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Volumn 11, Issue 3, 2016, Pages

Evolution of E. coli on [U-13C]glucose reveals a negligible isotopic influence on metabolism and physiology

Author keywords

[No Author keywords available]

Indexed keywords

ACETIC ACID; CARBON 13; GLUCOSE; OXYGEN; BACTERIAL DNA; CARBON;

EID: 84962602150     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0151130     Document Type: Article
Times cited : (47)

References (31)
  • 1
    • 84922448166 scopus 로고    scopus 로고
    • Methods and advances in metabolic flux analysis: A mini-review
    • 25613286
    • Antoniewicz MR. Methods and advances in metabolic flux analysis: a mini-review. J Ind Microbiol Biotechnol. 2015;42(3):317-25. doi: 10.1007/s10295-015-1585-x PMID: 25613286.
    • (2015) J Ind Microbiol Biotechnol. , vol.42 , Issue.3 , pp. 317-325
    • Antoniewicz, M.R.1
  • 2
    • 84887622596 scopus 로고    scopus 로고
    • Dynamic metabolic flux analysis-tools for probing transient states of metabolic networks
    • 23611566
    • Antoniewicz MR. Dynamic metabolic flux analysis-tools for probing transient states of metabolic networks. Curr Opin Biotechnol. 2013;24(6):973-8. doi: 10.1016/j.copbio.2013.03.018 PMID: 23611566.
    • (2013) Curr Opin Biotechnol. , vol.24 , Issue.6 , pp. 973-978
    • Antoniewicz, M.R.1
  • 3
    • 76749097100 scopus 로고    scopus 로고
    • Metabolic flux analysis and pharmaceutical production
    • 19861167
    • Boghigian BA, Seth G, Kiss R, Pfeifer BA. Metabolic flux analysis and pharmaceutical production. Metabolic engineering. 2010;12(2):81-95. doi: 10.1016/j.ymben. 2009.10.004 PMID: 19861167.
    • (2010) Metabolic engineering. , vol.12 , Issue.2 , pp. 81-95
    • Boghigian, B.A.1    Seth, G.2    Kiss, R.3    Pfeifer, B.A.4
  • 5
    • 0000147656 scopus 로고
    • Carbon isotope discrimination and photosynthesis
    • WOS: A1989U857900019
    • Farquhar GD, Ehleringer JR, Hubick KT. Carbon Isotope Discrimination and Photosynthesis. Annu Rev Plant Phys. 1989;40:503-37. doi: 10.1146/Annurev. Arplant.40.1.503 PMID: WOS: A1989U857900019.
    • (1989) Annu Rev Plant Phys. , vol.40 , pp. 503-537
    • Farquhar, G.D.1    Ehleringer, J.R.2    Hubick, K.T.3
  • 6
    • 84883803981 scopus 로고    scopus 로고
    • Kinetic isotope effects significantly influence intracellular metabolite (13) C labeling patterns and flux determination
    • 23828762 PubMed Central PMCID: PMC4045492
    • Wasylenko TM, Stephanopoulos G. Kinetic isotope effects significantly influence intracellular metabolite (13) C labeling patterns and flux determination. Biotechnology journal. 2013;8(9):1080-9. doi: 10. 1002/biot.201200276 PMID: 23828762; PubMed Central PMCID: PMC4045492.
    • (2013) Biotechnology journal. , vol.8 , Issue.9 , pp. 1080-1089
    • Wasylenko, T.M.1    Stephanopoulos, G.2
  • 7
    • 84879489028 scopus 로고    scopus 로고
    • Adaptive laboratory evolution-principles and applications for biotechnology
    • 23815749 Epub 2013/07/03, PubMed Central PMCID: PMC3716822
    • Dragosits M, Mattanovich D. Adaptive laboratory evolution-principles and applications for biotechnology. Microb Cell Fact. 2013;12:64. Epub 2013/07/03. doi: 10.1186/1475-2859-12-64 PMID: 23815749; PubMed Central PMCID: PMC3716822.
    • (2013) Microb Cell Fact. , vol.12 , pp. 64
    • Dragosits, M.1    Mattanovich, D.2
  • 8
    • 84890116570 scopus 로고    scopus 로고
    • Long-term dynamics of adaptation in asexual populations
    • 24231808
    • Wiser MJ, Ribeck N, Lenski RE. Long-term dynamics of adaptation in asexual populations. Science. 2013;342(6164):1364-7. doi: 10.1126/science.1243357 PMID: 24231808.
    • (2013) Science. , vol.342 , Issue.6164 , pp. 1364-1367
    • Wiser, M.J.1    Ribeck, N.2    Lenski, R.E.3
  • 9
    • 84917705874 scopus 로고    scopus 로고
    • Use of adaptive laboratory evolution to discover key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal medium
    • 25304508 PubMed Central PMCID: PMC4272732
    • La Croix RA, Sandberg TE, O'Brien EJ, Utrilla J, Ebrahim A, Guzman GI, et al. Use of adaptive laboratory evolution to discover key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal medium. Appl Environ Microbiol. 2015;81(1):17-30. doi: 10.1128/AEM.02246-14 PMID: 25304508; PubMed Central PMCID: PMC4272732.
    • (2015) Appl Environ Microbiol. , vol.81 , Issue.1 , pp. 17-30
    • La Croix, R.A.1    Sandberg, T.E.2    O'Brien, E.J.3    Utrilla, J.4    Ebrahim, A.5    Guzman, G.I.6
  • 10
    • 84907269737 scopus 로고    scopus 로고
    • Evolution of Escherichia coli to 42 degrees C and subsequent genetic engineering reveals adaptive mechanisms and novel mutations
    • 25015645 PubMed Central PMCID: PMC4166923
    • Sandberg TE, Pedersen M, La Croix RA, Ebrahim A, Bonde M, Herrgard MJ, et al. Evolution of Escherichia coli to 42 degrees C and subsequent genetic engineering reveals adaptive mechanisms and novel mutations. Molecular biology and evolution. 2014;31(10):2647-62. doi: 10.1093/molbev/msu209 PMID: 25015645; PubMed Central PMCID: PMC4166923.
    • (2014) Molecular Biology and Evolution , vol.31 , Issue.10 , pp. 2647-2662
    • Sandberg, T.E.1    Pedersen, M.2    La Croix, R.A.3    Ebrahim, A.4    Bonde, M.5    Herrgard, M.J.6
  • 11
    • 84856258903 scopus 로고    scopus 로고
    • The molecular diversity of adaptive convergence
    • 22282810 Epub 2012/01/28
    • Tenaillon O, Rodriguez-Verdugo A, Gaut RL, McDonald P, Bennett AF, Long AD, et al. The molecular diversity of adaptive convergence. Science. 2012;335(6067):457-61. Epub 2012/01/28. doi: 10.1126/science.1212986 PMID: 22282810.
    • (2012) Science. , vol.335 , Issue.6067 , pp. 457-461
    • Tenaillon, O.1    Rodriguez-Verdugo, A.2    Gaut, R.L.3    McDonald, P.4    Bennett, A.F.5    Long, A.D.6
  • 12
    • 80054773605 scopus 로고    scopus 로고
    • Cumulative number of cell divisions as a meaningful timescale for adaptive laboratory evolution of Escherichia coli
    • 22028828 PubMed Central PMCID: PMC3196513
    • Lee DH, Feist AM, Barrett CL, Palsson BO. Cumulative number of cell divisions as a meaningful timescale for adaptive laboratory evolution of Escherichia coli. PLoS One. 2011;6(10):e26172. doi: 10. 1371/journal.pone.0026172 PMID: 22028828; PubMed Central PMCID: PMC3196513.
    • (2011) PLoS One. , vol.6 , Issue.10 , pp. e26172
    • Lee, D.H.1    Feist, A.M.2    Barrett, C.L.3    Palsson, B.O.4
  • 13
    • 84875904855 scopus 로고    scopus 로고
    • EcoGene 3.0
    • 23197660 Database issue:, PubMed Central PMCID: PMC3531124
    • Zhou J, Rudd KE. EcoGene 3.0. Nucleic Acids Res. 2013;41(Database issue):D613-24. doi: 10.1093/nar/gks1235 PMID: 23197660; PubMed Central PMCID: PMC3531124.
    • (2013) Nucleic Acids Res. , vol.41 , pp. D613-D624
    • Zhou, J.1    Rudd, K.E.2
  • 14
    • 0027251266 scopus 로고
    • The Escherichia coli K-12 "wild types" W3110 and MG1655 have an rph frameshift mutation that leads to pyrimidine starvation due to low pyrE expression levels
    • 8501045 Epub 1993/06/01, PubMed Central PMCID: PMC204738
    • Jensen KF. The Escherichia coli K-12 "wild types" W3110 and MG1655 have an rph frameshift mutation that leads to pyrimidine starvation due to low pyrE expression levels. J Bacteriol. 1993;175(11):3401-7. Epub 1993/06/01. PMID: 8501045; PubMed Central PMCID: PMC204738.
    • (1993) J Bacteriol. , vol.175 , Issue.11 , pp. 3401-3407
    • Jensen, K.F.1
  • 15
    • 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
    • gb-2009-10-10-r118 19849850 Epub 2009/10/24, PubMed Central PMCID: PMC2784333
    • Conrad TM, Joyce AR, Applebee MK, Barrett CL, Xie B, Gao Y, et al. 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. 2009;10(10):R118. Epub 2009/10/24. doi: 10.1186/gb-2009-10-10-r118 gb-2009-10-10-r118 [pii]. PMID: 19849850; PubMed Central PMCID: PMC2784333.
    • (2009) Genome Biol. , vol.10 , Issue.10 , pp. R118
    • Conrad, T.M.1    Joyce, A.R.2    Applebee, M.K.3    Barrett, C.L.4    Xie, B.5    Gao, Y.6
  • 16
    • 84873635856 scopus 로고    scopus 로고
    • Evolutionary potential, crossstress behavior and the genetic basis of acquired stress resistance in Escherichia coli
    • 23385483 PubMed Central PMCID: PMC3588905
    • Dragosits M, Mozhayskiy V, Quinones-Soto S, Park J, Tagkopoulos I. Evolutionary potential, crossstress behavior and the genetic basis of acquired stress resistance in Escherichia coli. Mol Syst Biol. 2013;9:643. doi: 10.1038/msb.2012.76 PMID: 23385483; PubMed Central PMCID: PMC3588905.
    • (2013) Mol Syst Biol. , vol.9 , pp. 643
    • Dragosits, M.1    Mozhayskiy, V.2    Quinones-Soto, S.3    Park, J.4    Tagkopoulos, I.5
  • 17
    • 0034176967 scopus 로고    scopus 로고
    • Replication fork arrest and DNA recombination
    • 10754549 Epub 2000/04/08
    • Michel B. Replication fork arrest and DNA recombination. Trends Biochem Sci. 2000;25(4):173-8. Epub 2000/04/08. PMID: 10754549.
    • (2000) Trends Biochem Sci. , vol.25 , Issue.4 , pp. 173-178
    • Michel, B.1
  • 18
    • 0345687900 scopus 로고    scopus 로고
    • Slipped-strand mispairing can function as a phase variation mechanism in Escherichia coli
    • 14617664 PubMed Central PMCID: PMC262711
    • Torres-Cruz J, Van Der Woude MW. Slipped-strand mispairing can function as a phase variation mechanism in Escherichia coli. J Bacteriol. 2003;185(23):6990-4. PMID: 14617664; PubMed Central PMCID: PMC262711.
    • (2003) J Bacteriol. , vol.185 , Issue.23 , pp. 6990-6994
    • Torres-Cruz, J.1    Van Der Woude, M.W.2
  • 19
    • 33845648557 scopus 로고    scopus 로고
    • Bacterial contingency loci: The role of simple sequence DNA repeats in bacterial adaptation
    • 17094739
    • Moxon R, Bayliss C, Hood D. Bacterial contingency loci: the role of simple sequence DNA repeats in bacterial adaptation. Annual review of genetics. 2006;40:307-33. doi: 10.1146/annurev. genet.40. 110405.090442 PMID: 17094739.
    • (2006) Annual Review of genetics. , vol.40 , pp. 307-333
    • Moxon, R.1    Bayliss, C.2    Hood, D.3
  • 20
    • 14244270260 scopus 로고    scopus 로고
    • Analysis of gene expression in Escherichia coli in response to changes of growth-limiting nutrient in chemostat cultures
    • 15066832 PubMed Central PMCID: PMCPMC383082
    • Hua Q, Yang C, Oshima T, Mori H, Shimizu K. Analysis of gene expression in Escherichia coli in response to changes of growth-limiting nutrient in chemostat cultures. Appl Environ Microbiol. 2004;70(4):2354-66. PMID: 15066832; PubMed Central PMCID: PMCPMC383082.
    • (2004) Appl Environ Microbiol. , vol.70 , Issue.4 , pp. 2354-2366
    • Hua, Q.1    Yang, C.2    Oshima, T.3    Mori, H.4    Shimizu, K.5
  • 21
    • 84922245805 scopus 로고    scopus 로고
    • Integrated 13C-metabolic flux analysis of 14 parallel labeling experiments in Escherichia coli
    • 25596508
    • Crown SB, Long CP, Antoniewicz MR. Integrated 13C-metabolic flux analysis of 14 parallel labeling experiments in Escherichia coli. Metab Eng. 2015;28:151-8. doi: 10.1016/j.ymben. 2015.01.001 PMID: 25596508.
    • (2015) Metab Eng. , vol.28 , pp. 151-158
    • Crown, S.B.1    Long, C.P.2    Antoniewicz, M.R.3
  • 22
    • 84964949413 scopus 로고    scopus 로고
    • Impact of kinetic isotope effects in isotopic studies of metabolic systems
    • 26410690 PubMed Central PMCID: PMCPMC4583766
    • Millard P, Portais JC, Mendes P. Impact of kinetic isotope effects in isotopic studies of metabolic systems. BMC Syst Biol. 2015;9(1):64. doi: 10.1186/s12918-015-0213-8 PMID: 26410690; PubMed Central PMCID: PMCPMC4583766.
    • (2015) BMC Syst Biol. , vol.9 , Issue.1 , pp. 64
    • Millard, P.1    Portais, J.C.2    Mendes, P.3
  • 23
    • 84917686994 scopus 로고    scopus 로고
    • Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq
    • 24838886 PubMed Central PMCID: PMC4239701
    • Deatherage DE, Barrick JE. Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. Methods in molecular biology. 2014;1151:165-88. doi: 10.1007/978-1-4939-0554-6-12 PMID: 24838886; PubMed Central PMCID: PMC4239701.
    • (2014) Methods in Molecular Biology , vol.1151 , pp. 165-188
    • Deatherage, D.E.1    Barrick, J.E.2
  • 24
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • 22388286 PubMed Central PMCID: PMC3322381
    • Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nature methods. 2012;9(4):357-9. doi: 10.1038/nmeth.1923 PMID: 22388286; PubMed Central PMCID: PMC3322381.
    • (2012) Nature methods. , vol.9 , Issue.4 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 25
    • 84907920598 scopus 로고    scopus 로고
    • Parallel labeling experiments validate Clostridium acetobutylicum metabolic network model for C metabolic flux analysis
    • 25183671
    • Au J, Choi J, Jones SW, Venkataramanan KP, Antoniewicz MR. Parallel labeling experiments validate Clostridium acetobutylicum metabolic network model for C metabolic flux analysis. Metab Eng. 2014;26:23-33. PMID: 25183671. doi: 10.1016/j.ymben. 2014.08.002
    • (2014) Metab Eng. , vol.26 , pp. 23-33
    • Au, J.1    Choi, J.2    Jones, S.W.3    Venkataramanan, K.P.4    Antoniewicz, M.R.5
  • 26
    • 84892799105 scopus 로고    scopus 로고
    • Central metabolic responses to the overproduction of fatty acids in Escherichia coli based on 13C-metabolic flux analysis
    • 24122357
    • He L, Xiao Y, Gebreselassie N, Zhang F, Antoniewicz MR, Tang YJ, et al. Central metabolic responses to the overproduction of fatty acids in Escherichia coli based on 13C-metabolic flux analysis. Biotechnol Bioeng. 2014;111(3):575-85. doi: 10.1002/bit.25124 PMID: 24122357.
    • (2014) Biotechnol Bioeng. , vol.111 , Issue.3 , pp. 575-585
    • He, L.1    Xiao, Y.2    Gebreselassie, N.3    Zhang, F.4    Antoniewicz, M.R.5    Tang, Y.J.6
  • 27
    • 77953115788 scopus 로고    scopus 로고
    • Cost of unneeded proteins in E. Coli is reduced after several generations in exponential growth
    • 20434381 Epub 2010/05/04
    • Shachrai I, Zaslaver A, Alon U, Dekel E. Cost of unneeded proteins in E. coli is reduced after several generations in exponential growth. Mol Cell. 2010;38(5):758-67. Epub 2010/05/04. doi: 10.1016/j. molcel.2010.04.015 PMID: 20434381.
    • (2010) Mol Cell. , vol.38 , Issue.5 , pp. 758-767
    • Shachrai, I.1    Zaslaver, A.2    Alon, U.3    Dekel, E.4
  • 28
    • 34249297627 scopus 로고    scopus 로고
    • Metabolic flux analysis in a nonstationary system: Fed-batch fermentation of a high yielding strain of E. Coli producing 1, 3-propanediol
    • 17400499 PubMed Central PMCID: PMC2048574
    • Antoniewicz MR, Kraynie DF, Laffend LA, Gonzalez-Lergier J, Kelleher JK, Stephanopoulos G. Metabolic flux analysis in a nonstationary system: fed-batch fermentation of a high yielding strain of E. coli producing 1, 3-propanediol. Metab Eng. 2007;9(3):277-92. doi: 10.1016/j.ymben. 2007.01.003 PMID: 17400499; PubMed Central PMCID: PMC2048574.
    • (2007) Metab Eng. , vol.9 , Issue.3 , pp. 277-292
    • Antoniewicz, M.R.1    Kraynie, D.F.2    Laffend, L.A.3    Gonzalez-Lergier, J.4    Kelleher, J.K.5    Stephanopoulos, G.6
  • 29
    • 84907889105 scopus 로고    scopus 로고
    • Quantifying biomass composition by gas chromatography/mass spectrometry
    • 25208224
    • Long CP, Antoniewicz MR. Quantifying biomass composition by gas chromatography/mass spectrometry. Anal Chem. 2014;86(19):9423-7. doi: 10.1021/ac502734e PMID: 25208224.
    • (2014) Anal Chem. , vol.86 , Issue.19 , pp. 9423-9427
    • Long, C.P.1    Antoniewicz, M.R.2
  • 30
    • 79954522565 scopus 로고    scopus 로고
    • Measuring deuterium enrichment of glucose hydrogen atoms by gas chromatography/mass spectrometry
    • 21413777 PubMed Central PMCID: PMC3562696
    • Antoniewicz MR, Kelleher JK, Stephanopoulos G. Measuring deuterium enrichment of glucose hydrogen atoms by gas chromatography/mass spectrometry. Anal Chem. 2011;83(8):3211-6. doi: 10.1021/ac200012p PMID: 21413777; PubMed Central PMCID: PMC3562696.
    • (2011) Anal Chem. , vol.83 , Issue.8 , pp. 3211-3216
    • Antoniewicz, M.R.1    Kelleher, J.K.2    Stephanopoulos, G.3
  • 31
    • 0029664919 scopus 로고    scopus 로고
    • Correction of 13C mass isotopomer distributions for natural stable isotope abundance
    • 8799277 Epub 1996/03/01, 10.1002/SICI 1096-9888 199603 31:3<255::AID-JMS290>3.0. CO;2-3
    • Fernandez CA, Des Rosiers C, Previs SF, David F, Brunengraber H. Correction of 13C mass isotopomer distributions for natural stable isotope abundance. J Mass Spectrom. 1996;31(3):255-62. Epub 1996/03/01. 10.1002/(SICI) 1096-9888 (199603) 31:3<255::AID-JMS290>3.0. CO;2-3 [pii] doi: 10.1002/(SICI) 1096-9888 (199603) 31:3<255::AID-JMS290>3.0. CO;2-3 PMID: 8799277.
    • (1996) J Mass Spectrom. , vol.31 , Issue.3 , pp. 255-262
    • Fernandez, C.A.1    Des Rosiers, C.2    Previs, S.F.3    David, F.4    Brunengraber, H.5


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