Open Access Research article

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

Bogumiła C Marciniak1, Monika Pabijaniak1, Anne de Jong1, Robert Dűhring2, Gerald Seidel2, Wolfgang Hillen2 and Oscar P Kuipers13*

Author Affiliations

1 Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, Centrum voor Levenswetenschappen, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands

2 Lehrstuhl für Microbiologie, Institut für Biologie der Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany

3 Kluyver Center for Genomics of Industrial Fermentation, Delft/Groningen, The Netherlands

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BMC Genomics 2012, 13:401  doi:10.1186/1471-2164-13-401

Published: 17 August 2012

Additional files

Additional file 1:

Gene expression fold changes "CcpA induction" vs "no CcpA induction". Expression fold changes in three microarrays experiments with low, medium and high CcpA expression induction. Activated genes - positive values, repressed genes - negative values.

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Additional file 2:

Cre boxes predicted in the Bacillus subtilis genome using Genome2D software and 8.96 calculated cutoff.

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Additional file 3:

Cre boxes predicted with Genome2D software using cutoff 8.96 and found in upper and lower strand within −500 and +100 nucleotides from the start codon of the first gene of operon.

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Additional file 4:

List of significantly regulated first genes of operons (1.8 < fold change < −1.8) with cre boxes within −500 and +100 nucleotides from start codon. Significant fold changes are shown in bold. cre box to start codon and transcriptional start site (TSS) distances are calculated from conserved G residue in the middle of cre box to first nucleotide of start codon and to TSS, respectively. For cre box affinity determination criteria see main text.

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Additional file 5:

First genes of operons with cre sites. Start codon and further coding sequences are shown in lowercase and intergenic regions in uppercase. Underlined – predicted cre boxes, bold – cre boxes known from the literature, solid box – promoter known from the literature, dotted box – predicted promoter, dark grey shadow - transcriptional start site (TSS) known from the literature, light grey shadow – predicted TSS.

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