The PcrA/UvrD helicase binds directly to RNA polymerase (RNAP) but the structural basis for this interaction and its functional significance have remained unclear. In this work we used biochemical assays and hydrogen-deuterium exchange coupled to mass spectrometry to study the PcrA-RNAP complex. We find that PcrA binds tightly to a transcription elongation complex in a manner dependent on protein:protein interaction with the conserved PcrA C-terminal Tudor domain. The helicase binds predominantly to two positions on the surface of RNAP. The PcrA C-terminal domain engages a conserved region in a lineage-specific insert within the β subunit which we identify as a helicase interaction motif present in many other PcrA partner proteins, including the nucleotide excision repair factor UvrB. The catalytic core of the helicase binds near the RNA and DNA exit channels and blocking PcrA activity in vivo leads to the accumulation of R-loops. We propose a role for PcrA as an R-loop suppression factor that helps to minimise conflicts between transcription and other processes on DNA including replication.
Bibliographical noteFunding Information:
This work was funded by the European Union via the DNAREPAIRMAN innovative training network (Urrutia-Irazabal, Savery and Dillingham) and by a BBSRC ALERT grant (Ault and Sobott; BB/ M012573/1). We are grateful to Abigail Smith and Gwendolyn Brouwer for helpful discussions, to Harry Thompson for technical assistance with CD measurements, to Kate Heesom and Phil Lewis for technical assistance with TMT-MS, to Peter McGlynn, Heath Murray, Marie-Agnès Petit, Houra Mer-rikh and Christopher Merrikh for advice and the sharing of plasmids and strains used in this work, and to Peter Lewis for generously sharing the co-ordinates of the B. subtilis transcription elongation complex ahead of public release.
© Urrutia-Irazabal et al.