Investigating the Role of DNA Polymerase IV in the Resolution of R‐loops

Abstract

As the replication fork progresses through the DNA template, it may encounter a number of obstacles, one of which is the RNA transcription machinery. This encounter occurs because both processes utilize the same template and because the rate of replication (~1000 nt/s) is much faster than the rate of transcription (40–80 nt/s). The encounter of the two machineries, in either a co‐directional or a head‐on orientation, results in replication‐transcription collisions (RTCs). Failure to resolve these collisions leads to replication fork stalling and eventually cell death. One of the events required to resolve RTCs is the removal of RNA: DNA hybrids, known as R‐loops. In E. coli, RNase H1, coded by rnhA, is a member of a family of highly conserved endonucleases mediating resolution of R‐loops by cleaving the RNA strand on RNA: DNA hybrids. If not resolved, R‐loops cause genomic instability in the form of double‐stranded breaks through the collapse of the replication fork and accumulation of DNA lesions.In E. coli, both replication stalling and accumulation of DNA lesions leads to induction of the SOS response. Among the first genes to be upregulated is dinB, encoding DNA polymerase IV (DinB), becoming the most abundant DNA polymerase in the cell (~2500 nM). DinB main role is to synthesize DNA over template lesions. There is evidence to support the notion that DinB is involved in recombination, a mechanism that is used to repair double‐stranded breaks. In stressful conditions, DinB, due to its abundance, outcompetes other polymerases for the recombination intermediate and synthesizes DNA from it. Because of its abundance during SOS induction and its role in recombination, DinB may also be involved in the resolution of R‐loops. Here, we investigate the possible role of DinB in R‐loop resolution in a rnhA‐deletion strain. Loss of rnhA results in slow growth that is rescued by expression of DinB from a low copy plasmid. This data suggest DinB is multicopy suppressor of the rnhA deletion and that DinB plays a role in the resolution of R‐loops.Support or Funding InformationNational Institute of General Medical Sciences (RO1GM088230 to VG)This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.