메뉴 건너뛰기




Volumn 9, Issue 11, 2015, Pages 2360-2372

Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris

(14)  Zhou, Aifen a   Hillesland, Kristina L b   He, Zhili a   Schackwitz, Wendy c   Tu, Qichao a   Zane, Grant M d   Ma, Qiao a,e   Qu, Yuanyuan a,e   Stahl, David A f   Wall, Judy D d   Hazen, Terry C g,h   Fields, Matthew W i   Arkin, Adam P j   Zhou, Jizhong a,j,k  


Author keywords

[No Author keywords available]

Indexed keywords

ADAPTATION; BIOMASS ALLOCATION; CLONE; ENZYME ACTIVITY; EVOLUTIONARY BIOLOGY; GENE EXPRESSION; GENETIC ANALYSIS; GENOTYPE; GROWTH RATE; MOLECULAR ANALYSIS; MUTATION; POLYMORPHISM; PROTEIN; SALINITY TOLERANCE; SULFATE-REDUCING BACTERIUM;

EID: 84945471794     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2015.45     Document Type: Article
Times cited : (22)

References (48)
  • 2
    • 77955513081 scopus 로고    scopus 로고
    • Determinants of divergent adaptation and dobzhansky-muller interaction in experimental yeast populations
    • Anderson JB, Funt JThompson DA, Prabhu S, Socha A, Sirjusingh C, et al. (2010). Determinants of divergent adaptation and dobzhansky-muller interaction in experimental yeast populations. Curr Biol 20: 1383-1388
    • (2010) Curr Biol , vol.20 , pp. 1383-1388
    • Anderson, J.B.1    Funt, J.2    Thompson, D.A.3    Prabhu, S.4    Socha, A.5    Sirjusingh, C.6
  • 3
    • 77957746208 scopus 로고    scopus 로고
    • Genome-wide mutational diversity in an evolving population of Escherichia coli
    • Barrick J, Lenski R. (2009). Genome-wide mutational diversity in an evolving population of Escherichia coli. Cold Spring Harb Symp Quant Biol 74: 119-129
    • (2009) Cold Spring Harb Symp Quant Biol , vol.74 , pp. 119-129
    • Barrick, J.1    Lenski, R.2
  • 4
    • 84888001845 scopus 로고    scopus 로고
    • Genome dynamics during experimental evolution
    • Barrick JE, Lenski RE. (2013). Genome dynamics during experimental evolution. Nat Rev Genet 14: 827-839
    • (2013) Nat Rev Genet , vol.14 , pp. 827-839
    • Barrick, J.E.1    Lenski, R.E.2
  • 5
    • 79951808135 scopus 로고    scopus 로고
    • Next-generation sequencing as a tool to study microbial evolution
    • Brockhurst MA, Colegrave N, Rozen DE. (2011). Next-generation sequencing as a tool to study microbial evolution. Mol Ecol 20: 972-980
    • (2011) Mol Ecol , vol.20 , pp. 972-980
    • Brockhurst, M.A.1    Colegrave, N.2    Rozen, D.E.3
  • 6
    • 0030049824 scopus 로고    scopus 로고
    • Identification and molecular characterization of a putative regulatory locus that affects autolysis in staphylococcus aureus
    • Brunskill EW, Bayles KW. (1996). Identification and molecular characterization of a putative regulatory locus that affects autolysis in Staphylococcus aureus. J Bacteriol 178: 611-618
    • (1996) J Bacteriol , vol.178 , pp. 611-618
    • Brunskill, E.W.1    Bayles, K.W.2
  • 7
    • 0034780806 scopus 로고    scopus 로고
    • Bacterial fatty acid biosyn thesis targets for antibacterial drug discovery
    • Campbell JW, Cronan JE. (2001). Bacterial fatty acid biosynthesis: targets for antibacterial drug discovery. Ann Rev Microbiol 55: 305-332
    • (2001) Ann Rev Microbiol , vol.55 , pp. 305-332
    • Campbell, J.W.1    Cronan, J.E.2
  • 9
    • 33747337245 scopus 로고    scopus 로고
    • Temporal transcriptomic analysis as desulfovibrio vulgaris hildenborough transitions into stationary phase during electron donor depletion
    • Clark M, He Q, He Z, Huang K, Alm E, Wan X, et al. (2006). Temporal transcriptomic analysis as Desulfovibrio vulgaris Hildenborough transitions into stationary phase during electron donor depletion. Appl Environ Microbiol 72: 5578-5588
    • (2006) Appl Environ Microbiol , vol.72 , pp. 5578-5588
    • Clark, M.1    He, Q.2    He, Z.3    Huang, K.4    Alm, E.5    Wan, X.6
  • 10
    • 84859706260 scopus 로고    scopus 로고
    • Transcriptomic and proteomic analyses of desulfovibrio vulgaris biofilms: Carbon and energy flow contribute to the distinct biofilm growth state
    • Clark M, He Z, Redding A, Joachimiak MP, Keasling JD, Zhou JZ, et al. (2012 proteomic analyses of Desulfovibrio vulgaris biofilms: Carbon and energy flow contribute to the distinct biofilm growth state. BMC Genomics 13: 138
    • (2012) BMC Genomics , vol.13 , pp. 138
    • Clark, M.1    He, Z.2    Redding, A.3    Joachimiak, M.P.4    Keasling, J.D.5    Zhou, J.Z.6
  • 11
    • 84860663163 scopus 로고    scopus 로고
    • Evolutionary insight from wholegenome sequencing of experimentally evolved microbes
    • Dettman JR, Rodrigue N, Melnyk AH, Wong A, Bailey SF, Kassen R. (2012). Evolutionary insight from wholegenome sequencing of experimentally evolved microbes. Mol Ecol 21: 2058-2077
    • (2012) Mol Ecol , vol.21 , pp. 2058-2077
    • Dettman, J.R.1    Rodrigue, N.2    Melnyk, A.H.3    Wong, A.4    Bailey, S.F.5    Kassen, R.6
  • 12
    • 79955027266 scopus 로고    scopus 로고
    • Adaptation of saccharomyces cerevisiae to saline stress through laboratory evolution
    • Dhar R, SÄGesser R, Weikert C, Yuan J, Wagner A. (2011). Adaptation of Saccharomyces cerevisiae to saline stress through laboratory evolution. J Evol Biol 24: 1135-1153
    • (2011) J Evol Biol , vol.24 , pp. 1135-1153
    • Dhar, R.S.Ä.1    Gesser, R.2    Weikert, C.3    Yuan, J.4    Wagner, A.5
  • 13
    • 84873635856 scopus 로고    scopus 로고
    • Evolutionary potential, crossstress behavior and the genetic basis of acquired stress resistance in Escherichia coli
    • Dragosits M, Mozhayskiy V, Quinones-Soto S, Park J, Tagkopoulos I. (2013). Evolutionary potential, crossstress behavior and the genetic basis of acquired stress resistance in Escherichia coli. Mol Syst Biol 9: 643
    • (2013) Mol Syst Biol , vol.9 , pp. 643
    • Dragosits, M.1    Mozhayskiy, V.2    Quinones-Soto, S.3    Park, J.4    Tagkopoulos, I.5
  • 14
    • 0038441327 scopus 로고    scopus 로고
    • Evolution experiments with microorganisms: The dynamics and genetic bases of adaptation
    • Elena SF, Lenski RE. (2003). Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nat Rev Genet 4: 457-469
    • (2003) Nat Rev Genet , vol.4 , pp. 457-469
    • Elena, S.F.1    Lenski, R.E.2
  • 15
    • 84886550456 scopus 로고    scopus 로고
    • Strategies for the multiplex mapping of genes to traits
    • Garst A, Lynch M, Evans R, Gill R. (2013). Strategies for the multiplex mapping of genes to traits. Microb Cell Fact 12: 99
    • (2013) Microb Cell Fact , vol.12 , pp. 99
    • Garst, A.1    Lynch, M.2    Evans, R.3    Gill, R.4
  • 16
    • 77649215646 scopus 로고    scopus 로고
    • Global transcriptional, physiological, and metabolite analyses of the responses of desulfovibrio vulgaris hildenborough to salt adaptation
    • He Z, Zhou A, Baidoo E, He Q, Joachimiak MP, Benke P, et al. (2010). Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris Hildenborough to salt adaptation. Appl Environ Microbiol 76: 1574-1586
    • (2010) Appl Environ Microbiol , vol.76 , pp. 1574-1586
    • He, Z.1    Zhou, A.2    Baidoo, E.3    He, Q.4    Joachimiak, M.P.5    Benke, P.6
  • 17
    • 33751544539 scopus 로고    scopus 로고
    • Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale
    • Herring C Raghunathan A, Honisch C, Patel T, Applebee M, Joyce A, et al. (2006). Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nat Genet 38 1406-1412
    • (2006) Nat Genet , vol.38 , pp. 1406-1412
    • Herring, C.1    Raghunathan, A.2    Honisch, C.3    Patel, T.4    Applebee, M.5    Joyce, A.6
  • 18
    • 73249117149 scopus 로고    scopus 로고
    • Development of a markerless genetic exchange system for desulfovibrio vulgaris hildenborough and its use in generating a strain with increased transformation efficiency
    • Keller KL, Bender KS, Wall JD. (2009). Development of a markerless genetic exchange system for Desulfovibrio vulgaris Hildenborough and its use in generating a strain with increased transformation efficiency. Ann Rev Microbiol 75: 7682-7691
    • (2009) Ann Rev Microbiol , vol.75 , pp. 7682-7691
    • Keller, K.L.1    Bender, K.S.2    Wall, J.D.3
  • 19
    • 84878275641 scopus 로고    scopus 로고
    • Speedy speciation in a bacterial microcosm: New species can arise as frequently as adaptations within a species
    • Koeppel AF, Wertheim JO, Barone L, Gentile N, Krizanc D, Cohan FM. (2013). Speedy speciation in a bacterial microcosm: new species can arise as frequently as adaptations within a species. ISME J 7 1080-1091
    • (2013) ISME J , vol.7 , pp. 1080-1091
    • Koeppel, A.F.1    Wertheim, J.O.2    Barone, L.3    Gentile, N.4    Krizanc, D.5    Cohan, F.M.6
  • 20
    • 77955112220 scopus 로고    scopus 로고
    • Bacterial stimulus perception and signal transduction: Response to osmotic stress
    • Krämer R. (2010). Bacterial stimulus perception and signal transduction: response to osmotic stress. Chem Record 10: 217-229
    • (2010) Chem Record , vol.10 , pp. 217-229
    • Krämer, R.1
  • 21
    • 84883132678 scopus 로고    scopus 로고
    • Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations
    • Lang GI, Rice DP, Hickman MJ, Sodergren E, Weinstock GM, Botstein D, et al. (2013). Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations. Nature 500: 571-574
    • (2013) Nature , vol.500 , pp. 571-574
    • Lang, G.I.1    Rice, D.P.2    Hickman, M.J.3    Sodergren, E.4    Weinstock, G.M.5    Botstein, D.6
  • 22
    • 55549097836 scopus 로고    scopus 로고
    • Mapping short DNA sequencing reads and calling variants using mapping quality scores
    • Li H, Ruan J, Durbin R. (2008). Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18: 1851-1858
    • (2008) Genome Res , vol.18 , pp. 1851-1858
    • Li, H.1    Ruan, J.2    Durbin, R.3
  • 23
    • 0028032013 scopus 로고
    • Reduction of chromate by desulfovibrio vulgaris and its c3 cytochrome
    • Lovley DR, Phillips EJP. (1994). Reduction of chromate by Desulfovibrio vulgaris and its c3 cytochrome. Appl Environ Microbiol 60: 726-728
    • (1994) Appl Environ Microbiol , vol.60 , pp. 726-728
    • Lovley, D.R.1    Phillips, E.J.P.2
  • 24
    • 0041305844 scopus 로고    scopus 로고
    • Identification of histidine kinases that act as sensors in the perception of salt stress in synechocystis sp
    • Marin K, Suzuki I, Yamaguchi K, Ribbeck K, Yamamoto H, Kanesaki Y, et al. (2003). Identification of histidine kinases that act as sensors in the perception of salt stress in Synechocystis sp. PCC 6803. Proc Natl Acad Sci USA 100: 9061-9066
    • (2003) PCC 6803. Proc Natl Acad Sci USA , vol.100 , pp. 9061-9066
    • Marin, K.1    Suzuki, I.2    Yamaguchi, K.3    Ribbeck, K.4    Yamamoto, H.5    Kanesaki, Y.6
  • 25
    • 0037059058 scopus 로고    scopus 로고
    • The membrane protein feob contains an intramolecular g protein essential for fe(II) uptake in bacteria
    • Marlovits TC, Haase W, Herrmann C, Aller SG, Unger VM . (2002). The membrane protein FeoB contains an intramolecular G protein essential for Fe(II) uptake in bacteria. Proc Natl Acad Sci USA 99: 16243-16248
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 16243-16248
    • Marlovits, T.C.1    Haase, W.2    Herrmann, C.3    Aller, S.G.4    Unger, V.M.5
  • 26
    • 0035910286 scopus 로고    scopus 로고
    • The crystal structure of beta-ketoacyl-Acyl carrier protein synthase II from Synechocystis sp. at 1.54A resolution and its relationship to other condensing enzymes
    • Moche M, Dehesh K, Edwards P, Lindqvist Y. (2001). The crystal structure of beta-ketoacyl-Acyl carrier protein synthase II from Synechocystis sp. at 1.54A resolution and its relationship to other condensing enzymes. J Mol Biol 305: 491-503
    • (2001) J Mol Biol , vol.305 , pp. 491-503
    • Moche, M.1    Dehesh, K.2    Edwards, P.3    Lindqvist, Y.4
  • 27
    • 33744776637 scopus 로고    scopus 로고
    • Salt stress in desulfovibrio vulgaris hildenborough: An integrated genomics approach
    • Mukhopadhyay A, He Z, Alm E, Arkin A, Baidoo E, Borglin S, et al. (2006). Salt stress in Desulfovibrio vulgaris Hildenborough: an integrated genomics approach. J Bacteriol 188: 4068-4078
    • (2006) J Bacteriol , vol.188 , pp. 4068-4078
    • Mukhopadhyay, A.1    He, Z.2    Alm, E.3    Arkin, A.4    Baidoo, E.5    Borglin, S.6
  • 29
    • 0034213941 scopus 로고    scopus 로고
    • The emergence and maintenance of diversity: Insights from experimental bacterial populations
    • Rainey PB, Buckling A, Kassen R, Travisano M. (2000). The emergence and maintenance of diversity: insights from experimental bacterial populations. Trends Ecol Evol 15: 243-247
    • (2000) Trends Ecol Evol , vol.15 , pp. 243-247
    • Rainey, P.B.1    Buckling, A.2    Kassen, R.3    Travisano, M.4
  • 30
    • 80053912671 scopus 로고    scopus 로고
    • Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium
    • Rajeev L, Luning E, Dehal P, Price M, Arkin A, Mukhopadhyay A. (2011). Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium. Genome Biol 12: R99
    • (2011) Genome Biol , vol.12 , pp. R99
    • Rajeev, L.1    Luning, E.2    Dehal, P.3    Price, M.4    Arkin, A.5    Mukhopadhyay, A.6
  • 31
    • 33646498780 scopus 로고    scopus 로고
    • Organic compatible solutes of halotolerant and halophilic microorganisms
    • Roberts M. (2005). Organic compatible solutes of halotolerant and halophilic microorganisms. Saline Syst 1: 5
    • (2005) Saline Syst , vol.1 , pp. 5
    • Roberts, M.1
  • 32
    • 79961049020 scopus 로고    scopus 로고
    • Large-scale comparative phenotypic and genomic analyses reveal ecological preferences of shewanella species and identify metabolic pathways conserved at the genus level
    • Rodrigues JLM, Serres MH, Tiedje JM. (2011). Large-scale comparative phenotypic and genomic analyses reveal ecological preferences of Shewanella species and identify metabolic pathways conserved at the genus Level. Appl Environl Microbiol 77: 5352-5360
    • (2011) Appl Environl Microbiol , vol.77 , pp. 5352-5360
    • Rodrigues, J.L.M.1    Serres, M.H.2    Tiedje, J.M.3
  • 33
    • 72949085559 scopus 로고    scopus 로고
    • The properties of adaptive walks in evolving populations of fungus
    • Schoustra SE, Bataillon T, Gifford DR, Kassen R. (2009). The properties of adaptive walks in evolving populations of fungus. PLoS Biol 7: e1000250
    • (2009) PLoS Biol , vol.7 , pp. e1000250
    • Schoustra, S.E.1    Bataillon, T.2    Gifford, D.R.3    Kassen, R.4
  • 34
    • 73449104573 scopus 로고    scopus 로고
    • Compensatory evolution of gene regulation in response to stress by Escherichia coli lacking rpos
    • Stoebel DM, Hokamp K, Last MS, Dorman CJ. (2009). Compensatory evolution of gene regulation in response to stress by Escherichia coli lacking RpoS. PLoS Genet 5: e1000671
    • (2009) PLoS Genet , vol.5 , pp. e1000671
    • Stoebel, D.M.1    Hokamp, K.2    Last, M.S.3    Dorman, C.J.4
  • 35
    • 84859911840 scopus 로고    scopus 로고
    • Laboratory evolution of geobacter sulfurreducens for enhanced growth on lactate via a single-basepair substitution in a transcriptional regulator
    • Summers ZM, Ueki T, Ismail W, Haveman SA, Lovley DR. (2012). Laboratory evolution of Geobacter sulfurreducens for enhanced growth on lactate via a single-basepair substitution in a transcriptional regulator. ISME J 6: 975-983
    • (2012) ISME J , vol.6 , pp. 975-983
    • Summers, Z.M.1    Ueki, T.2    Ismail, W.3    Haveman, S.A.4    Lovley, D.R.5
  • 37
    • 0031876504 scopus 로고    scopus 로고
    • Repeated evolution of an acetate-crossfeeding polymorphism in longterm populations of Escherichia coli
    • Treves DS, Manning S, Adams J. (1998). Repeated evolution of an acetate-crossfeeding polymorphism in longterm populations of Escherichia coli. Mol Biol Evol 15: 789-797
    • (1998) Mol Biol Evol , vol.15 , pp. 789-797
    • Treves, D.S.1    Manning, S.2    Adams, J.3
  • 38
    • 0036837968 scopus 로고    scopus 로고
    • Carbon monoxide cycling by desulfovibrio vulgaris hildenborough
    • Voordouw G. (2002). Carbon monoxide cycling by Desulfovibrio vulgaris Hildenborough. J Bacteriol 184: 5903-5911
    • (2002) J Bacteriol , vol.184 , pp. 5903-5911
    • Voordouw, G.1
  • 40
    • 84861849986 scopus 로고    scopus 로고
    • The inner membrane histidine kinase envz senses osmolality via helix-coil transitions in the cytoplasm
    • Wang LC, Morgan LK, Godakumbura P, Kenney LJ, Anand GS. (2012). The inner membrane histidine kinase EnvZ senses osmolality via helix-coil transitions in the cytoplasm. EMBO J 31: 2648-2659
    • (2012) EMBO J , vol.31 , pp. 2648-2659
    • Wang, L.C.1    Morgan, L.K.2    Godakumbura, P.3    Kenney, L.J.4    Anand, G.S.5
  • 42
    • 0347994900 scopus 로고    scopus 로고
    • High-resolution yeast phenomics resolves different physiological features in the saline response
    • Warringer J, Ericson E, Fernandez L, Nerman O, Blomberg A. (2003). High-resolution yeast phenomics resolves different physiological features in the saline response. Proc Natl Acad Sci USA 100: 15724-15729
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 15724-15729
    • Warringer, J.1    Ericson, E.2    Fernandez, L.3    Nerman, O.4    Blomberg, A.5
  • 43
    • 84901358601 scopus 로고    scopus 로고
    • Evolved osmotolerant Escherichia coli mutants frequently exhibit defective n-Acetylglucosamine catabolism and point mutations in cell shape-regulating protein mreb
    • Winkler JD, Garcia C, Olson M, Callaway E, Kao KC. (2014). Evolved osmotolerant Escherichia coli mutants frequently exhibit defective N-Acetylglucosamine catabolism and point mutations in cell shape-regulating protein MreB. Appl Environl Microbiol 80: 3729-3740
    • (2014) Appl Environl Microbiol , vol.80 , pp. 3729-3740
    • Winkler, J.D.1    Garcia, C.2    Olson, M.3    Callaway, E.4    Kao, K.C.5
  • 44
    • 14844363079 scopus 로고    scopus 로고
    • The number of mutations selected during adaptation in a laboratory population of saccharomyces cerevisiae
    • Zeyl C. (2005). The number of mutations selected during adaptation in a laboratory population of Saccharomyces cerevisiae. Genetics 169: 1825-1831
    • (2005) Genetics , vol.169 , pp. 1825-1831
    • Zeyl, C.1
  • 45
    • 84883161070 scopus 로고    scopus 로고
    • Characterization of nacl tolerance in desulfovibrio vulgaris hildenborough through experimental evolution
    • Zhou A, Baidoo E, He Z, Mukhopadhyay A, Baumohl JK, Benke P, et al. (2013). Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution. ISME J 7: 1790-1802
    • (2013) ISME J , vol.7 , pp. 1790-1802
    • Zhou, A.1    Baidoo, E.2    He, Z.3    Mukhopadhyay, A.4    Baumohl, J.K.5    Benke, P.6
  • 47
    • 79956076088 scopus 로고    scopus 로고
    • How sulphate-reducing microorganisms cope with stress: Lessons from systems biology
    • Zhou J, He Q, Hemme CL, Mukhopadhyay A, Hillesland K, Zhou A, et al. (2011). How sulphate-reducing microorganisms cope with stress: lessons from systems biology. Nat Rev Microbiol 9: 452-466
    • (2011) Nat Rev Microbiol , vol.9 , pp. 452-466
    • Zhou, J.1    He, Q.2    Hemme, C.L.3    Mukhopadhyay, A.4    Hillesland, K.5    Zhou, A.6
  • 48
    • 67650576959 scopus 로고    scopus 로고
    • Functions of the clostridium acetobutylicium fabf and fabz proteins in unsaturated fatty acid biosynthesis
    • Zhu L, Cheng J, Luo B, Feng S, Lin J, Wang S, et al. (2009). Functions of the Clostridium acetobutylicium FabF and FabZ proteins in unsaturated fatty acid biosynthesis. BMC Microbiol 9: 119
    • (2009) BMC Microbiol , vol.9 , pp. 119
    • Zhu, L.1    Cheng, J.2    Luo, B.3    Feng, S.4    Lin, J.5    Wang, S.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.