TY - JOUR
T1 - Specificity of the DNA mismatch repair system (MMR) and mutagenesis bias in bacteria
AU - Long, Hongan
AU - Miller, Samuel F.
AU - Williams, Emily
AU - Lynch, Michael
N1 - Publisher Copyright:
© 2018 Oxford University Press. All Rights Reserved.
PY - 2018/10/1
Y1 - 2018/10/1
N2 - 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.
AB - 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.
KW - DNA mismatch repair
KW - Mutation rate and spectrum
KW - Neutral evolution
KW - Spontaneous mutation
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U2 - 10.1093/molbev/msy134
DO - 10.1093/molbev/msy134
M3 - Article
C2 - 29939310
AN - SCOPUS:85054978614
SN - 0737-4038
VL - 35
SP - 2414
EP - 2421
JO - Molecular biology and evolution
JF - Molecular biology and evolution
IS - 10
ER -