Preferential D-loop Extension by a Translesion DNA Polymerase Underlies Error-Prone Recombination

Although homologous recombination (HR) is considered an accurate form of DNA repair, genetics suggest that Escherichia coli (E. coli) translesion DNA polymerase (pol) IV (DinB) promotes error-prone recombination during stress which allows cells to overcome adverse conditions. How pol IV functions and is regulated during recombination under stress, however, is unknown. We show that pol IV is highly proficient in error-prone recombination, and is preferentially recruited to D-loops at stress-induced concentrations in vitro. Unexpectedly, we find that high-fidelity pol II switches to exonuclease mode at D-loops which is stimulated by topological stress and reduced deoxy-ribonucleotide pools observed during stationary-phase. The exonuclease activity of pol II enables it to compete with pol IV which likely suppresses error-prone recombination. These findings indicate that preferential D-loop extension by pol IV facilitates error-prone recombination and explain how pol II reduces such errors in vivo. Homologous recombination (HR) repairs double-strand breaks (DSBs) by directing replication to copy sequence information from a homologous donor (Fig. 1a)1–4. For example, following formation of a DSB, nucleases resect the DNA resulting in a 3 ’ single-strand DNA (ssDNA) tail. RecA type recombinases form a filament along the tail whic