Genome-wide binding profiles of the Bacillus subtilis transition state regulator AbrB and its homolog Abh reveals their interactive role in transcriptional regulation

Nucleic Acids Res. 2011 Jan;39(2):414-28. doi: 10.1093/nar/gkq780. Epub 2010 Sep 3.

Abstract

AbrB is a global transcriptional regulator of Bacillus subtilis that represses the expression of many genes during exponential growth. Here, we demonstrate that AbrB and its homolog Abh bind to hundreds of sites throughout the entire B. subtilis genome during exponential growth. Comparison of regional binding of AbrB and Abh in wild-type, ΔabrB and Δabh backgrounds revealed that they bind as homomer and/or heteromer forms with different specificities and affinities. We found four AbrB and Abh binding patterns were major. Three of these contain pairs of TGGNA motifs connected by A/T-rich sequences, differing in arrangement and spacing. We also assessed the direct involvement of these complexes in the control of gene expression. Our data indicate that AbrB usually acts as a repressor, and that the ability of Abh to act as a transcriptional regulator was limited. We found that changes to AbrB/Abh levels affect their binding at several promoters and consequently transcriptional regulation. Surprisingly, most AbrB/Abh binding events had no impact on transcription, suggesting an interesting possibility that AbrB/Abh binding is analogous to nucleoid-associated protein binding in Escherichia coli.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacillus subtilis / genetics*
  • Bacillus subtilis / metabolism
  • Bacterial Proteins / metabolism*
  • Base Sequence
  • Binding Sites
  • Consensus Sequence
  • DNA-Binding Proteins / metabolism*
  • Dimerization
  • Gene Expression Regulation, Bacterial*
  • Genome, Bacterial
  • Protein Binding
  • Transcription Factors / metabolism*
  • Transcription, Genetic*

Substances

  • AbrB protein, Bacillus subtilis
  • Bacterial Proteins
  • DNA-Binding Proteins
  • Transcription Factors