TY - JOUR
T1 - The rate and spectrum of spontaneous mutations in Mycobacterium smegmatis, a bacterium naturally devoid of the postreplicative mismatch repair pathway
AU - Kucukyildirim, Sibel
AU - Long, Hongan
AU - Sung, Way
AU - Miller, Samuel F.
AU - Doak, Thomas G.
AU - Lynch, Michael
N1 - Funding Information:
We thank Emily Williams for helpful technical support. This research was supported by a Multidisciplinary University Research Initiative award (W911NF-09-1-0444) from the US Army Research Office and a National Institutes of Health (NIH) grant (GM036827) to M.L.
Publisher Copyright:
© 2016 Kucukyildirim et al.
PY - 2016/7/1
Y1 - 2016/7/1
N2 - Mycobacterium smegmatis is a bacterium that is naturally devoid of known postreplicative DNA mismatch repair (MMR) homologs, mutS and mutL, providing an opportunity to investigate how the mutation rate and spectrum has evolved in the absence of a highly conserved primary repair pathway. Mutation accumulation experiments of M. smegmatis yielded a base-substitution mutation rate of 5.27 × 10-10 per site per generation, or 0.0036 per genome per generation, which is surprisingly similar to the mutation rate in MMRfunctional unicellular organisms. Transitions were found more frequently than transversions, with the A:T/G:C transition rate significantly higher than the G:C→A:T transition rate, opposite to what is observed in most studied bacteria.We also found that the transition-mutation rate of M. smegmatis is significantly lower than that of other naturally MMR-devoid or MMR-knockout organisms. Two possible candidates that could be responsible for maintaining high DNA fidelity in this MMR-deficient organism are the ancestral-like DNA polymerase DnaE1, which contains a highly efficient DNA proofreading histidinol phosphatase (PHP) domain, and/or the existence of a uracil-DNA glycosylase B (UdgB) homolog that might protect the GC-rich M. smegmatis genome against DNA damage arising from oxidation or deamination. Our results suggest that M. smegmatis has a noncanonical Dam (DNA adenine methylase) methylation system, with target motifs differing from those previously reported. The mutation features of M. smegmatis provide further evidence that genomes harbor alternative routes for improving replication fidelity, even in the absence of major repair pathways.
AB - Mycobacterium smegmatis is a bacterium that is naturally devoid of known postreplicative DNA mismatch repair (MMR) homologs, mutS and mutL, providing an opportunity to investigate how the mutation rate and spectrum has evolved in the absence of a highly conserved primary repair pathway. Mutation accumulation experiments of M. smegmatis yielded a base-substitution mutation rate of 5.27 × 10-10 per site per generation, or 0.0036 per genome per generation, which is surprisingly similar to the mutation rate in MMRfunctional unicellular organisms. Transitions were found more frequently than transversions, with the A:T/G:C transition rate significantly higher than the G:C→A:T transition rate, opposite to what is observed in most studied bacteria.We also found that the transition-mutation rate of M. smegmatis is significantly lower than that of other naturally MMR-devoid or MMR-knockout organisms. Two possible candidates that could be responsible for maintaining high DNA fidelity in this MMR-deficient organism are the ancestral-like DNA polymerase DnaE1, which contains a highly efficient DNA proofreading histidinol phosphatase (PHP) domain, and/or the existence of a uracil-DNA glycosylase B (UdgB) homolog that might protect the GC-rich M. smegmatis genome against DNA damage arising from oxidation or deamination. Our results suggest that M. smegmatis has a noncanonical Dam (DNA adenine methylase) methylation system, with target motifs differing from those previously reported. The mutation features of M. smegmatis provide further evidence that genomes harbor alternative routes for improving replication fidelity, even in the absence of major repair pathways.
KW - GC bias
KW - Mutation accumulation
KW - Mycobacteria
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U2 - 10.1534/g3.116.030130
DO - 10.1534/g3.116.030130
M3 - Article
C2 - 27194804
AN - SCOPUS:84978422201
SN - 2160-1836
VL - 6
SP - 2157
EP - 2163
JO - G3: Genes, Genomes, Genetics
JF - G3: Genes, Genomes, Genetics
IS - 7
ER -