Xenogeneic silencing strategies in bacteria are dictated by RNA polymerase promiscuity

David Forrest, Emily A Warman, Amanda M Erkelens, Remus T Dame, David C Grainger

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Horizontal gene transfer facilitates dissemination of favourable traits among bacteria. However, foreign DNA can also reduce host fitness: incoming sequences with a higher AT content than the host genome can misdirect transcription. Xenogeneic silencing proteins counteract this by modulating RNA polymerase binding. In this work, we compare xenogeneic silencing strategies of two distantly related model organisms: Escherichia coli and Bacillus subtilis. In E. coli, silencing is mediated by the H-NS protein that binds extensively across horizontally acquired genes. This prevents spurious non-coding transcription, mostly intragenic in origin. By contrast, binding of the B. subtilis Rok protein is more targeted and mostly silences expression of functional mRNAs. The difference reflects contrasting transcriptional promiscuity in E. coli and B. subtilis, largely attributable to housekeeping RNA polymerase σ factors. Thus, whilst RNA polymerase specificity is key to the xenogeneic silencing strategy of B. subtilis, transcriptional promiscuity must be overcome to silence horizontally acquired DNA in E. coli.

Original languageEnglish
Article number1149
JournalNature Communications
Issue number1
Publication statusPublished - 3 Mar 2022

Bibliographical note

© 2022. The Author(s).


  • Bacillus subtilis/genetics
  • Bacterial Proteins/genetics
  • DNA
  • DNA-Directed RNA Polymerases/genetics
  • Escherichia coli/genetics
  • Gene Expression Regulation, Bacterial
  • Transcription, Genetic


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