Replication-Transcription Conflicts Generate R-Loops that Orchestrate Bacterial Stress Survival and Pathogenesis

Cell. 2017 Aug 10;170(4):787-799.e18. doi: 10.1016/j.cell.2017.07.044.


Replication-transcription collisions shape genomes, influence evolution, and promote genetic diseases. Although unclear why, head-on transcription (lagging strand genes) is especially disruptive to replication and promotes genomic instability. Here, we find that head-on collisions promote R-loop formation in Bacillus subtilis. We show that pervasive R-loop formation at head-on collision regions completely blocks replication, elevates mutagenesis, and inhibits gene expression. Accordingly, the activity of the R-loop processing enzyme RNase HIII at collision regions is crucial for stress survival in B. subtilis, as many stress response genes are head-on to replication. Remarkably, without RNase HIII, the ability of the intracellular pathogen Listeria monocytogenes to infect and replicate in hosts is weakened significantly, most likely because many virulence genes are head-on to replication. We conclude that the detrimental effects of head-on collisions stem primarily from excessive R-loop formation and that the resolution of these structures is critical for bacterial stress survival and pathogenesis.

Keywords: DNA replication; Listeria; R-loops; RNase H; accelerated evolution; gene orientation; pathogenesis; replication restart; replication-transcription conflicts; stress response.

MeSH terms

  • Animals
  • Bacillus subtilis / physiology*
  • DNA Replication Timing
  • DNA Replication*
  • Female
  • Gene Expression
  • Gene Knockout Techniques
  • Listeria monocytogenes / genetics
  • Listeria monocytogenes / pathogenicity
  • Listeria monocytogenes / physiology*
  • Listeriosis / microbiology
  • Mice
  • Stress, Physiological
  • Transcription, Genetic*
  • Virulence