Transcriptional analysis of Bacillus cereus ATCC 14579 and its ccpA deletion strain grown with and without glucose
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ABSTRACT:
ORGANISM(S): Bacillus cereus ATCC 14579
PROVIDER: GSE20057 | GEO | 2015/01/05
SECONDARY ACCESSION(S): PRJNA124327
REPOSITORIES: GEO
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Project description:In Bacillus cereus the catabolite control protein CcpA was shown to be involved in optimizing the efficiency of glucose catabolism by activating genes encoding glycolytic enzymes including a non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase that mediates conversion of D-glyceraldehyde 3-phosphate to 3-phospho-D-glycerate in one single step, and by repressing genes encoding the citric acid cycle and gluconeogenic enzymes. Two B. cereus-specific CcpA-regulated operons were identified, encoding enzymes involved in the catabolism of fuculose/arabinose and aspartate. In addition, a genome search using the CRE-site consensus predicted the B. cereus CcpA regulon to include 10 PTS-system gene clusters as well as genes coding for overflow metabolic enzymes leading to acetoin and acetate. Notably, catabolite repression of the genes encoding non-hemolytic enterotoxin (Nhe) and hemolytic (Hbl) enterotoxin appeared CcpA-dependent, and for the corresponding enterotoxin operons, putative CRE-sites were identified. This points to metabolic control of enterotoxin gene expression and suggests that CcpA-mediated glucose sensing provides an additional mode of control to PlcR activated expression of nhe and hbl genes in B. cereus. Keywords: Time course analysis by comparing transriptomes of the wildtype and the ccpA deleton strain. The wildtype (B. cereus ATCC 14579) and ccpA deletion strain were sampled during aerobic growth in Brain heart infusion broth. Samples of wildtype and ccpA deletion strain were compared at 4 time points, i.e. early exponential (OD600 0.2), mid-exponential (OD600 0.8), transition phase (OD600 4), and stationary phase (OD600 8). For each time point biological duplo's were obtained, which were subsequently differently labelled to perform a dye swap.
2010-05-25 | E-GEOD-7843 | biostudies-arrayexpress
Project description:In Bacillus cereus the catabolite control protein CcpA was shown to be involved in optimizing the efficiency of glucose catabolism by activating genes encoding glycolytic enzymes including a non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase that mediates conversion of D-glyceraldehyde 3-phosphate to 3-phospho-D-glycerate in one single step, and by repressing genes encoding the citric acid cycle and gluconeogenic enzymes. Two B. cereus-specific CcpA-regulated operons were identified, encoding enzymes involved in the catabolism of fuculose/arabinose and aspartate. In addition, a genome search using the CRE-site consensus predicted the B. cereus CcpA regulon to include 10 PTS-system gene clusters as well as genes coding for overflow metabolic enzymes leading to acetoin and acetate. Notably, catabolite repression of the genes encoding non-hemolytic enterotoxin (Nhe) and hemolytic (Hbl) enterotoxin appeared CcpA-dependent, and for the corresponding enterotoxin operons, putative CRE-sites were identified. This points to metabolic control of enterotoxin gene expression and suggests that CcpA-mediated glucose sensing provides an additional mode of control to PlcR activated expression of nhe and hbl genes in B. cereus. Keywords: Time course analysis by comparing transriptomes of the wildtype and the ccpA deleton strain.
2008-03-28 | GSE7843 | 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:Transcriptional analysis of Bacillus cereus ATCC 14579 and its ccpA deletion strain grown with and without glucose
| PRJNA124327 | ENA
Project description:CcpA is a global regulator of transcription in Gram-positive bacteria that controls gene expression in response to carbohydrate availability. Using the fructan hydrolase (fruA) gene of S. mutans as a model, we demonstrate that CcpA does indeed play a major role in carbohydrate catabolite repression. Using DNA microarrays, the expression of at least 170 genes differed in CcpA-deficient cells compared to the parental strains when cells are grown in the presence of glucose, but only 90 genes showed altered expression when cells were cultivated in the poorly-repressing substrate galactose. Interestingly, 90 genes were differently expressed in wild-type S. mutans in response to cultivation in glucose versus galactose, but the expression of over 500 genes was altered when growth in glucose and galactose were compared in the CcpA-deficient strain. The results support a major role for CcpA in regulation of gene expression, but reveal that a substantial CcpA-independent network exists in S. mutans to regulate gene expression in response to carbohydrate source. Keywords: Catabolite repression, sugar transport, biofilm, virulence, stress response
2008-05-01 | GSE8850 | 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. The transcriptomes of strain Newman and its isogenic ccpA-deleted mutant were determined in early exponential growth and 30 min after the addition of 10 mM glucose, under controlled pH conditions. In the absence of glucose, the wild type grew slightly faster than the mutant, reaching an OD600 of 1 approximately 20 min earlier than the mutant. Adding 10 mM glucose at OD600 1 increased the growth rate of the wild type but had only a minor effect on that of the mutant. 60 min after glucose addition, glucose was depleted down to 0.3 mM by the wild type, while still 3 mM glucose was left in the culture of the mutant. Despite increased glucose consumption rates in the wild type, acetate production was only slightly enhanced compared to the mutant. No lactate was excreted at any time point sampled. Acidification of the medium upon glucose metabolism was prevented by buffering, maintaining a pH of 7.5 for both strains and under both growth conditions for at least 2 h after glucose addition, allowing to rule out any pH effects.
2010-06-24 | E-GEOD-12614 | biostudies-arrayexpress
Project description:The Bacillus cereus ATCC 14579 alternative σ factor σZ and its putative regulon have been characterized. σZ shows overall similarity with ECF σ factors and sigZ constitutes an operon together with asfZ encoding its putative anti-σ factor. Expression analysis revealed sigZ to be induced by an array of stresses, including exposure to ethanol, alkaline pH and heat shock, and a typical promoter binding site for the sigZ-operon was identified by 5’RACE. Phenotypic characterization of B. cereus ATCC 14579 and its sigZ-deletion strain revealed diminished growth performance and sporulation capacity. The σZ-regulon was successfully established by transcriptome analysis of a nisin inducible sigZ-overexpression strain. Overexpression of sigZ was shown to affect expression of 42 genes, including 33 genes encoding proteins located in the extracytoplasm. The identified σZ regulon contained genes encoding proteins situated in the extracytoplasm involved in cell surface modifications and transport. The regulation of genes encoding cell surface modification proteins implies σZ to be involved in the regulation of interaction of B. cereus ATCC 14579 with its environments, which includes human intestinal cells, possibly influencing its virulence status. Keywords: Comparative transcriptome study
2008-05-11 | GSE9860 | GEO
Project description:Assessment of CcpA-mediated catabolite control of metabolism and enterotoxin production in Bacillus cereus ATCC 14579
| PRJNA99971 | ENA
Project description:The stress response of B. cereus ATCC 14579 is monitored true time, showing an enormous response in gene expression. Keywords: Stress response, comparative transcriptome analysis.
2008-05-11 | GSE9855 | GEO
Project description:Comparison of the B cereus codY deletion mutant with wild type strain (ATCC 14579)
2012-07-05 | GSE31017 | GEO