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

Kevin S. Lang, Ashley N. Hall, Christopher N. Merrikh, Mark Ragheb, Hannah Tabakh, Alex J. Pollock, Joshua J. Woodward, Julia E. Dreifus, Houra Merrikh

Research output: Contribution to journalArticlepeer-review

126 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)787-799.e18
Issue number4
StatePublished - Aug 10 2017
Externally publishedYes

Bibliographical note

Funding Information:
We would like to thank the members of the Merrikh lab for helpful discussions and Richard Losick for his generous gift of the Pspank(hy)-luxABCDE plasmid, pAH60. We thank Bonny Brewer for helpful discussions about the analysis of 2D gels. We thank Jay Shendure and Choli Lee for assistance in sequencing the DRIP-seq libraries. Finally, a special thank you to Sarah Mangiameli for performing the fluctuation tests on the mutation rate data. This work was supported by the Cell and Molecular Biology Training Grant T32 GM 007270 to A.N.H., the National Institutes of Health grants AI116669 and AI108698 and the Pew Scholars Program in the Biomedical Sciences to J.J.W. as well as the National Institute of Health New Innovator Award (DP2GM110773) and National Science Foundation grant MCB1243492 to H.M.

Publisher Copyright:
© 2017 Elsevier Inc.


  • DNA replication
  • Listeria
  • R-loops
  • RNase H
  • accelerated evolution
  • gene orientation
  • pathogenesis
  • replication restart
  • replication-transcription conflicts
  • stress response


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