메뉴 건너뛰기




Volumn 6, Issue 5, 2012, Pages 975-983

Laboratory evolution of Geobacter sulfurreducens for enhanced growth on lactate via a single-base-pair substitution in a transcriptional regulator

Author keywords

evolution; genome sequencing; geobacter; subsurface

Indexed keywords

BACTERIAL DNA; GROUND WATER; LACTIC ACID;

EID: 84859911840     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2011.166     Document Type: Article
Times cited : (32)

References (58)
  • 1
    • 77954948121 scopus 로고    scopus 로고
    • Interference with histidyltRNA synthetase by a CRISPR spacer sequence as a factor in the evolution of Pelobacter carbinolicus
    • Aklujkar M, Lovley DR. (2010). Interference with histidyltRNA synthetase by a CRISPR spacer sequence as a factor in the evolution of Pelobacter carbinolicus. BMC Evol Biol 10: 230.
    • (2010) BMC Evol Biol , vol.10 , pp. 230
    • Aklujkar, M.1    Lovley, D.R.2
  • 3
    • 30344472977 scopus 로고    scopus 로고
    • Adaptive evolution by optimizing expression levels in different environments
    • DOI 10.1016/j.tim.2005.11.005, PII S0966842X05003100
    • Babu MM, Aravind L. (2006). Adaptive evolution by optimizing expression levels in different environments. Trends Microbiol 14: 11-14. (Pubitemid 43063186)
    • (2006) Trends in Microbiology , vol.14 , Issue.1 , pp. 11-14
    • Babu, M.M.1    Aravind, L.2
  • 5
    • 0018419825 scopus 로고
    • Methanogens: Reevaluation of a unique biological group
    • Balch WE, Fox GE, Magrum LJ, Woese CR, Wolfe RS. (1979). Methanogens: Reevaluation of a unique biological group. Microbiol Rev 43: 260-296. (Pubitemid 9231879)
    • (1979) Microbiological Reviews , vol.43 , Issue.2 , pp. 260-296
    • Balch, W.E.1    Fox, G.E.2    Magrum, L.J.3
  • 6
    • 70350641005 scopus 로고    scopus 로고
    • Genome evolution and adaptation in a long-term experiment with Escherichia coli
    • Barrick JE, Yu DS, Yoon SH, Jeong H, Oh TK, Schneider D et al. (2009). Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461: 1243-1247.
    • (2009) Nature , vol.461 , pp. 1243-1247
    • Barrick, J.E.1    Yu, D.S.2    Yoon, S.H.3    Jeong, H.4    Oh, T.K.5    Schneider, D.6
  • 7
    • 79951808135 scopus 로고    scopus 로고
    • Nextgeneration sequencing as a tool to study microbial evolution
    • Brockhurst MA, Colegrave N, Rozen DE. (2010). Nextgeneration sequencing as a tool to study microbial evolution. Mol Ecol 20: 972-980.
    • (2010) Mol Ecol , vol.20 , pp. 972-980
    • Brockhurst, M.A.1    Colegrave, N.2    Rozen, D.E.3
  • 10
    • 78650546051 scopus 로고    scopus 로고
    • RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media
    • Conrad TM, Frazier M, Joyce AR, Cho BK, Knight EM, Lewis NE et al. (2010). RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media. Proc Natl Acad Sci USA 107: 20500-20505.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 20500-20505
    • Conrad, T.M.1    Frazier, M.2    Joyce, A.R.3    Cho, B.K.4    Knight, E.M.5    Lewis, N.E.6
  • 11
    • 75349114758 scopus 로고    scopus 로고
    • Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations
    • Conrad TM, Joyce AR, Applebee MK, Barrett CL, Xie B, Gao Y et al. (2009). Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations. Genome Biol 10: R118.
    • (2009) Genome Biol , vol.10
    • Conrad, T.M.1    Joyce, A.R.2    Applebee, M.K.3    Barrett, C.L.4    Xie, B.5    Gao, Y.6
  • 14
    • 15544376421 scopus 로고    scopus 로고
    • Long-term experimental evolution in Escherichia coli. XII. DNA topology as a key target of selection
    • DOI 10.1534/genetics.104.035717
    • Crozat E, Philippe N, Lenski RE, Geiselmann J, Schneider D. (2005). Long-term experimental evolution in Escherichia coli. XII. DNA topology as a key target of selection. Genetics 169: 523-532. (Pubitemid 40404290)
    • (2005) Genetics , vol.169 , Issue.2 , pp. 523-532
    • Crozat, E.1    Philippe, N.2    Lenski, R.E.3    Geiselmann, J.4    Schneider, D.5
  • 16
    • 23144432213 scopus 로고    scopus 로고
    • Optimality and evolutionary tuning of the expression level of a protein
    • DOI 10.1038/nature03842
    • Dekel E, Alon U. (2005). Optimality and evolutionary tuning of the expression level of a protein. Nature 436: 588-592. (Pubitemid 41112935)
    • (2005) Nature , vol.436 , Issue.7050 , pp. 588-592
    • Dekel, E.1    Alon, U.2
  • 17
    • 0035125986 scopus 로고    scopus 로고
    • In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data
    • DOI 10.1038/84379
    • Edwards JS, Ibarra RU, Palsson BO. (2001). In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotechnol 19: 125-130. (Pubitemid 32144439)
    • (2001) Nature Biotechnology , vol.19 , Issue.2 , pp. 125-130
    • Edwards, J.S.1    Ibarra, R.U.2    Palsson, B.O.3
  • 18
    • 0020793569 scopus 로고
    • A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity
    • Feinberg AP, Vogelstein B. (1983). A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochem 132: 6-13.
    • (1983) Anal Biochem , vol.132 , pp. 6-13
    • Feinberg, A.P.1    Vogelstein, B.2
  • 20
    • 0036276689 scopus 로고    scopus 로고
    • Potential for bioremediation of uranium-contaminated aquifers with microbial U(VI) reduction
    • Finneran K, Anderson R, Nevin K, Lovley D. (2002). Potential for bioremediation of uranium-contaminated aquifers with microbial U(VI) reduction. Soil Sediment Contam 11: 339-357. (Pubitemid 34617010)
    • (2002) Soil and Sediment Contamination , vol.11 , Issue.3 , pp. 339-357
    • Finneran, K.T.1    Anderson, R.T.2    Nevin, K.P.3    Lovley, D.R.4
  • 22
    • 25844495901 scopus 로고    scopus 로고
    • Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states
    • DOI 10.1101/gr.3832305
    • Fong SS, Joyce AR, Palsson BO. (2005b). Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states. Genome Res 15: 1365-1372. (Pubitemid 41400902)
    • (2005) Genome Research , vol.15 , Issue.10 , pp. 1365-1372
    • Fong, S.S.1    Joyce, A.R.2    Palsson, B.O.3
  • 23
    • 6944224154 scopus 로고    scopus 로고
    • Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes
    • DOI 10.1038/ng1432
    • Fong SS, Palsson BO. (2004). Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes. Nat Genet 36: 1056-1058. (Pubitemid 41184464)
    • (2004) Nature Genetics , vol.36 , Issue.10 , pp. 1056-1058
    • Fong, S.S.1    Palsson, B.O.2
  • 24
    • 0033681074 scopus 로고    scopus 로고
    • Oxidation of acetate through reactions of the citric acid cycle by Geobacter sulfurreducens in pure culture and in syntrophic coculture
    • Galushko AS, Schink B. (2000). Oxidation of acetate through reactions of the citric acid cycle by Geobacter sulfurreducens in pure culture and in syntrophic coculture. Arch Microbiol 174: 314-321.
    • (2000) Arch Microbiol , vol.174 , pp. 314-321
    • Galushko, A.S.1    Schink, B.2
  • 26
    • 28244484693 scopus 로고    scopus 로고
    • Developments in bioremediation of soils and sediments polluted with metals and radionuclides: 2. Field research on bioremediation of metals and radionuclides
    • DOI 10.1007/s11157-005-2170-y
    • Hazen TC, Tabak HH. (2005). Developments in bioremediation of soils and sediments polluted with metals and radionuclides: 2. Field research on bioremediation of metals and radionuclides. Rev Environ Sci Biotech 4: 157-183. (Pubitemid 41712753)
    • (2005) Re-views in Environmental Science and Biotechnology , vol.4 , Issue.3 , pp. 157-183
    • Hazen, T.C.1    Tabak, H.H.2
  • 28
    • 58549102477 scopus 로고    scopus 로고
    • Transcriptome of Geobacter uraniireducens growing in uraniumcontaminated subsurface sediments
    • Holmes DE, O'Neil RA, Chavan MA, N'Guessan LA, Vrionis HA, Perpetua LA et al. (2009). Transcriptome of Geobacter uraniireducens growing in uraniumcontaminated subsurface sediments. ISME J 3: 216-230.
    • (2009) ISME J , vol.3 , pp. 216-230
    • Holmes, D.E.1    O'Neil, R.A.2    Chavan, M.A.3    N'Guessan, L.A.4    Vrionis, H.A.5    Perpetua, L.A.6
  • 29
    • 0037079023 scopus 로고    scopus 로고
    • Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth
    • DOI 10.1038/nature01149
    • Ibarra RU, Edwards JS, Palsson BO. (2002). Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 420: 186-189. (Pubitemid 35340123)
    • (2002) Nature , vol.420 , Issue.6912 , pp. 186-189
    • Ibarra, R.U.1    Edwards, J.S.2    Palsson, B.O.3
  • 30
    • 33748335479 scopus 로고    scopus 로고
    • Unraveling adaptive evolution: How a single point mutation affects the protein coregulation network
    • DOI 10.1038/ng1867, PII NG1867
    • Knight CG, Zitzmann N, Prabhakar S, Antrobus R, Dwek R, Hebestreit H et al. (2006). Unraveling adaptive evolution: How a single point mutation affects the protein coregulation network. Nat Genet 38: 1015-1022. (Pubitemid 44325926)
    • (2006) Nature Genetics , vol.38 , Issue.9 , pp. 1015-1022
    • Knight, C.G.1    Zitzmann, N.2    Prabhakar, S.3    Antrobus, R.4    Dwek, R.5    Hebestreit, H.6    Rainey, P.B.7
  • 32
    • 33646129914 scopus 로고    scopus 로고
    • The IclR family of transcriptional activators and repressors can be defined by a single profile
    • Krell T, Molina-Henares AJ, Ramos JL. (2006). The IclR family of transcriptional activators and repressors can be defined by a single profile. Protein Sci 15: 1207-1213.
    • (2006) Protein Sci , vol.15 , pp. 1207-1213
    • Krell, T.1    Molina-Henares, A.J.2    Ramos, J.L.3
  • 33
    • 77954265373 scopus 로고    scopus 로고
    • Adaptive evolution of Escherichia coli K-12 MG1655 during growth on a Nonnative carbon source, L-1,2-propanediol
    • Lee DH, Palsson BO. (2010). Adaptive evolution of Escherichia coli K-12 MG1655 during growth on a Nonnative carbon source, L-1,2-propanediol. Appl Environ Microbiol 76: 4158-4168.
    • (2010) Appl Environ Microbiol , vol.76 , pp. 4158-4168
    • Lee, D.H.1    Palsson, B.O.2
  • 34
    • 2142763872 scopus 로고    scopus 로고
    • Cleaning up with genomics: Applying molecular biology to bioremediation
    • Lovley DR. (2003). Cleaning up with genomics: Applying molecular biology to bioremediation. Nat Rev Microbiol 1: 35-44.
    • (2003) Nat Rev Microbiol , vol.1 , pp. 35-44
    • Lovley, D.R.1
  • 35
    • 0029540914 scopus 로고
    • Deep subsurface microbial processes
    • Lovley DR, Chapelle FH. (1995). Deep subsurface microbial processes. Revi Geophys 33: 365-381. (Pubitemid 26456977)
    • (1995) Reviews of Geophysics , vol.33 , Issue.3 , pp. 365-381
    • Lovley, D.R.1    Chapelle, F.H.2
  • 37
    • 78650298909 scopus 로고    scopus 로고
    • In situ to in silico and back: Elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling
    • Mahadevan R, Palsson BO, Lovley DR. (2011). In situ to in silico and back: Elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling. Nat Rev Microbiol 9: 39-50.
    • (2011) Nat Rev Microbiol , vol.9 , pp. 39-50
    • Mahadevan, R.1    Palsson, B.O.2    Lovley, D.R.3
  • 38
    • 0036841380 scopus 로고    scopus 로고
    • Broad-host-range cre-lox system for antibiotic marker recycling in Gram-negative bacteria
    • Marx CJ, Lidstrom ME. (2002). Broad-host-range cre-lox system for antibiotic marker recycling in gram-negative bacteria. Biotechniques 33: 1062-1067. (Pubitemid 35285540)
    • (2002) BioTechniques , vol.33 , Issue.5 , pp. 1062-1067
    • Marx, C.J.1    Lidstrom, M.E.2
  • 40
    • 33644964124 scopus 로고    scopus 로고
    • Members of the IclR family of bacterial transcriptional regulators function as activators and/or repressors
    • Molina-Henares AJ, Krell T, Eugenia Guazzaroni M, Segura A, Ramos JL. (2006). Members of the IclR family of bacterial transcriptional regulators function as activators and/or repressors. FEMS Microbiol Rev 30: 157-186.
    • (2006) FEMS Microbiol Rev , vol.30 , pp. 157-186
    • Molina-Henares, A.J.1    Krell, T.2    Eugenia Guazzaroni, M.3    Segura, A.4    Ramos, J.L.5
  • 41
    • 42149145227 scopus 로고    scopus 로고
    • Sustained removal of uranium from contaminated groundwater following stimulation of dissimilatory metal reduction
    • DOI 10.1021/es071960p
    • N'Guessan AL, Vrionis HA, Resch CT, Long PE, Lovley DR. (2008). Sustained removal of uranium from contaminated groundwater following stimulation of dissimilatory metal reduction. Environ Sci Technol 42: 2999-3004. (Pubitemid 351536945)
    • (2008) Environmental Science and Technology , vol.42 , Issue.8 , pp. 2999-3004
    • N'Guessan, A.L.1    Vrionis, H.A.2    Resch, C.T.3    Long, P.E.4    Lovley, D.R.5
  • 42
    • 33747849237 scopus 로고    scopus 로고
    • Parallel changes in global protein profiles during long-term experimental evolution in Escherichia coli
    • DOI 10.1534/genetics.105.049619
    • Pelosi L, Kuhn L, Guetta D, Garin J, Geiselmann J, Lenski RE et al. (2006). Parallel changes in global protein profiles during long-term experimental evolution in Escherichia coli. Genetics 173: 1851-1869. (Pubitemid 44285668)
    • (2006) Genetics , vol.173 , Issue.4 , pp. 1851-1869
    • Pelosi, L.1    Kuhn, L.2    Guetta, D.3    Garin, J.4    Geiselmann, J.5    Lenski, R.E.6    Schneider, D.7
  • 43
    • 34548769341 scopus 로고    scopus 로고
    • Evolution of global regulatory networks during a long-term experiment with Escherichia coli
    • DOI 10.1002/bies.20629
    • Philippe N, Crozat E, Lenski RE, Schneider D. (2007). Evolution of global regulatory networks during a longterm experiment with Escherichia coli. Bioessays 29: 846-860. (Pubitemid 47424895)
    • (2007) BioEssays , vol.29 , Issue.9 , pp. 846-860
    • Philippe, N.1    Crozat, E.2    Lenski, R.E.3    Schneider, D.4
  • 44
    • 21344461500 scopus 로고    scopus 로고
    • Extracellular electron transfer via microbial nanowires
    • DOI 10.1038/nature03661
    • Reguera G,McCarthy KD, Mehta T, Nicoll JS, TuominenMT, Lovley DR. (2005). Extracellular electron transfer via microbial nanowires. Nature 435: 1098-1101. (Pubitemid 40910516)
    • (2005) Nature , vol.435 , Issue.7045 , pp. 1098-1101
    • Reguera, G.1    McCarthy, K.D.2    Mehta, T.3    Nicoll, J.S.4    Tuominen, M.T.5    Lovley, D.R.6
  • 46
    • 69849084132 scopus 로고    scopus 로고
    • Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation
    • Scheibe TD, Mahadevan R, Fang Y, Garg S, Long PE, Lovley DR. (2009). Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation. Microb Biotechnol 2: 274-286.
    • (2009) Microb Biotechnol , vol.2 , pp. 274-286
    • Scheibe, T.D.1    Mahadevan, R.2    Fang, Y.3    Garg, S.4    Long, P.E.5    Lovley, D.R.6
  • 47
    • 40149105737 scopus 로고    scopus 로고
    • Computational and experimental analysis of redundancy in the central metabolism of Geobacter sulfurreducens
    • Segura D, Mahadevan R, Juarez K, Lovley DR. (2008). Computational and experimental analysis of redundancy in the central metabolism of Geobacter sulfurreducens. PLoS Comput Biol 4: E36.
    • (2008) PLoS Comput Biol , vol.4
    • Segura, D.1    Mahadevan, R.2    Juarez, K.3    Lovley, D.R.4
  • 48
    • 0036811766 scopus 로고    scopus 로고
    • Fitness evolution and the rise of mutator alleles in experimental Escherichia coli populations
    • Shaver AC, Dombrowski PG, Sweeney JY, Treis T, Zappala RM, Sniegowski PD. (2002). Fitness evolution and the rise of mutator alleles in experimental Escherichia coli populations. Genetics 162: 557-566. (Pubitemid 35365023)
    • (2002) Genetics , vol.162 , Issue.2 , pp. 557-566
    • Shaver, A.C.1    Dombrowski, P.G.2    Sweeney, J.Y.3    Treis, T.4    Zappala, R.M.5    Sniegowski, P.D.6
  • 50
    • 67650904950 scopus 로고    scopus 로고
    • Understanding the adaptive growth strategy of Lactobacillus plantarum by in silico optimisation
    • Teusink B, Wiersma A, Jacobs L, Notebaart RA, Smid EJ. (2009). Understanding the adaptive growth strategy of Lactobacillus plantarum by in silico optimisation. PLoS Comput Biol 5: E1000410.
    • (2009) PLoS Comput Biol , vol.5
    • Teusink, B.1    Wiersma, A.2    Jacobs, L.3    Notebaart, R.A.4    Smid, E.J.5
  • 51
    • 78650778559 scopus 로고    scopus 로고
    • A c-type cytochrome and a transcriptional regulator responsible for enhanced extracellular electron transfer in Geobacter sulfurreducens revealed by adaptive evolution
    • Tremblay PL, Summers ZM, Glaven RH, Nevin KP, Zengler K, Barrett CL et al. (2011). A c-type cytochrome and a transcriptional regulator responsible for enhanced extracellular electron transfer in Geobacter sulfurreducens revealed by adaptive evolution. Environ Microbiol 13: 13-23.
    • (2011) Environ Microbiol , vol.13 , pp. 13-23
    • Tremblay, P.L.1    Summers, Z.M.2    Glaven, R.H.3    Nevin, K.P.4    Zengler, K.5    Barrett, C.L.6
  • 52
    • 0031876504 scopus 로고    scopus 로고
    • Repeated evolution of an acetate-crossfeeding polymorphism in long-term populations of Escherichia coli
    • Treves DS, Manning S, Adams J. (1998). Repeated evolution of an acetate-crossfeeding polymorphism in long-term populations of Escherichia coli. Mol Biol Evol 15: 789-797. (Pubitemid 28321878)
    • (1998) Molecular Biology and Evolution , vol.15 , Issue.7 , pp. 789-797
    • Treves, D.S.1    Manning, S.2    Adams, J.3
  • 53
    • 0037155137 scopus 로고    scopus 로고
    • Transcriptional activation of a heat-shock gene, lonD, of Myxococcus xanthus by a two component histidine-aspartate phosphorelay system
    • DOI 10.1074/jbc.M110155200
    • Ueki T, Inouye S. (2002). Transcriptional activation of a heat-shock gene, lonD, of Myxococcus xanthus by a two component histidine-aspartate phosphorelay system. J Biol Chem 277: 6170-6177. (Pubitemid 34968406)
    • (2002) Journal of Biological Chemistry , vol.277 , Issue.8 , pp. 6170-6177
    • Ueki, T.1    Inouye, S.2
  • 54
    • 25444465658 scopus 로고    scopus 로고
    • Identification of a gene involved in polysaccharide export as a transcription target of FruA, an essential factor for Myxococcus xanthus development
    • DOI 10.1074/jbc.M507191200
    • Ueki T, Inouye S. (2005). Identification of a gene involved in polysaccharide export as a transcription target of FruA, an essential factor for Myxococcus xanthus development. J Biol Chem 280: 32279-32284. (Pubitemid 41361836)
    • (2005) Journal of Biological Chemistry , vol.280 , Issue.37 , pp. 32279-32284
    • Ueki, T.1    Inouye, S.2
  • 55
    • 0036736638 scopus 로고    scopus 로고
    • The apparent clock-like evolution of Escherichia coli in glucoselimited chemostats is reproducible at large but not at small population sizes and can be explained with Monod kinetics
    • Wick LM, Weilenmann H, Egli T. (2002). The apparent clock-like evolution of Escherichia coli in glucoselimited chemostats is reproducible at large but not at small population sizes and can be explained with Monod kinetics. Microbiology 148: 2889-2902.
    • (2002) Microbiology , vol.148 , pp. 2889-2902
    • Wick, L.M.1    Weilenmann, H.2    Egli, T.3
  • 56
    • 34548415488 scopus 로고    scopus 로고
    • Genome-wide similarity search for transcription factors and their binding sites in a metal-reducing prokaryote Geobacter sulfurreducens
    • DOI 10.1016/j.biosystems.2006.10.006, PII S0303264706002103
    • Yan B, Lovley DR, Krushkal J. (2007). Genome-wide similarity search for transcription factors and their binding sites in a metal-reducing prokaryote Geobacter sulfurreducens. Biosystems 90: 421-441. (Pubitemid 47362461)
    • (2007) BioSystems , vol.90 , Issue.2 , pp. 421-441
    • Yan, B.1    Lovley, D.R.2    Krushkal, J.3
  • 58
    • 78751584992 scopus 로고    scopus 로고
    • Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments
    • Zhuang K, Izallalen M, Mouser P, Richter H, Risso C, Mahadevan R et al. (2010). Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments. ISME J 5: 305-316.
    • (2010) ISME J , vol.5 , pp. 305-316
    • Zhuang, K.1    Izallalen, M.2    Mouser, P.3    Richter, H.4    Risso, C.5    Mahadevan, R.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.