RNase J1 is the major 5'-to-3' bacterial exoribonuclease. We demonstrate that in its absence, RNA polymerases (RNAPs) are redistributed on DNA, with increased RNAP occupancy on some genes without a parallel increase in transcriptional output. This suggests that some of these RNAPs represent stalled, non-transcribing complexes. We show that RNase J1 is able to resolve these stalled RNAP complexes by a "torpedo" mechanism, whereby RNase J1 degrades the nascent RNA and causes the transcription complex to disassemble upon collision with RNAP. A heterologous enzyme, yeast Xrn1 (5'-to-3' exonuclease), is less efficient than RNase J1 in resolving stalled Bacillus subtilis RNAP, suggesting that the effect is RNase-specific. Our results thus reveal a novel general principle, whereby an RNase can participate in genome-wide surveillance of stalled RNAP complexes, preventing potentially deleterious transcription-replication collisions.

Department of Cell Biology Faculty of Science Charles University Prague Czech Republic

Division of Biomolecular Physics Institute of Physics Charles University Prague 2 Czech Republic

Institute of Microbiology of the Czech Academy of Sciences Prague 4 Czech Republic

UMR8261 CNRS Université de Paris Institut de Biologie Physico Chimique Paris France

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EMBO J. 2020 Feb 3;39(3):e104112. doi: 10.15252/embj.2019104112. PubMed

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