High- and low-affinity cre boxes for CcpA binding in Bacillus subtilis revealed by genome-wide analysis

In Bacillus subtilis and its relatives carbon catabolite control, a mechanism enabling to reach maximal efficiency of carbon and energy sources metabolism, is achieved by the global regulator CcpA (carbon catabolite protein A). CcpA in a complex with HPr-Ser-P (seryl-phosphorylated form of histidine...

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Published in:	BMC genomics Vol. 13; no. 1; p. 401
Main Authors:	Marciniak, Bogumiła C, Pabijaniak, Monika, de Jong, Anne, Dűhring, Robert, Seidel, Gerald, Hillen, Wolfgang, Kuipers, Oscar P
Format:	Journal Article
Language:	English
Published:	England BioMed Central Ltd 17-08-2012 BioMed Central BMC
Subjects:	Analysis Bacillus subtilis Bacillus subtilis - genetics Bacillus subtilis - metabolism Bacterial genetics Bacterial Proteins - metabolism Bacteriology Binding Sites Carbon Carbon catabolite protein A Carbon sources Catabolite responsive elements (cre) affinity Catabolites CcpA Cell culture Chromosomes Conserved sequence Cre box motif Energy metabolism Gene expression Gene Expression Regulation, Bacterial Genes Genetic aspects Genetic research Genome, Bacterial - genetics Genome-Wide Association Study Genomics Histidine Kinases Microbiology Operons Physiological aspects Promoters Protein binding Protein turnover Proteins Regulatory sequences Transcription United States
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Summary:	In Bacillus subtilis and its relatives carbon catabolite control, a mechanism enabling to reach maximal efficiency of carbon and energy sources metabolism, is achieved by the global regulator CcpA (carbon catabolite protein A). CcpA in a complex with HPr-Ser-P (seryl-phosphorylated form of histidine-containing protein, HPr) binds to operator sites called catabolite responsive elements, cre. Depending on the cre box position relative to the promoter, the CcpA/HPr-Ser-P complex can either act as a positive or a negative regulator. The cre boxes are highly degenerate semi-palindromes with a lowly conserved consensus sequence. So far, studies aimed at revealing how CcpA can bind such diverse sites were focused on the analysis of single cre boxes. In this study, a genome-wide analysis of cre sites was performed in order to identify differences in cre sequence and position, which determine their binding affinity. The transcriptomes of B. subtilis cultures with three different CcpA expression levels were compared. The higher the amount of CcpA in the cells, the more operons possessing cre sites were differentially regulated. The cre boxes that mediated regulation at low CcpA levels were designated as strong (high affinity) and those which responded only to high amounts of CcpA, as weak (low affinity). Differences in the sequence and position in relation to the transcription start site between strong and weak cre boxes were revealed. Certain residues at specific positions in the cre box as well as, to a certain extent, a more palindromic nature of cre sequences and the location of cre in close vicinity to the transcription start site contribute to the strength of CcpA-dependent regulation. The main factors contributing to cre regulatory efficiencies, enabling subtle differential control of various subregulons of the CcpA regulon, are identified.
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ISSN:	1471-2164 1471-2164
DOI:	10.1186/1471-2164-13-401