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Preferential D-loop extension by a translesion DNA polymerase underlies error-prone recombination

Nature Structural & Molecular Biology volume 20, pages 748–755 (2013)Cite this article

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Abstract

Although homologous recombination is considered an accurate form of DNA repair, genetics suggest that the Escherichia coli translesion DNA polymerase IV (Pol IV, also known as DinB) promotes error-prone recombination during stress, which allows cells to overcome adverse conditions. However, how Pol IV functions and is regulated during recombination under stress is unknown. We show that Pol IV is highly proficient in error-prone recombination and is preferentially recruited to displacement loops (D loops) at stress-induced concentrations in vitro. We also found that high-fidelity Pol II switches to exonuclease mode at D loops, which is stimulated by topological stress and reduced deoxyribonucleotide pool concentration during stationary phase. The exonuclease activity of Pol II enables it to compete with Pol IV, which probably 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.

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Figure 1: Pol IV is highly proficient and error prone in recombination-directed replication.
Figure 2: High levels of Pol IV comparable to those in SOS-induced cells facilitate its recruitment to D loops.
Figure 3: Pol II switches to an active exonuclease mode at D loops.
Figure 4: Pol II requires a functional exonuclease domain to compete with Pol IV at D loops.
Figure 5: Levels of Pol IV corresponding to RpoS-induced cells allow it to limit Pol II exonuclease activity at D loops.
Figure 6: Model of translesion DNA polymerase activity at D loops during stress.

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Acknowledgements

We thank M. Skangalis, D. Zhang and O. Yurieva for technical support. This work was supported by the US National Institutes of Health (grants to M.E.O. (GM38839), R.T.P. (K99CA160648) and M.F.G. (GM21422 and ES012259)) and the Howard Hughes Medical Institute.

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  1. Richard T Pomerantz & Isabel Kurth

    Present address: Present addresses: Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania, USA (R.T.P.) and RGenix, Brooklyn, New York, USA (I.K.).,

Authors and Affiliations

  1. The Rockefeller University, Howard Hughes Medical Institute, New York, New York, USA

    Richard T Pomerantz, Isabel Kurth & Mike E O'Donnell

  2. Department of Biological Sciences, University of Southern California, Los Angeles, California, USA

    Myron F Goodman

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R.T.P. conceived the idea for the study, wrote the manuscript and performed and interpreted all experiments, with the exception of those in Figure 3i,j, which were performed by I.K. M.E.O. and M.F.G. provided editorial input.

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Correspondence to Mike E O'Donnell.

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Pomerantz, R., Kurth, I., Goodman, M. et al. Preferential D-loop extension by a translesion DNA polymerase underlies error-prone recombination. Nat Struct Mol Biol 20, 748–755 (2013). https://doi.org/10.1038/nsmb.2573

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