title: The Rate and Spectrum of Spontaneous Mutations in Mycobacterium smegmatis, a Bacterium Naturally Devoid of the Postreplicative Mismatch Repair Pathway.
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 MMR-functional 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.
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405 Department of Biology, Hacettepe University, Ankara, 06800 Turkey sibelkucukyildirim@gmail.com.
authors.forename: Sibel
authors.initials: S
authors.lastname: Kucukyildirim
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405.
authors.forename: Hongan
authors.initials: H
authors.lastname: Long
authors.affiliation: Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, North Carolina, 28223.
authors.forename: Way
authors.initials: W
authors.lastname: Sung
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405.
authors.forename: Samuel F
authors.initials: SF
authors.lastname: Miller
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405 National Center for Genome Analysis Support, Indiana University, Bloomington, Indiana 47405.
authors.forename: Thomas G
authors.initials: TG
authors.lastname: Doak
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405.
authors.forename: Michael
authors.initials: M
authors.lastname: Lynch
mesh_terms: D004249:DNA Damage; D053843:DNA Mismatch Repair; D004258:DNA Polymerase III / Q000235:genetics / Q000378:metabolism; D004260:DNA Repair; D004261:DNA Replication; D004269:DNA, Bacterial / Q000235:genetics* / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D059645:Mutation Rate; D020102:Mycobacterium smegmatis / Q000235:genetics* / Q000378:metabolism; D017354:Point Mutation; D000072417:Protein Domains; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific) / Q000235:genetics / Q000378:metabolism; D051981:Uracil-DNA Glycosidase / Q000235:genetics / Q000378:metabolism
chemical_list: D004269:DNA, Bacterial; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific); C074904:DNA polymerase III, alpha subunit; D004258:DNA Polymerase III; D051981:Uracil-DNA Glycosidase
keywords: GC bias; Mycobacteria; mutation accumulation