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The Evolution of RecD Outside of the RecBCD Complex

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Abstract

The common understanding of the function of RecD, as derived predominantly from studies in Escherichia coli, is that RecD is one of three enzymes in the RecBCD double-stranded break repair DNA recombination complex. However, comparative genomics has revealed that many organisms possess a recD gene even though the other members of the complex, recB and recC, are not present. Further, bioinformatic analyses have shown that there is substantial sequence dissimilarity between recD genes associated with recB and recC (recD1), and those that are not associated with recBC (recD2). Deinococcus radiodurans, known for its extraordinary DNA repair capability, is one such organism that does not possess either recB or recC, and yet does possess a recD gene. The recD of D. radiodurans was deleted and this mutant was shown to have a capacity to repair double-stranded DNA breaks equivalent to wild-type. The phylogenetic history of recD was studied using a dataset of 120 recD genes from 91 fully sequenced species. The analysis focused upon the role of gene duplication and functional genomic context in the evolution of recD2, which appears to have undergone numerous independent events resulting in duplicate recD2 genes. The role of RecD as part of the RecBCD complex appears to have a divergence from an earlier ancestral RecD function still preserved in many species including D. radiodurans.

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Acknowledgments

This research was supported by the Office of Science (BER), U.S. Department of Energy, Grant No. DE-FC02-02ER63453. We graciously acknowledge Dr. John Battista and Dr. Mary Lidstrom for generously providing reagents. We thank Mr. Jim Puhl of NIST for his help with the ionizing radiation experiments. We are grateful to members of the Synthetic Biology group at the J. Craig Venter Institute, especially Dr. John Glass, Dr. Chuck Merryman and Ms. Cindi Pfannkoch for stimulating discussions. We thank Mikkel Algire and Radha Krishnakumar for critical reading of this manuscript. We thank Jonathan Badger for his phylipFasta script and general help and advice on constructing a recD phylogeny.

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Authors and Affiliations

  1. J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, 20850, USA

    Michael Montague, Ray-Yuan Chuang & Sanjay Vashee

  2. NuPotential Inc, Baton Rouge, LA, 70803, USA

    Christian Barnes

  3. J. Craig Venter Institute, San Diego, CA, 92121, USA

    Hamilton O. Smith

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  1. Michael Montague
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  2. Christian Barnes
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  3. Hamilton O. Smith
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  4. Ray-Yuan Chuang
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  5. Sanjay Vashee
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Correspondence to Ray-Yuan Chuang or Sanjay Vashee.

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Montague, M., Barnes, C., Smith, H.O. et al. The Evolution of RecD Outside of the RecBCD Complex. J Mol Evol 69, 360–371 (2009). https://doi.org/10.1007/s00239-009-9290-x

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