메뉴 건너뛰기




Volumn 6, Issue 7, 2016, Pages 2157-2163

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

Author keywords

GC bias; Mutation accumulation; Mycobacteria

Indexed keywords

DNA POLYMERASE; HISTIDINOL PHOSPHATASE; PROTEIN DNAE1; UNCLASSIFIED DRUG; URACIL DNA GLYCOSIDASE; URACIL DNA GLYCOSIDASE B; BACTERIAL DNA; DNA DIRECTED DNA POLYMERASE GAMMA; DNA POLYMERASE III, ALPHA SUBUNIT; SITE SPECIFIC DNA METHYLTRANSFERASE (ADENINE SPECIFIC);

EID: 84978422201     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.116.030130     Document Type: Article
Times cited : (38)

References (90)
  • 1
    • 34447564992 scopus 로고    scopus 로고
    • Mutation rate variation in multicellular eukaryotes: causes and consequences
    • Baer, C. F., M. M. Miyamoto, and D. R. Denver, 2007 Mutation rate variation in multicellular eukaryotes: causes and consequences. Nat. Rev. Genet. 8: 619-631.
    • (2007) Nat. Rev. Genet. , vol.8 , pp. 619-631
    • Baer, C.F.1    Miyamoto, M.M.2    Denver, D.R.3
  • 2
    • 33846597082 scopus 로고    scopus 로고
    • Physical and functional interactions between Escherichia coli MutY glycosylase and mismatch repair protein MutS
    • Bai, H., and A.-L. Lu, 2007 Physical and functional interactions between Escherichia coli MutY glycosylase and mismatch repair protein MutS. J. Bacteriol. 189: 902-910.
    • (2007) J. Bacteriol. , vol.189 , pp. 902-910
    • Bai, H.1    Lu, A.-L.2
  • 3
    • 0001057383 scopus 로고
    • The viability of near-normal irradiated chromosomes
    • Bateman, A. J., 1959 The viability of near-normal irradiated chromosomes. Int. J. Radiat. Biol. 1: 170-180.
    • (1959) Int. J. Radiat. Biol. , vol.1 , pp. 170-180
    • Bateman, A.J.1
  • 4
    • 84953775974 scopus 로고    scopus 로고
    • Genome wide estimates of mutation rates and spectrum in Schizosaccharomyces pombe indicate CpG sites are highly mutagenic despite the absence of DNA methylation
    • Behringer, M. G., and D. W. Hall, 2015 Genome wide estimates of mutation rates and spectrum in Schizosaccharomyces pombe indicate CpG sites are highly mutagenic despite the absence of DNA methylation. G3 (Bethesda) 6: 149-160.
    • (2015) G3 (Bethesda) , vol.6 , pp. 149-160
    • Behringer, M.G.1    Hall, D.W.2
  • 5
    • 0035448545 scopus 로고    scopus 로고
    • The evolution of mycobacterial pathogenicity: clues from comparative genomics
    • Brosch, R., A. S. Pym, S. V. Gordon, and S. T. Cole, 2001 The evolution of mycobacterial pathogenicity: clues from comparative genomics. Trends Microbiol. 9: 452-458.
    • (2001) Trends Microbiol. , vol.9 , pp. 452-458
    • Brosch, R.1    Pym, A.S.2    Gordon, S.V.3    Cole, S.T.4
  • 6
    • 69549116107 scopus 로고    scopus 로고
    • BreakDancer: an algorithm for high-resolution mapping of genomic structural variation
    • Chen, K., J. W. Wallis, M. D. McLellan, D. E. Larson, J. M. Kalicki et al., 2009 BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat. Methods 6: 677-681.
    • (2009) Nat. Methods , vol.6 , pp. 677-681
    • Chen, K.1    Wallis, J.W.2    McLellan, M.D.3    Larson, D.E.4    Kalicki, J.M.5
  • 7
    • 84857877933 scopus 로고    scopus 로고
    • Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing
    • Clark, T. A., I. A. Murray, R. D. Morgan, A. O. Kislyuk, K. E. Spittle et al., 2012 Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing. Nucleic Acids Res. 40: e29.
    • (2012) Nucleic Acids Res. , vol.40
    • Clark, T.A.1    Murray, I.A.2    Morgan, R.D.3    Kislyuk, A.O.4    Spittle, K.E.5
  • 8
    • 0032508046 scopus 로고    scopus 로고
    • Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
    • Cole, S. T., R. Brosch, J. Parkhill, T. Garnier, C. Churcher et al., 1998 Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393: 537-544.
    • (1998) Nature , vol.393 , pp. 537-544
    • Cole, S.T.1    Brosch, R.2    Parkhill, J.3    Garnier, T.4    Churcher, C.5
  • 9
    • 34250900982 scopus 로고    scopus 로고
    • Base-excision repair of oxidative DNA damage
    • David, S. S., V. L. O'Shea, and S. Kundu, 2007 Base-excision repair of oxidative DNA damage. Nature 447: 941-950.
    • (2007) Nature , vol.447 , pp. 941-950
    • David, S.S.1    O'Shea, V.L.2    Kundu, S.3
  • 10
    • 78650114501 scopus 로고    scopus 로고
    • Mismatch repair modulation of MutY activity drives Bacillus subtilis stationary-phase mutagenesis
    • Debora, B. N., L. E. Vidales, R. Ramirez, M. Ramirez, E. A. Robleto et al., 2011 Mismatch repair modulation of MutY activity drives Bacillus subtilis stationary-phase mutagenesis. J. Bacteriol. 193: 236-245.
    • (2011) J. Bacteriol. , vol.193 , pp. 236-245
    • Debora, B.N.1    Vidales, L.E.2    Ramirez, R.3    Ramirez, M.4    Robleto, E.A.5
  • 12
    • 79955483667 scopus 로고    scopus 로고
    • A framework for variation discovery and genotyping using next-generation DNA sequencing data
    • DePristo, M. A., E. Banks, R. Poplin, and K. V. GarimellaMaguire, J. R. et al., 2011 A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43: 491-498.
    • (2011) Nat. Genet. , vol.43 , pp. 491-498
    • DePristo, M.A.1    Banks, E.2    Poplin, R.3    Garimella, K.V.4    Maguire, J.R.5
  • 13
    • 84937043154 scopus 로고    scopus 로고
    • The rate and molecular spectrum of spontaneous mutations in the GC-rich multichromosome genome of Burkholderia cenocepacia
    • Dillon, M. M., W. Sung, M. Lynch, and V. S. Cooper, 2015 The rate and molecular spectrum of spontaneous mutations in the GC-rich multichromosome genome of Burkholderia cenocepacia. Genetics 200: 935-946.
    • (2015) Genetics , vol.200 , pp. 935-946
    • Dillon, M.M.1    Sung, W.2    Lynch, M.3    Cooper, V.S.4
  • 15
    • 0025886466 scopus 로고
    • A constant rate of spontaneous mutation in DNA-based microbes
    • Drake, J. W., 1991 A constant rate of spontaneous mutation in DNA-based microbes. Proc. Natl. Acad. Sci. USA 88: 7160-7164.
    • (1991) Proc. Natl. Acad. Sci. USA , vol.88 , pp. 7160-7164
    • Drake, J.W.1
  • 16
    • 0020461949 scopus 로고
    • Specific mutator effects of ung (uracil-DNA glycosylase) mutations in Escherichia coli
    • Duncan, B. K., and B. Weiss, 1982 Specific mutator effects of ung (uracil-DNA glycosylase) mutations in Escherichia coli. J. Bacteriol. 151: 750-755.
    • (1982) J. Bacteriol. , vol.151 , pp. 750-755
    • Duncan, B.K.1    Weiss, B.2
  • 17
    • 34447546660 scopus 로고    scopus 로고
    • The distribution of fitness effects of new mutations
    • Eyre-Walker, A., and P. D. Keightley, 2007 The distribution of fitness effects of new mutations. Nat. Rev. Genet. 8: 610-618.
    • (2007) Nat. Rev. Genet. , vol.8 , pp. 610-618
    • Eyre-Walker, A.1    Keightley, P.D.2
  • 18
    • 84941668361 scopus 로고    scopus 로고
    • The spontaneous mutation rate in the fission yeast Schizosaccharomyces pombe
    • Farlow, A., H. Long, S. Arnoux, W. Sung, T. G. Doak et al., 2015 The spontaneous mutation rate in the fission yeast Schizosaccharomyces pombe. Genetics 201: 737-744.
    • (2015) Genetics , vol.201 , pp. 737-744
    • Farlow, A.1    Long, H.2    Arnoux, S.3    Sung, W.4    Doak, T.G.5
  • 19
    • 79955460244 scopus 로고    scopus 로고
    • Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection
    • Ford, C. B., P. L. Lin, M. R. Chase, R. R. Shah, O. Iartchouk et al., 2011 Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection. Nat. Genet. 43: 482-486.
    • (2011) Nat. Genet. , vol.43 , pp. 482-486
    • Ford, C.B.1    Lin, P.L.2    Chase, M.R.3    Shah, R.R.4    Iartchouk, O.5
  • 20
    • 84879682699 scopus 로고    scopus 로고
    • Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis
    • Ford, C. B., R. R. Shah, M. K. Maeda, S. Gagneux, M. B. Murray et al., 2013 Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis. Nat. Genet. 45: 784-790.
    • (2013) Nat. Genet. , vol.45 , pp. 784-790
    • Ford, C.B.1    Shah, R.R.2    Maeda, M.K.3    Gagneux, S.4    Murray, M.B.5
  • 21
    • 84867383562 scopus 로고    scopus 로고
    • The presence of the DNA repair genes mutM, mutY, mutL, and mutS is related to proteome size in bacterial genomes
    • Garcia-Gonzales, A., R. J. Rivera-Rivera, and S. E. Massey, 2012 The presence of the DNA repair genes mutM, mutY, mutL, and mutS is related to proteome size in bacterial genomes. Front. Genet. 3: 1-11.
    • (2012) Front. Genet. , vol.3 , pp. 1-11
    • Garcia-Gonzales, A.1    Rivera-Rivera, R.J.2    Massey, S.E.3
  • 22
    • 84966300362 scopus 로고    scopus 로고
    • Fundamentals of Molecular Evolution
    • Sinauer Associates, Sunderland, MA.
    • Graur, D., and W. H. Li, 2000 Fundamentals of Molecular Evolution, Sinauer Associates, Sunderland, MA.
    • (2000)
    • Graur, D.1    Li, W.H.2
  • 23
    • 77951697965 scopus 로고    scopus 로고
    • Spontaneous mutation accumulation studies in evolutionary genetics
    • Halligan, D. L., and P. D. Keightley, 2009 Spontaneous mutation accumulation studies in evolutionary genetics. Annu. Rev. Ecol. Evol. Syst. 40: 151-172.
    • (2009) Annu. Rev. Ecol. Evol. Syst. , vol.40 , pp. 151-172
    • Halligan, D.L.1    Keightley, P.D.2
  • 24
    • 20844442964 scopus 로고    scopus 로고
    • Variation in efficiency of DNA mismatch repair at different sites in the yeast genome
    • Hawk, J. D., L. Stefanovic, J. C. Boyer, T. D. Petes, and R. A. Farber, 2005 Variation in efficiency of DNA mismatch repair at different sites in the yeast genome. Proc. Natl. Acad. Sci. USA 102: 8639-8643.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 8639-8643
    • Hawk, J.D.1    Stefanovic, L.2    Boyer, J.C.3    Petes, T.D.4    Farber, R.A.5
  • 25
    • 0029119607 scopus 로고
    • DNA methylation in mycobacteria: absence of methylation at GATC (Dam) and CCA/TGG (Dcm) sequences
    • Hemavathy, K. C., and V. Nagaraja, 1995 DNA methylation in mycobacteria: absence of methylation at GATC (Dam) and CCA/TGG (Dcm) sequences. FEMS Immunol. Med. Microbiol. 11: 291-296.
    • (1995) FEMS Immunol. Med. Microbiol. , vol.11 , pp. 291-296
    • Hemavathy, K.C.1    Nagaraja, V.2
  • 26
    • 78049445172 scopus 로고    scopus 로고
    • Evidence that mutation is universally biased towards AT in bacteria
    • Hershberg, R., and D. A. Petrov, 2010 Evidence that mutation is universally biased towards AT in bacteria. PLoS Genet. 6: e1001115.
    • (2010) PLoS Genet. , vol.6
    • Hershberg, R.1    Petrov, D.A.2
  • 27
    • 0141996214 scopus 로고    scopus 로고
    • Crystal structure of a family 4 uracil-DNA glycosylase from Thermus thermophilus HB8
    • Hoseki, J., A. Okamoto, R. Masui, T. Shibata, Y. Inoue et al., 2003 Crystal structure of a family 4 uracil-DNA glycosylase from Thermus thermophilus HB8. J. Mol. Biol. 333: 515-526.
    • (2003) J. Mol. Biol. , vol.333 , pp. 515-526
    • Hoseki, J.1    Okamoto, A.2    Masui, R.3    Shibata, T.4    Inoue, Y.5
  • 28
    • 84949501486 scopus 로고
    • Univariate Discrete Distributions
    • Wiley-Interscience, Hoboken , NJ.
    • Johnson, N. L., and A. W. Kemp, 1993 Univariate Discrete Distributions, Wiley-Interscience, Hoboken , NJ.
    • (1993)
    • Johnson, N.L.1    Kemp, A.W.2
  • 29
    • 67650064592 scopus 로고    scopus 로고
    • Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines
    • Keightley, P. D., U. Trivedi, M. Thomson, F. Oliver, S. Kumar et al., 2009 Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines. Genome Res. 19: 1195-1201.
    • (2009) Genome Res. , vol.19 , pp. 1195-1201
    • Keightley, P.D.1    Trivedi, U.2    Thomson, M.3    Oliver, F.4    Kumar, S.5
  • 30
    • 84901295203 scopus 로고    scopus 로고
    • Estimation of the spontaneous mutation rate per nucleotide site in a Drosophila melanogaster full-sib family
    • Keightley, P. D., R. W. Ness, D. L. Halligan, and P. R. Haddrill, 2014 Estimation of the spontaneous mutation rate per nucleotide site in a Drosophila melanogaster full-sib family. Genetics 196: 313-320.
    • (2014) Genetics , vol.196 , pp. 313-320
    • Keightley, P.D.1    Ness, R.W.2    Halligan, D.L.3    Haddrill, P.R.4
  • 32
    • 0029026635 scopus 로고
    • DNA polymerase III holoenzyme: structure and function of a chromosomal replicating machine
    • Kelman, Z., and M. O'Donnell, 1995 DNA polymerase III holoenzyme: structure and function of a chromosomal replicating machine. Annu. Rev. Biochem. 64: 171-200.
    • (1995) Annu. Rev. Biochem. , vol.64 , pp. 171-200
    • Kelman, Z.1    O'Donnell, M.2
  • 33
    • 0029931416 scopus 로고    scopus 로고
    • Estimate of the genomic mutation rate deleterious to overall fitness in E
    • Kibota, T. T., and M. Lynch, 1996 Estimate of the genomic mutation rate deleterious to overall fitness in E. coli. Nature 381: 694-696.
    • (1996) coli. Nature , vol.381 , pp. 694-696
    • Kibota, T.T.1    Lynch, M.2
  • 34
    • 0038104364 scopus 로고    scopus 로고
    • Competition between MutY and mismatch repair at A-C mispairs in vivo
    • Kim, M., T. Huang, and J. H. Miller, 2003 Competition between MutY and mismatch repair at A-C mispairs in vivo. J. Bacteriol. 185: 4626-4629.
    • (2003) J. Bacteriol. , vol.185 , pp. 4626-4629
    • Kim, M.1    Huang, T.2    Miller, J.H.3
  • 35
    • 84959609205 scopus 로고    scopus 로고
    • On the evolutionary adjustment of spontaneous mutation rates
    • Kimura, M., 2009 On the evolutionary adjustment of spontaneous mutation rates. Genet. Res. 9: 23.
    • (2009) Genet. Res. , vol.9 , pp. 23
    • Kimura, M.1
  • 36
    • 2342419732 scopus 로고    scopus 로고
    • DNA replication fidelity
    • Kunkel, T. A., 2004 DNA replication fidelity. J. Biol. Chem. 279: 16895-16898.
    • (2004) J. Biol. Chem. , vol.279 , pp. 16895-16898
    • Kunkel, T.A.1
  • 38
    • 84896523433 scopus 로고    scopus 로고
    • Mutation rates, spectra, and genome-wide distribution of spontaneous mutations in mismatch repair deficient yeast
    • Lang, G. I., L. Parsons, and A. E. Gammie, 2013 Mutation rates, spectra, and genome-wide distribution of spontaneous mutations in mismatch repair deficient yeast. G3 (Bethesda) 3: 1453-1465.
    • (2013) G3 (Bethesda) , vol.3 , pp. 1453-1465
    • Lang, G.I.1    Parsons, L.2    Gammie, A.E.3
  • 39
    • 84867339877 scopus 로고    scopus 로고
    • Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing
    • Lee, H., E. Popodi, H. Tang, and P. L. Foster, 2012 Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing. Proc. Natl. Acad. Sci. USA 109: E2774-E2783.
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109 , pp. E2774-E2783
    • Lee, H.1    Popodi, E.2    Tang, H.3    Foster, P.L.4
  • 40
    • 80052396623 scopus 로고    scopus 로고
    • New family of deamination repair enzymes in uracil-DNA glycosylase superfamily
    • Lee, H. W., B. N. Dominy, and W. Cao, 2011 New family of deamination repair enzymes in uracil-DNA glycosylase superfamily. J. Biol. Chem. 286: 31282-31287.
    • (2011) J. Biol. Chem. , vol.286 , pp. 31282-31287
    • Lee, H.W.1    Dominy, B.N.2    Cao, W.3
  • 41
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li, H., and R. Durbin, 2009 Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 42
  • 43
    • 84943608703 scopus 로고    scopus 로고
    • Background mutational features of the radiation-resistant bacterium Deinococcus radiodurans.
    • Long, H., S. Kucukyildirim, W. Sung, E. Williams, H. Lee et al., 2015a Background mutational features of the radiation-resistant bacterium Deinococcus radiodurans. Mol. Biol. Evol. 32: 2383-2392.
    • (2015) Mol. Biol. Evol. , vol.32 , pp. 2383-2392
    • Long, H.1    Kucukyildirim, S.2    Sung, W.3    Williams, E.4    Lee, H.5
  • 44
    • 84928236984 scopus 로고    scopus 로고
    • Mutation rate, spectrum, topology, and context-dependency in the DNA mismatch repair (MMR) deficient Pseudomonas fluorescens ATCC948
    • Long, H., W. Sung, S. F. Miller, M. Ackerman, T. G. Doak et al., 2015b Mutation rate, spectrum, topology, and context-dependency in the DNA mismatch repair (MMR) deficient Pseudomonas fluorescens ATCC948. Genome Biol. Evol. 7: 262-271.
    • (2015) Genome Biol. Evol. , vol.7 , pp. 262-271
    • Long, H.1    Sung, W.2    Miller, S.F.3    Ackerman, M.4    Doak, T.G.5
  • 45
    • 84855910162 scopus 로고    scopus 로고
    • Roles of endonuclease V, uracil-DNA glycosylase, and mismatch repair in Bacillus subtilis DNA base-deamination-induced mutagenesis
    • López-Olmos, K., M. P. Hernández, J. A. Contreras-Garduño, E. A. Robleto, P. Setlow et al., 2012 Roles of endonuclease V, uracil-DNA glycosylase, and mismatch repair in Bacillus subtilis DNA base-deamination-induced mutagenesis. J. Bacteriol. 194: 243-252.
    • (2012) J. Bacteriol. , vol.194 , pp. 243-252
    • López-Olmos, K.1    Hernández, M.P.2    Contreras-Garduño, J.A.3    Robleto, E.A.4    Setlow, P.5
  • 46
    • 34250709215 scopus 로고    scopus 로고
    • The Origins of Genome Architecture
    • Sinauer Associates, Sunderland, MA.
    • Lynch, M., 2007 The Origins of Genome Architecture, Sinauer Associates, Sunderland, MA.
    • (2007)
    • Lynch, M.1
  • 47
    • 77955090647 scopus 로고    scopus 로고
    • Evolution of the mutation rate
    • Lynch, M., 2010 Evolution of the mutation rate. Trends Genet. 26: 345-352.
    • (2010) Trends Genet. , vol.26 , pp. 345-352
    • Lynch, M.1
  • 48
    • 80052736277 scopus 로고    scopus 로고
    • The lower bound to the evolution of mutation rates
    • Lynch, M., 2011 The lower bound to the evolution of mutation rates. Genome Biol. Evol. 3: 1107-1118.
    • (2011) Genome Biol. Evol. , vol.3 , pp. 1107-1118
    • Lynch, M.1
  • 49
    • 84869212334 scopus 로고    scopus 로고
    • Evolutionary layering and the limits to cellular perfection
    • Lynch, M., 2012 Evolutionary layering and the limits to cellular perfection. Proc. Natl. Acad. Sci. USA 109: 18851-18856.
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109 , pp. 18851-18856
    • Lynch, M.1
  • 50
  • 51
    • 77749301852 scopus 로고    scopus 로고
    • Synergistic effects of UdgB and Ung in mutation prevention and protection against commonly encountered DNA damaging agents in Mycobacterium smegmatis
    • Malshetty, V. S., R. Jain, T. Srinath, K. Kurthkoti, and U. Varshney, 2010 Synergistic effects of UdgB and Ung in mutation prevention and protection against commonly encountered DNA damaging agents in Mycobacterium smegmatis. Microbiology 156: 940-949.
    • (2010) Microbiology , vol.156 , pp. 940-949
    • Malshetty, V.S.1    Jain, R.2    Srinath, T.3    Kurthkoti, K.4    Varshney, U.5
  • 52
    • 77956295988 scopus 로고    scopus 로고
    • The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data
    • McKenna, A. H. M., E. Banks, A. Sivachenko, K. Cibulskis, A. Kernytsky et al., 2010 The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20: 1297-1303.
    • (2010) Genome Res. , vol.20 , pp. 1297-1303
    • McKenna, A.H.M.1    Banks, E.2    Sivachenko, A.3    Cibulskis, K.4    Kernytsky, A.5
  • 53
    • 0035479142 scopus 로고    scopus 로고
    • Deletional bias and the evolution of bacterial genomes
    • Mira, A., H. Ochman, and N. A. Moran, 2001 Deletional bias and the evolution of bacterial genomes. Trends Genet. 17: 589-596.
    • (2001) Trends Genet. , vol.17 , pp. 589-596
    • Mira, A.1    Ochman, H.2    Moran, N.A.3
  • 54
    • 85007151998 scopus 로고    scopus 로고
    • Complete genome sequences of a Mycobacterium smegmatis laboratory strain (MC2 155) and isoniazid-resistant (4XR1/R2) mutant strains
    • Mohan, A., J. Padiadpu, P. Baloni, and N. Chandra, 2015 Complete genome sequences of a Mycobacterium smegmatis laboratory strain (MC2 155) and isoniazid-resistant (4XR1/R2) mutant strains. Genome Announc. 3: e01520-e01514.
    • (2015) Genome Announc. , vol.3 , pp. e01520-e01514
    • Mohan, A.1    Padiadpu, J.2    Baloni, P.3    Chandra, N.4
  • 55
    • 70549103951 scopus 로고    scopus 로고
    • Comparative genomic and phylogeographic analysis of Mycobacterium leprae
    • Monot, M., N. Honore, T. Garnier, N. Zidane, D. Sherafi et al., 2009 Comparative genomic and phylogeographic analysis of Mycobacterium leprae. Nat. Genet. 41: 1282-1289.
    • (2009) Nat. Genet. , vol.41 , pp. 1282-1289
    • Monot, M.1    Honore, N.2    Garnier, T.3    Zidane, N.4    Sherafi, D.5
  • 56
    • 0002129633 scopus 로고
    • The genetic structure of natural populations of Drosophila melanogaster I. Spontaneous mutation rate of polygenes controlling viability.
    • Mukai, T., 1964 The genetic structure of natural populations of Drosophila melanogaster. I. Spontaneous mutation rate of polygenes controlling viability. Genetics 50: 1-19.
    • (1964) Genetics , vol.50 , pp. 1-19
    • Mukai, T.1
  • 57
    • 33747830026 scopus 로고
    • Artificial transmutation of the gene
    • Muller, H. J., 1927 Artificial transmutation of the gene. Science 66: 84-87.
    • (1927) Science , vol.66 , pp. 84-87
    • Muller, H.J.1
  • 58
    • 0000775877 scopus 로고
    • The measurement of gene mutation rate in Drosophila, its high variability, and its dependence upon temperature
    • Muller, H. J., 1928 The measurement of gene mutation rate in Drosophila, its high variability, and its dependence upon temperature. Genetics 13: 279-357.
    • (1928) Genetics , vol.13 , pp. 279-357
    • Muller, H.J.1
  • 59
    • 84946572905 scopus 로고    scopus 로고
    • Extensive de novo mutation rate variation between individuals and across the genome of Chlamydomonas reinhardtii
    • Ness, R. W., A. D. Morgan, R. B. Vasanthakrishnan, N. Colegrave, and P. D. Keightley, 2015 Extensive de novo mutation rate variation between individuals and across the genome of Chlamydomonas reinhardtii. Genome Res. 25: 1739-1749.
    • (2015) Genome Res. , vol.25 , pp. 1739-1749
    • Ness, R.W.1    Morgan, A.D.2    Vasanthakrishnan, R.B.3    Colegrave, N.4    Keightley, P.D.5
  • 60
    • 0021910963 scopus 로고
    • Sequence specificity of isolated DNA-adenine methylases from Mycobacterium smegmatis (butyricum) and Shigella sonnei 47 cells
    • Nikolaskaya, I. I., N. G. Lopatina, E. V. Sharkova, and S. V. Suchkov, P. Somody et al., 1985 Sequence specificity of isolated DNA-adenine methylases from Mycobacterium smegmatis (butyricum) and Shigella sonnei 47 cells. Biochem. Int. 10: 405-413.
    • (1985) Biochem. Int. , vol.10 , pp. 405-413
    • Nikolaskaya, I.I.1    Lopatina, N.G.2    Sharkova, E.V.3    Suchkov, S.V.4    Somody, P.5
  • 61
    • 74849090833 scopus 로고    scopus 로고
    • The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana
    • Ossowski, S., K. Schneeberger, J. I. Lucas-Lledó, N. Warthmann, R. M. Clark et al., 2010 The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327: 92-94.
    • (2010) Science , vol.327 , pp. 92-94
    • Ossowski, S.1    Schneeberger, K.2    Lucas-Lledó, J.I.3    Warthmann, N.4    Clark, R.M.5
  • 62
    • 0034734383 scopus 로고    scopus 로고
    • Structure and function in the uracil-DNA glycosylase superfamily
    • Pearl, L. H., 2000 Structure and function in the uracil-DNA glycosylase superfamily. Mutat. Res. 460: 165-181.
    • (2000) Mutat. Res. , vol.460 , pp. 165-181
    • Pearl, L.H.1
  • 63
    • 0032530427 scopus 로고    scopus 로고
    • Uracil DNA glycosylase from Mycobacterium smegmatis and its distinct biochemical properties
    • Purnapatre, K., and U. Varshney, 1998 Uracil DNA glycosylase from Mycobacterium smegmatis and its distinct biochemical properties. Eur. J. Biochem. 256: 580-588.
    • (1998) Eur. J. Biochem. , vol.256 , pp. 580-588
    • Purnapatre, K.1    Varshney, U.2
  • 64
    • 84963641621 scopus 로고    scopus 로고
    • R: A Language and Environment for Statistical Computing
    • R Foundation for Statistical Computing, Vienna, Austria.
    • R Development Core Team, 2014 R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing, Vienna, Austria.
    • (2014)
  • 65
    • 84930090059 scopus 로고    scopus 로고
    • DNA replication fidelity in Mycobacterium tuberculosis is mediated by an ancestral prokaryotic proofreader
    • Rock, J. M., U. F. Lang, M. R. Chase, C. B. Ford, E. R. Gerrick et al., 2015 DNA replication fidelity in Mycobacterium tuberculosis is mediated by an ancestral prokaryotic proofreader. Nat. Genet. 47: 677-681.
    • (2015) Nat. Genet. , vol.47 , pp. 677-681
    • Rock, J.M.1    Lang, U.F.2    Chase, M.R.3    Ford, C.B.4    Gerrick, E.R.5
  • 66
    • 0037124349 scopus 로고    scopus 로고
    • A novel uracil-DNA glycosylase with broad substrate specificity and an unusual active site
    • Sartori, A. A., S. Fitz-Gibbon, H. Yang, J. H. Miller, and J. Jiricny, 2002 A novel uracil-DNA glycosylase with broad substrate specificity and an unusual active site. EMBO J. 21: 3182-3191.
    • (2002) EMBO J. , vol.21 , pp. 3182-3191
    • Sartori, A.A.1    Fitz-Gibbon, S.2    Yang, H.3    Miller, J.H.4    Jiricny, J.5
  • 67
    • 0027482444 scopus 로고
    • Base selection, proofreading, and mismatch repair during DNA replication in Escherichia coli
    • Schaaper, R. M., 1993 Base selection, proofreading, and mismatch repair during DNA replication in Escherichia coli. J. Biol. Chem. 268: 23762-23765.
    • (1993) J. Biol. Chem. , vol.268 , pp. 23762-23765
    • Schaaper, R.M.1
  • 68
    • 0025953766 scopus 로고
    • Spontaneous mutation in the Escherichia coli lac I gene
    • Schaaper, R. M., and R. L. Dunn, 1991 Spontaneous mutation in the Escherichia coli lac I gene. Genetics 129: 317-326.
    • (1991) Genetics , vol.129 , pp. 317-326
    • Schaaper, R.M.1    Dunn, R.L.2
  • 69
    • 0024374370 scopus 로고
    • The bacteriophage T2 and T4 DNA-[N6-adenine] methyltransferase (Dam) sequence specificities are not identical
    • Schlagman, S. L., and S. Hattman, 1989 The bacteriophage T2 and T4 DNA-[N6-adenine] methyltransferase (Dam) sequence specificities are not identical. Nucleic Acids Res. 17: 9101-9112.
    • (1989) Nucleic Acids Res. , vol.17 , pp. 9101-9112
    • Schlagman, S.L.1    Hattman, S.2
  • 70
    • 84930226215 scopus 로고    scopus 로고
    • The interaction of mycobacterial protein Rv2966c with host chromatin is mediated through non-CpG methylation and histone H3/H4 binding
    • Sharma, G., S. Upadhyay, M. Srilalitha, V. K. Nandicoori, and S. Khosla, 2015 The interaction of mycobacterial protein Rv2966c with host chromatin is mediated through non-CpG methylation and histone H3/H4 binding. Nucleic Acids Res. 43: 3922-3937.
    • (2015) Nucleic Acids Res. , vol.43 , pp. 3922-3937
    • Sharma, G.1    Upadhyay, S.2    Srilalitha, M.3    Nandicoori, V.K.4    Khosla, S.5
  • 71
    • 84884753898 scopus 로고    scopus 로고
    • DNA methylation impacts gene expression and ensures hypoxic survival of Mycobacterium tuberculosis
    • Shell, S. S., E. G. Prestwich, S. H. Baek, R. R. Shah, C. M. Sassetti et al., 2013 DNA methylation impacts gene expression and ensures hypoxic survival of Mycobacterium tuberculosis. PLoS Pathog. 9: e1003419.
    • (2013) PLoS Pathog. , vol.9
    • Shell, S.S.1    Prestwich, E.G.2    Baek, S.H.3    Shah, R.R.4    Sassetti, C.M.5
  • 72
    • 75249096198 scopus 로고    scopus 로고
    • To catch a killer What can mycobacterial models teach us about Mycobacterium tuberculosis pathogenesis?
    • Shiloh, M. U., and P. A. DiGiuseppe Champion, 2010 To catch a killer. What can mycobacterial models teach us about Mycobacterium tuberculosis pathogenesis? Curr. Opin. Microbiol. 13: 86-92.
    • (2010) Curr. Opin. Microbiol. , vol.13 , pp. 86-92
    • Shiloh, M.U.1    DiGiuseppe Champion, P.A.2
  • 73
    • 67649407565 scopus 로고    scopus 로고
    • Myths and misconceptions: the origin and evolution of Mycobacterium tuberculosis
    • Smith, N. H., R. G. Hewinson, K. Kremer, R. Brosch, and S. V. Gordon, 2009 Myths and misconceptions: the origin and evolution of Mycobacterium tuberculosis. Nat. Rev. Microbiol. 7: 537-544.
    • (2009) Nat. Rev. Microbiol. , vol.7 , pp. 537-544
    • Smith, N.H.1    Hewinson, R.G.2    Kremer, K.3    Brosch, R.4    Gordon, S.V.5
  • 74
    • 0025081151 scopus 로고
    • Isolation and characterization of efficient plasmid transformation mutants of Mycobacterium smegmatis
    • Snapper, S. B., R. E. Melton, S. Mustafa, T. Kieser, and W. R. Jacobs, Jr., 1990 Isolation and characterization of efficient plasmid transformation mutants of Mycobacterium smegmatis. Mol. Microbiol. 4: 1911-1919.
    • (1990) Mol. Microbiol. , vol.4 , pp. 1911-1919
    • Snapper, S.B.1    Melton, R.E.2    Mustafa, S.3    Kieser, T.4    Jacobs, W.R.5
  • 75
    • 84874623094 scopus 로고    scopus 로고
    • Mutation rates: how low can you go? Curr
    • Sniegowski, P., and Y. Raynes, 2013 Mutation rates: how low can you go? Curr. Biol. 23: R147-R149.
    • (2013) Biol. , vol.23 , pp. R147-R149
    • Sniegowski, P.1    Raynes, Y.2
  • 76
    • 0030931719 scopus 로고    scopus 로고
    • Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination
    • Sreevatsan, S., X. Pan, K. E. Stockbauer, N. D. Connell, B. N. Kreiswirth et al., 1997 Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination. Proc. Natl. Acad. Sci. USA 94: 9869-9874.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 9869-9874
    • Sreevatsan, S.1    Pan, X.2    Stockbauer, K.E.3    Connell, N.D.4    Kreiswirth, B.N.5
  • 77
    • 34548534747 scopus 로고    scopus 로고
    • Substrate specificities and functional characterization of a thermo-tolerant uracil DNA glycosylase (UdgB) from Mycobacterium tuberculosis
    • Srinath, T., S. K. Bharti, and U. Varshney, 2007 Substrate specificities and functional characterization of a thermo-tolerant uracil DNA glycosylase (UdgB) from Mycobacterium tuberculosis. DNA Repair (Amst.) 6: 1517-1528.
    • (2007) DNA Repair (Amst.) , vol.6 , pp. 1517-1528
    • Srinath, T.1    Bharti, S.K.2    Varshney, U.3
  • 79
    • 0037052965 scopus 로고    scopus 로고
    • A novel type of uracil-DNA glycosylase mediating repair of hydrolytic DNA damage in the extremely thermophilic eubacterium Thermus thermophilus
    • Starkuviene, V., and H.-J. Fritz, 2002 A novel type of uracil-DNA glycosylase mediating repair of hydrolytic DNA damage in the extremely thermophilic eubacterium Thermus thermophilus. Nucleic Acids Res. 30: 2097-2102.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 2097-2102
    • Starkuviene, V.1    Fritz, H.-J.2
  • 81
    • 84868579284 scopus 로고    scopus 로고
    • Extraordinary genome stability in the ciliate Paramecium tetraurelia
    • Sung, W., A. E. Tucker, T. G. Doak, E. Choi, W. K. Thomas et al., 2012b Extraordinary genome stability in the ciliate Paramecium tetraurelia. Proc. Natl. Acad. Sci. USA 109: 19339-19344.
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109 , pp. 19339-19344
    • Sung, W.1    Tucker, A.E.2    Doak, T.G.3    Choi, E.4    Thomas, W.K.5
  • 82
    • 84936850349 scopus 로고    scopus 로고
    • Asymmetric context-dependent mutation patterns revealed through mutation-accumulation experiments
    • Sung, W., M. S. Ackerman, J.-F. Gout, S. F. Miller, E.Williams et al., 2015 Asymmetric context-dependent mutation patterns revealed through mutation-accumulation experiments. Mol. Biol. Evol. 32: 1672-1683.
    • (2015) Mol. Biol. Evol. , vol.32 , pp. 1672-1683
    • Sung, W.1    Ackerman, M.S.2    Gout, J.-F.3    Miller, S.F.4    Williams, E.5
  • 83
    • 84923070685 scopus 로고    scopus 로고
    • The BER necessities: the repair of DNA damage in human-adapted bacterial pathogens
    • van der Veen, S., and C. M. Tang, 2015 The BER necessities: the repair of DNA damage in human-adapted bacterial pathogens. Nat. Rev. Microbiol. 13: 83-94.
    • (2015) Nat. Rev. Microbiol. , vol.13 , pp. 83-94
    • van der Veen, S.1    Tang, C.M.2
  • 84
    • 0036628726 scopus 로고    scopus 로고
    • Biological consequences of free radical-damaged DNA bases
    • Wallace, S. S., 2002 Biological consequences of free radical-damaged DNA bases. Free Radic. Biol. Med. 33: 1-14.
    • (2002) Free Radic. Biol. Med. , vol.33 , pp. 1-14
    • Wallace, S.S.1
  • 85
    • 70350469035 scopus 로고    scopus 로고
    • The uracil DNA glycosylase UdgB of Mycobacterium smegmatis protects the organism from the mutagenic effects of cytosine and adenine deamination
    • Wanner, R. M., D. Castor, C. Güthlein, E. C. Böttger, B. Springer et al., 2009 The uracil DNA glycosylase UdgB of Mycobacterium smegmatis protects the organism from the mutagenic effects of cytosine and adenine deamination. J. Bacteriol. 191: 6312-6319.
    • (2009) J. Bacteriol. , vol.191 , pp. 6312-6319
    • Wanner, R.M.1    Castor, D.2    Güthlein, C.3    Böttger, E.C.4    Springer, B.5
  • 86
    • 84856220271 scopus 로고    scopus 로고
    • Mutation rate inferred from synonymous substitutions in a long-term evolution experiment with Escherichia coli
    • Wielgoss, S., J. E. Barrick, O. Tenaillon, S. Cruveiller, B. Chane-Woon-Ming et al., 2011 Mutation rate inferred from synonymous substitutions in a long-term evolution experiment with Escherichia coli. G3 (Bethesda) 1: 183-186.
    • (2011) G3 (Bethesda) , vol.1 , pp. 183-186
    • Wielgoss, S.1    Barrick, J.E.2    Tenaillon, O.3    Cruveiller, S.4    Chane-Woon-Ming, B.5
  • 87
    • 70350694443 scopus 로고    scopus 로고
    • Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
    • Ye, K., M. H. Schulz, Q. Long, R. Apweiler, and Z. Ning, 2009 Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25: 2865-2871.
    • (2009) Bioinformatics , vol.25 , pp. 2865-2871
    • Ye, K.1    Schulz, M.H.2    Long, Q.3    Apweiler, R.4    Ning, Z.5
  • 88
    • 0034707047 scopus 로고    scopus 로고
    • The DNA damage response: putting checkpoints in perspective
    • Zhou, B. B., and S. J. Elledge, 2000 The DNA damage response: putting checkpoints in perspective. Nature 408: 433-439.
    • (2000) Nature , vol.408 , pp. 433-439
    • Zhou, B.B.1    Elledge, S.J.2
  • 89
    • 84966424770 scopus 로고    scopus 로고
    • Precision methylome characterization of Mycobacterium tuberculosis complex (MTBC) using PacBio single-molecule real-time (SMRT) technology
    • Zhu, L., J. Zhong, X. Jia, G. Liu, Y. Kang et al., 2016 Precision methylome characterization of Mycobacterium tuberculosis complex (MTBC) using PacBio single-molecule real-time (SMRT) technology. Nucleic Acids Res. 44: 730-743.
    • (2016) Nucleic Acids Res. , vol.44 , pp. 730-743
    • Zhu, L.1    Zhong, J.2    Jia, X.3    Liu, G.4    Kang, Y.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.