A degenerate tripartite DNA-binding site required for activation of ComA-dependent quorum response gene expression in Bacillus subtilis

J Mol Biol. 2008 Aug 29;381(2):261-75. doi: 10.1016/j.jmb.2008.06.035. Epub 2008 Jun 18.


In Bacillus subtilis, the transcription factor ComA activates several biological processes in response to increasing population density. Extracellular peptide signaling is used to coordinate the activity of ComA with population density. At low culture densities, when the concentration of signaling peptides is lowest, ComA is largely inactive. At higher densities, when the concentration of signaling peptides is higher, ComA is active and activates the transcription of at least nine operons involved in the development of competence and in the production of degradative enzymes and antibiotics. We found that ComA binds a degenerate tripartite sequence consisting of three DNA-binding determinants or "recognition elements." Mutational analyses showed that all three recognition elements are required for transcription activation in vivo and for specific DNA binding by ComA in vitro. Degeneracy of the recognition elements in the ComA-binding site is an important regulatory feature for coordinating transcription with population density (i.e., promoters containing an optimized binding site have high activity at low culture density and are no longer regulated in the normal-density-dependent manner). We found that purified ComA forms a dimer in solution, and we propose a model for how two dimers of ComA bind to an odd number of DNA-binding determinants to activate transcription of target genes. This DNA-protein architecture for transcription activation appears to be conserved for ComA homologs in other Bacillus species.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Bacillus subtilis / genetics
  • Bacillus subtilis / metabolism*
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism*
  • Base Sequence
  • Binding Sites / genetics
  • DNA, Bacterial / genetics
  • DNA, Bacterial / metabolism*
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism*
  • Dimerization
  • Electrophoretic Mobility Shift Assay
  • Gene Expression Regulation, Bacterial
  • Peptide Synthases / genetics
  • Peptide Synthases / metabolism
  • Phosphoprotein Phosphatases / genetics
  • Phosphoprotein Phosphatases / metabolism
  • Promoter Regions, Genetic / genetics
  • Protein Binding
  • Quorum Sensing / genetics*
  • Sequence Analysis, DNA
  • Transcription, Genetic
  • Transcriptional Activation


  • Bacterial Proteins
  • ComA protein, Bacteria
  • DNA, Bacterial
  • DNA-Binding Proteins
  • rapA protein, Bacillus subtilis
  • Phosphoprotein Phosphatases
  • Peptide Synthases
  • surfactin synthetase