Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis

Science. 2012 Mar 2;335(6072):1103-6. doi: 10.1126/science.1206848.


Bacteria adapt to environmental stimuli by adjusting their transcriptomes in a complex manner, the full potential of which has yet to be established for any individual bacterial species. Here, we report the transcriptomes of Bacillus subtilis exposed to a wide range of environmental and nutritional conditions that the organism might encounter in nature. We comprehensively mapped transcription units (TUs) and grouped 2935 promoters into regulons controlled by various RNA polymerase sigma factors, accounting for ~66% of the observed variance in transcriptional activity. This global classification of promoters and detailed description of TUs revealed that a large proportion of the detected antisense RNAs arose from potentially spurious transcription initiation by alternative sigma factors and from imperfect control of transcription termination.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptation, Physiological
  • Algorithms
  • Bacillus subtilis / genetics*
  • Bacillus subtilis / physiology*
  • Binding Sites
  • Gene Expression Profiling
  • Gene Expression Regulation, Bacterial*
  • Gene Regulatory Networks
  • Oligonucleotide Array Sequence Analysis
  • Promoter Regions, Genetic*
  • RNA, Antisense / genetics
  • RNA, Antisense / metabolism
  • RNA, Bacterial / genetics
  • RNA, Bacterial / metabolism
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Regulon
  • Sigma Factor / metabolism
  • Terminator Regions, Genetic
  • Transcription, Genetic*
  • Transcriptome*


  • RNA, Antisense
  • RNA, Bacterial
  • RNA, Messenger
  • Sigma Factor

Associated data

  • GEO/GSE27219
  • GEO/GSE27303
  • GEO/GSE27419
  • GEO/GSE27652