The rate and spectrum of spontaneous mutations in Mycobacterium smegmatis, a bacterium naturally devoid of the postreplicative mismatch repair pathway

Sibel Kucukyildirim, Hongan Long, Way Sung, Samuel F. Miller, Thomas G. Doak, Michael Lynch

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)2157-2163
Number of pages7
JournalG3: Genes, Genomes, Genetics
Volume6
Issue number7
DOIs
StatePublished - Jul 1 2016
Externally publishedYes

Fingerprint

Mycobacterium smegmatis
DNA Mismatch Repair
Mutation Rate
Bacteria
Mutation
Genome
Histidinol-Phosphatase
Site-Specific DNA-Methyltransferase (Adenine-Specific)
Uracil-DNA Glycosidase
Deamination
DNA
DNA-Directed DNA Polymerase
Methylation
DNA Damage

Keywords

  • GC bias
  • Mutation accumulation
  • Mycobacteria

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Genetics(clinical)

Cite this

The rate and spectrum of spontaneous mutations in Mycobacterium smegmatis, a bacterium naturally devoid of the postreplicative mismatch repair pathway. / Kucukyildirim, Sibel; Long, Hongan; Sung, Way; Miller, Samuel F.; Doak, Thomas G.; Lynch, Michael.

In: G3: Genes, Genomes, Genetics, Vol. 6, No. 7, 01.07.2016, p. 2157-2163.

Research output: Contribution to journalArticle

Kucukyildirim, Sibel ; Long, Hongan ; Sung, Way ; Miller, Samuel F. ; Doak, Thomas G. ; Lynch, Michael. / The rate and spectrum of spontaneous mutations in Mycobacterium smegmatis, a bacterium naturally devoid of the postreplicative mismatch repair pathway. In: G3: Genes, Genomes, Genetics. 2016 ; Vol. 6, No. 7. pp. 2157-2163.
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