Paper

Transcriptome Analysis of Temporal Regulation of Carbon Metabolism by CcpA in Bacillus subtilis Reveals Additional Target Genes
Andrzej T. Lulko, Girbe Buist, Jan Kok, Oscar P. Kuipers

Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands

Address of Corresponding Author

J Mol Microbiol Biotechnol 2007;12:82-95 (DOI: 10.1159/000096463)

  Key Words

• CcpA
• CCR
• CCA
• cre
• DNA microarrays
• Time series
• Bacillus subtilis
• man
• opu
• yhb

  Abstract

The pleiotropic regulator of carbon metabolism in Gram-positive bacteria, CcpA, regulates gene expression by binding to so-called cre elements, which are located either upstream or in promoter regions, or in open-reading frames. In this study we compared the transcriptomes of Bacillus subtilis 168 and its ccpA deletion mutant during growth in glucose-containing rich medium. Although growth was similar, glucose was completely consumed by the wild-type strain in the stationary phase, while it was still present in the culture of the mutant. At that stage, direct and indirect effects on gene expression were observed. During exponential growth, CcpA mainly influences the carbohydrate and energy metabolism, whereas from transition phase onwards its function expands on a broader range of physiological processes including nucleotide metabolism, cell motility and protein synthesis. A genome wide search revealednew putative cre sites, which could function in vivo according to our transcriptome data. Comparison of our data with published transcriptome data of ccpA mutant analysis in the exponential growth phase confirmed earlier identified CcpA regulon members. It also allowed identification of potential new CcpA-repressed genes, amongst others ycgN and the ydh operon. Novel activated members include opuE andthe opuAABC, yhb and man operons, which all have a putative cre site that appears to be dependent on helical topology. A comparative analysis of these genes with the known activated genes i.e.ackA and pta revealed the presence of a possible upstream activating region (UAR) as has been shown to be functional for the activation of ackA. The data suggest that at later growth phases CcpA may regulate gene expression by itself or complexed with other, yet unknown cofactors.

Copyright © 2007 S. Karger AG, Basel

  Author Contacts

Oscar P. Kuipers
Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30
NL-9751 NN Haren (The Netherlands)
Tel. +31 50 363 2093, Fax +31 50 363 2348, E-Mail o.p.kuipers@rug.nl

  Article Information

The supplementary tables and graphs mentioned in this article as well as the slide images and raw data are available from http://molgen.biol.rug.nl/publication/ccpa_bsub_data/

Number of Print Pages : 14
Number of Figures : 6, Number of Tables : 1, Number of References : 57