Specificity of the DNA mismatch repair system (MMR) and mutagenesis bias in bacteria

Hongan Long, Samuel F. Miller, Emily Williams, Michael Lynch

Research output: Contribution to journalArticlepeer-review

29 Scopus citations


The mutation rate of an organism is influenced by the interaction of evolutionary forces such as natural selection and genetic drift. However, the mutation spectrum (i.e., the frequency distribution of different types of mutations) can be heavily influenced by DNA repair. Using mutation-accumulation lines of the extremophile bacterium Deinococcus radiodurans DmutS1 and the model soil bacterium Pseudomonas fluorescens wild-type and MMR (Methyl-dependent Mismatch Repair-deficient) strains, we report the mutational features of these two important bacteria. We find that P. fluorescens has one of the highest MMR repair efficiencies among tested bacteria. We also discover that MMR of D. radiodurans preferentially repairs deletions, contrary to all other bacteria examined. We then, for the first time, quantify genome-wide efficiency and specificity of MMR in repairing different genomic regions and mutation types, by evaluating the P. fluorescens and D. radiodurans mutation data sets, along with previously reported ones of Bacillus subtilis subsp. subtilis, Escherichia coli, Vibrio cholerae, and V. fischeri. MMR in all six bacteria shares two general features: 1) repair efficiency is influenced by the neighboring base composition for both transitions and transversions, not limited to transversions as previously reported; and 2) MMR only recognizes indels <4 bp in length. This study demonstrates the power of mutation accumulation lines in quantifying DNA repair and mutagenesis patterns.

Original languageEnglish (US)
Pages (from-to)2414-2421
Number of pages8
JournalMolecular biology and evolution
Issue number10
StatePublished - Oct 1 2018


  • DNA mismatch repair
  • Mutation rate and spectrum
  • Neutral evolution
  • Spontaneous mutation

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics


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