-binding motif and repressed after up-shift with isoleucine and to a lesser extent guanidine. Transcription of the quorum sensing system agr followed a similar expression pattern. The codY dependent repression of agr is in line with the concomitant influence of CodY on typical agr regulated genes such as cap, spa fnbA and coa. However, transcriptional analysis revealed that most of these virulence genes (e.g. cap, fnbA, spa hla) are also regulated by CodY in an agr negative background. Microarray analysis revealed the large majority of codY-repressed genes are involved in amino-acid transport and metabolism, genes showing codY dependent activation were mainly involved in nucleotide transport and metabolism or virulence. In summary, CodY in S. aureus not only acts as repressor for genes involved in nitrogen metabolism but also contributes to virulence gene regulation by supporting as well as substituting agr function. The microarray was manufactured by in situ synthesis of 10'807 long oligonucleotide probes , selected as previously described (Charbonnier, 2005). It covers >98% of all ORFs annotated in strains N315 and Mu50 , MW2, COL , NCTC8325, USA300 , MRSA252 an MSSA476 including their respective plasmids.
2008-11-06 | E-GEOD-12340 | biostudies-arrayexpress
Project description:More than 200 direct CodY target genes in Staphylococcus aureus were identified by genome-wide analysis of in vitro DNA binding. This analysis, which was confirmed for some genes by DNase I footprinting assays, revealed that CodY is a direct regulator of numerous transcription units associated with amino acid biosynthesis, transport of macromolecules and virulence. The virulence genes regulated by CodY fell into three groups. One group was dependent on the Agr system for its expression; these genes were indirectly regulated by CodY through its repression of the agr locus. A second group was regulated directly by CodY. The third group, which includes genes for alpha-toxin and capsule synthesis, was regulated by CodY in two ways, i.e., by direct repression and by repression of the agr locus. Since S. aureus CodY was activated in vitro by the branched chain amino acids and GTP, CodY appears to link changes in intracellular metabolite pools with the induction of numerous adaptive responses, including virulence.
2010-04-01 | GSE20973 | GEO
Project description:Background The catabolite control protein A (CcpA) is a member of the LacI/GalR family of transcriptional regulators controlling carbon-metabolism pathways in low-GC Gram positive bacteria. It functions as a catabolite repressor or activator, allowing the bacteria to utilize the preferred carbon source over secondary carbon sources. This study is the first CcpA-dependent transcriptome and proteome analysis in S. aureus wild type and ccpA-deleted mutant, focussing on short-time effects of glucose under stable pH conditions. Results The addition of glucose to exponentially growing S. aureus increased enzymes of glycolytic pathway, indicating a higher glycolytic activity, while proteins required for the complete oxidation in the TCA cycle were repressed via CcpA. Phosphotransacetylase and acetate kinase, converting acetylCoA to acetate with a concomitant substrate-level phosphorylation were neither regulated by glucose nor by CcpA. Most CcpA directly repressed genes were involved in utilization of amino acids as secondary carbon sources. More genes were found to be differentially expressed by CcpA in a glucose-independent manner than in the classical, glucose dependent way, suggesting that glucose-independent regulation by CcpA may be of particular importance in S. aureus. In the presence of glucose, CcpA was found to regulate expression of genes involved in metabolism, but that of genes coding for virulence determinants. Conclusions This study identified the CcpA regulon of exponentially growing S. aureus, for the first time. As in other bacteria, the CcpA-regulon of S. aureus comprised a large amount of metabolic genes but also some 50 genes associated with virulence. CcpA seemed to work in a glucose- as well as glucose-independent way.
2008-12-20 | GSE12614 | GEO
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
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