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Volumn 14, Issue 1, 2015, Pages

An ancient Chinese wisdom for metabolic engineering: Yin-Yang

Author keywords

ATP; Energy metabolism; Flux analysis; Free energy; Maintenance loss; Semi biosynthesis

Indexed keywords

ADENOSINE TRIPHOSPHATE; CARBON;

EID: 84928315635     PISSN: None     EISSN: 14752859     Source Type: Journal    
DOI: 10.1186/s12934-015-0219-3     Document Type: Article
Times cited : (37)

References (53)
  • 1
    • 84891385829 scopus 로고    scopus 로고
    • Transcription activator-like effector nucleases (TALENs): a highly efficient and versatile tool for genome editing
    • Sun N, Zhao H. Transcription activator-like effector nucleases (TALENs): a highly efficient and versatile tool for genome editing. Biotechnol Bioeng. 2013;110:1811-21.
    • (2013) Biotechnol Bioeng , vol.110 , pp. 1811-1821
    • Sun, N.1    Zhao, H.2
  • 2
    • 84874608929 scopus 로고    scopus 로고
    • RNA-guided editing of bacterial genomes using CRISPR-Cas systems
    • Jiang W, Bikard D, Cox D, Zhang F, Marraffini LA. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotech. 2013;31:233-9.
    • (2013) Nat Biotech , vol.31 , pp. 233-239
    • Jiang, W.1    Bikard, D.2    Cox, D.3    Zhang, F.4    Marraffini, L.A.5
  • 3
    • 67650519133 scopus 로고    scopus 로고
    • The RNA-induced silencing complex: a versatile gene-silencing machine
    • Pratt AJ, MacRae IJ. The RNA-induced silencing complex: a versatile gene-silencing machine. J Biol Chem. 2009;284:17897-901.
    • (2009) J Biol Chem , vol.284 , pp. 17897-17901
    • Pratt, A.J.1    MacRae, I.J.2
  • 4
    • 84874687019 scopus 로고    scopus 로고
    • Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression
    • Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell. 2013;152:1173-83.
    • (2013) Cell , vol.152 , pp. 1173-1183
    • Qi, L.S.1    Larson, M.H.2    Gilbert, L.A.3    Doudna, J.A.4    Weissman, J.S.5    Arkin, A.P.6
  • 5
    • 68949161807 scopus 로고    scopus 로고
    • Programming cells by multiplex genome engineering and accelerated evolution
    • Wang HH, Isaacs FJ, Carr PA, Sun ZZ, Xu G, Forest CR, et al. Programming cells by multiplex genome engineering and accelerated evolution. Nature. 2009;460:894-8.
    • (2009) Nature , vol.460 , pp. 894-898
    • Wang, H.H.1    Isaacs, F.J.2    Carr, P.A.3    Sun, Z.Z.4    Xu, G.5    Forest, C.R.6
  • 6
    • 79960502359 scopus 로고    scopus 로고
    • Precise manipulation of chromosomes in Vivo enables genome-wide codon replacement
    • Isaacs FJ, Carr PA, Wang HH, Lajoie MJ, Sterling B, Kraal L, et al. Precise manipulation of chromosomes in Vivo enables genome-wide codon replacement. Science. 2011;333:348-53.
    • (2011) Science , vol.333 , pp. 348-353
    • Isaacs, F.J.1    Carr, P.A.2    Wang, H.H.3    Lajoie, M.J.4    Sterling, B.5    Kraal, L.6
  • 7
    • 71849086611 scopus 로고    scopus 로고
    • Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde
    • Atsumi S, Higashide W, Liao JC. Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde. Nat Biotech. 2009;27:1177-80.
    • (2009) Nat Biotech , vol.27 , pp. 1177-1180
    • Atsumi, S.1    Higashide, W.2    Liao, J.C.3
  • 8
    • 70449336249 scopus 로고    scopus 로고
    • Engineering a platform for photosynthetic isoprene production in Cyanobacteria, using Synechocystis as the model organism
    • Lindberg P, Park S, Melis A. Engineering a platform for photosynthetic isoprene production in Cyanobacteria, using Synechocystis as the model organism. Metab Eng. 2010;12:70-9.
    • (2010) Metab Eng , vol.12 , pp. 70-79
    • Lindberg, P.1    Park, S.2    Melis, A.3
  • 11
    • 84872436756 scopus 로고    scopus 로고
    • Microbial life under extreme energy limitation
    • Hoehler TM, Jorgensen BB. Microbial life under extreme energy limitation. Nat Rev Micro. 2013;11:83-94.
    • (2013) Nat Rev Micro , vol.11 , pp. 83-94
    • Hoehler, T.M.1    Jorgensen, B.B.2
  • 12
    • 0035917865 scopus 로고    scopus 로고
    • Cooperation and competition in the evolution of ATP-producing pathways
    • Pfeiffer T, Schuster S, Bonhoeffer S. Cooperation and competition in the evolution of ATP-producing pathways. Science. 2001;292:504-7.
    • (2001) Science , vol.292 , pp. 504-507
    • Pfeiffer, T.1    Schuster, S.2    Bonhoeffer, S.3
  • 13
    • 33745310267 scopus 로고    scopus 로고
    • Resource competition and social conflict in experimental populations of yeast
    • MacLean RC, Gudelj I. Resource competition and social conflict in experimental populations of yeast. Nature. 2006;441:498-501.
    • (2006) Nature , vol.441 , pp. 498-501
    • MacLean, R.C.1    Gudelj, I.2
  • 14
    • 0037079023 scopus 로고    scopus 로고
    • Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth
    • Ibarra RU, Edwards JS, Palsson BO. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature. 2002;420:186-9.
    • (2002) Nature , vol.420 , pp. 186-189
    • Ibarra, R.U.1    Edwards, J.S.2    Palsson, B.O.3
  • 15
    • 20044375201 scopus 로고    scopus 로고
    • Large-scale in vivo flux analysis shows rigidity and suboptimal performance of Bacillus subtilis metabolism
    • Fischer E, Sauer U. Large-scale in vivo flux analysis shows rigidity and suboptimal performance of Bacillus subtilis metabolism. Nat Genet. 2005;37:636-40.
    • (2005) Nat Genet , vol.37 , pp. 636-640
    • Fischer, E.1    Sauer, U.2
  • 16
    • 0026416683 scopus 로고
    • Plasmid presence changes the relative levels of many host cell proteins and ribosome components in recombinant Escherichia coli
    • Birnbaum S, Bailey JE. Plasmid presence changes the relative levels of many host cell proteins and ribosome components in recombinant Escherichia coli. Biotechnol Bioeng. 1991;37:736-45.
    • (1991) Biotechnol Bioeng , vol.37 , pp. 736-745
    • Birnbaum, S.1    Bailey, J.E.2
  • 17
    • 33845315054 scopus 로고    scopus 로고
    • Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism
    • Wang Z, Xiang L, Shao J, Wegrzyn A, Wegrzyn G. Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism. Microb Cell Fact. 2006;5:34.
    • (2006) Microb Cell Fact , vol.5 , pp. 34
    • Wang, Z.1    Xiang, L.2    Shao, J.3    Wegrzyn, A.4    Wegrzyn, G.5
  • 18
    • 64549091131 scopus 로고    scopus 로고
    • Identification of cellular objective for elucidating the physiological state of plasmid-bearing Escherichia coli using genome-scale in silico analysis
    • Ow DS-W, Lee D-Y, Yap MG-S, Oh SK-W. Identification of cellular objective for elucidating the physiological state of plasmid-bearing Escherichia coli using genome-scale in silico analysis. Biotechnol Prog. 2009;25:61-7.
    • (2009) Biotechnol Prog , vol.25 , pp. 61-67
    • Ow, D.S.-W.1    Lee, D.-Y.2    Yap, M.G.-S.3    Oh, S.K.-W.4
  • 20
    • 77955102352 scopus 로고    scopus 로고
    • Quantifying E. coli Proteome and transcriptome with single-molecule sensitivity in single cells
    • Taniguchi Y, Choi PJ, Li G-W, Chen H, Babu M, Hearn J, et al. Quantifying E. coli Proteome and transcriptome with single-molecule sensitivity in single cells. Science. 2010;329:533-8.
    • (2010) Science , vol.329 , pp. 533-538
    • Taniguchi, Y.1    Choi, P.J.2    Li, G.-W.3    Chen, H.4    Babu, M.5    Hearn, J.6
  • 21
    • 80051474345 scopus 로고    scopus 로고
    • Quantification of metabolic limitations during recombinant protein production in Escherichia coli
    • Heyland J, Blank LM, Schmid A. Quantification of metabolic limitations during recombinant protein production in Escherichia coli. J Biotechnol. 2011;155:178-84.
    • (2011) J Biotechnol , vol.155 , pp. 178-184
    • Heyland, J.1    Blank, L.M.2    Schmid, A.3
  • 22
    • 0028146781 scopus 로고
    • Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110
    • Varma A, Palsson BO. Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Appl Environ Microbiol. 1994;60:3724-31.
    • (1994) Appl Environ Microbiol , vol.60 , pp. 3724-3731
    • Varma, A.1    Palsson, B.O.2
  • 23
    • 0033588791 scopus 로고    scopus 로고
    • Estimation of P-to-O ratio in Bacillus subtilis and its influence on maximum riboflavin yield
    • Sauer U, Bailey JE. Estimation of P-to-O ratio in Bacillus subtilis and its influence on maximum riboflavin yield. Biotechnol Bioeng. 1999;64:750-4.
    • (1999) Biotechnol Bioeng , vol.64 , pp. 750-754
    • Sauer, U.1    Bailey, J.E.2
  • 24
    • 84870872107 scopus 로고    scopus 로고
    • Kinetic Modeling and isotopic investigation of isobutanol fermentation by two engineered Escherichia coli strains
    • Xiao Y, Feng X, Varman AM, He L, Yu H, Tang YJ. Kinetic Modeling and isotopic investigation of isobutanol fermentation by two engineered Escherichia coli strains. Ind Eng Chem Res. 2012;51:15855-63.
    • (2012) Ind Eng Chem Res , vol.51 , pp. 15855-15863
    • Xiao, Y.1    Feng, X.2    Varman, A.M.3    He, L.4    Yu, H.5    Tang, Y.J.6
  • 25
    • 78650647970 scopus 로고    scopus 로고
    • Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli
    • Atsumi S, Wu TY, Machado IMP, Huang WC, Chen PY, Pellegrini M, et al. Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli. Mol Syst Biol. 2010;6:449.
    • (2010) Mol Syst Biol , vol.6 , pp. 449
    • Atsumi, S.1    Wu, T.Y.2    Machado, I.M.P.3    Huang, W.C.4    Chen, P.Y.5    Pellegrini, M.6
  • 27
    • 84920903437 scopus 로고    scopus 로고
    • Improving Microbial Biogasoline Production in Escherichia coli Using Tolerance Engineering
    • Foo JL, Jensen HM, Dahl RH, George K, Keasling JD, Lee TS, et al. Improving Microbial Biogasoline Production in Escherichia coli Using Tolerance Engineering. mBio. 2014;5(6):e01932-14.
    • (2014) mBio , vol.5 , Issue.6 , pp. e01932-e02014
    • Foo, J.L.1    Jensen, H.M.2    Dahl, R.H.3    George, K.4    Keasling, J.D.5    Lee, T.S.6
  • 28
    • 18844371475 scopus 로고    scopus 로고
    • Cellulose utilization by Clostridium thermocellum: bioenergetics and hydrolysis product assimilation
    • Zhang Y-HP, Lynd LR. Cellulose utilization by Clostridium thermocellum: bioenergetics and hydrolysis product assimilation. Proc Natl Acad Sci USA. 2005;102:7321-5.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 7321-7325
    • Zhang, Y.-H.P.1    Lynd, L.R.2
  • 29
    • 33845442201 scopus 로고    scopus 로고
    • Engineering yeast transcription machinery for improved ethanol tolerance and production
    • Alper H, Moxley J, Nevoigt E, Fink GR, Stephanopoulos G. Engineering yeast transcription machinery for improved ethanol tolerance and production. Science. 2006;314:1565-8.
    • (2006) Science , vol.314 , pp. 1565-1568
    • Alper, H.1    Moxley, J.2    Nevoigt, E.3    Fink, G.R.4    Stephanopoulos, G.5
  • 31
    • 84925497895 scopus 로고    scopus 로고
    • Engineering Clostridium acetobutylicum with a histidine kinase knockout for enhanced n-butanol tolerance and production
    • Xu M, Zhao J, Yu L, Tang IC, Xue C, Yang S-T. Engineering Clostridium acetobutylicum with a histidine kinase knockout for enhanced n-butanol tolerance and production. Appl Microbiol Biot. 2015;99:1011-22.
    • (2015) Appl Microbiol Biot , vol.99 , pp. 1011-1022
    • Xu, M.1    Zhao, J.2    Yu, L.3    Tang, I.C.4    Xue, C.5    Yang, S.-T.6
  • 32
    • 80054069179 scopus 로고    scopus 로고
    • A comprehensive genome-scale reconstruction of Escherichia coli metabolism-2011
    • Orth J, Conrad T, Na J, Lerman J, Nam H, Feist A, et al. A comprehensive genome-scale reconstruction of Escherichia coli metabolism-2011. Mol Syst Biol. 2011;7:535.
    • (2011) Mol Syst Biol , vol.7 , pp. 535
    • Orth, J.1    Conrad, T.2    Na, J.3    Lerman, J.4    Nam, H.5    Feist, A.6
  • 34
    • 75749125061 scopus 로고    scopus 로고
    • Microbial production of fatty-acid-derived fuels and chemicals from plant biomass
    • Steen EJ, Kang Y, Bokinsky G, Hu Z, Schirmer A, McClure A, et al. Microbial production of fatty-acid-derived fuels and chemicals from plant biomass. Nature. 2010;463:559-62.
    • (2010) Nature , vol.463 , pp. 559-562
    • Steen, E.J.1    Kang, Y.2    Bokinsky, G.3    Hu, Z.4    Schirmer, A.5    McClure, A.6
  • 36
    • 84862159261 scopus 로고    scopus 로고
    • Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions
    • Orth J, Palsson B. Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions. BMC Syst Biol. 2012;6:30.
    • (2012) BMC Syst Biol , vol.6 , pp. 30
    • Orth, J.1    Palsson, B.2
  • 37
    • 38049001166 scopus 로고    scopus 로고
    • Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels
    • Atsumi S, Hanai T, Liao JC. Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature. 2008;451:86-9.
    • (2008) Nature , vol.451 , pp. 86-89
    • Atsumi, S.1    Hanai, T.2    Liao, J.C.3
  • 38
    • 0030967563 scopus 로고    scopus 로고
    • Enhanced hydrogen production in altered mixed acid fermentation of glucose by Enterobacter aerogenes
    • Rachman MA, Furutani Y, Nakashimada Y, Kakizono T, Nishio N. Enhanced hydrogen production in altered mixed acid fermentation of glucose by Enterobacter aerogenes. J Ferment Bioeng. 1997;83:358-63.
    • (1997) J Ferment Bioeng , vol.83 , pp. 358-363
    • Rachman, M.A.1    Furutani, Y.2    Nakashimada, Y.3    Kakizono, T.4    Nishio, N.5
  • 39
    • 42949144463 scopus 로고    scopus 로고
    • Chapter Fifteen - Applications of the VHb Gene vgb for Improved Microbial Fermentation Processes
    • Edited by Robert KP: Academic Press
    • Wei X-X, Chen G-Q. Chapter Fifteen - Applications of the VHb Gene vgb for Improved Microbial Fermentation Processes. In Method Enzymol. Volume Volume 436. Edited by Robert KP: Academic Press; 2008: 273-287
    • (2008) Method Enzymol , vol.436 , pp. 273-287
    • Wei, X.-X.1    Chen, G.-Q.2
  • 41
    • 84859950774 scopus 로고    scopus 로고
    • ATP drives direct photosynthetic production of 1-butanol in cyanobacteria
    • Lan EI, Liao JC. ATP drives direct photosynthetic production of 1-butanol in cyanobacteria. Proc Natl Acad Sci. 2012;109:6018-23.
    • (2012) Proc Natl Acad Sci , vol.109 , pp. 6018-6023
    • Lan, E.I.1    Liao, J.C.2
  • 42
    • 77950195893 scopus 로고    scopus 로고
    • Metabolic flux control at the pyruvate node in an anaerobic Escherichia coli strain with an Active Pyruvate Dehydrogenase
    • Wang Q, Ou MS, Kim Y, Ingram LO, Shanmugam KT. Metabolic flux control at the pyruvate node in an anaerobic Escherichia coli strain with an Active Pyruvate Dehydrogenase. Appl Environ Microb. 2010;76:2107-14.
    • (2010) Appl Environ Microb , vol.76 , pp. 2107-2114
    • Wang, Q.1    Ou, M.S.2    Kim, Y.3    Ingram, L.O.4    Shanmugam, K.T.5
  • 43
    • 0037417864 scopus 로고    scopus 로고
    • Engineering the metabolism of Escherichia coli W3110 for the conversion of sugar to redox-neutral and oxidized products: Homoacetate production
    • Causey TB, Zhou S, Shanmugam KT, Ingram LO. Engineering the metabolism of Escherichia coli W3110 for the conversion of sugar to redox-neutral and oxidized products: Homoacetate production. Proc Natl Acad Sci. 2003;100:825-32.
    • (2003) Proc Natl Acad Sci , vol.100 , pp. 825-832
    • Causey, T.B.1    Zhou, S.2    Shanmugam, K.T.3    Ingram, L.O.4
  • 44
    • 33846108255 scopus 로고    scopus 로고
    • Towards synthesis of a minimal cell
    • Forster AC, Church GM. Towards synthesis of a minimal cell. Mol Syst Biol. 2006;2:45.
    • (2006) Mol Syst Biol , vol.2 , pp. 45
    • Forster, A.C.1    Church, G.M.2
  • 45
    • 45749137679 scopus 로고    scopus 로고
    • Minimal Escherichia coli cell for the most efficient production of ethanol from Hexoses and Pentoses
    • Trinh CT, Unrean P, Srienc F. Minimal Escherichia coli cell for the most efficient production of ethanol from Hexoses and Pentoses. Appl Environ Microb. 2008;74:3634-43.
    • (2008) Appl Environ Microb , vol.74 , pp. 3634-3643
    • Trinh, C.T.1    Unrean, P.2    Srienc, F.3
  • 47
    • 84899051891 scopus 로고    scopus 로고
    • Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development
    • Paddon CJ, Keasling JD. Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development. Nat Rev Micro. 2014;12:355-67.
    • (2014) Nat Rev Micro , vol.12 , pp. 355-367
    • Paddon, C.J.1    Keasling, J.D.2
  • 49
    • 79952604817 scopus 로고    scopus 로고
    • Evaluating factors that influence microbial synthesis yields by linear regression with numerical and ordinal variables
    • Colletti PF, Goyal Y, Varman AM, Feng X, Wu B, Tang YJ. Evaluating factors that influence microbial synthesis yields by linear regression with numerical and ordinal variables. Biotechnol Bioeng. 2011;108:893-901.
    • (2011) Biotechnol Bioeng , vol.108 , pp. 893-901
    • Colletti, P.F.1    Goyal, Y.2    Varman, A.M.3    Feng, X.4    Wu, B.5    Tang, Y.J.6
  • 50
    • 83255164998 scopus 로고    scopus 로고
    • Cell-free synthetic biology: thinking outside the cell
    • Hodgman CE, Jewett MC. Cell-free synthetic biology: thinking outside the cell. Metab Eng. 2012;14:261-9.
    • (2012) Metab Eng , vol.14 , pp. 261-269
    • Hodgman, C.E.1    Jewett, M.C.2
  • 51
    • 61349097193 scopus 로고    scopus 로고
    • Spontaneous high-yield production of hydrogen from cellulosic materials and water catalyzed by enzyme cocktails
    • Ye X, Wang Y, Hopkins RC, Adams MWW, Evans BR, Mielenz JR, et al. Spontaneous high-yield production of hydrogen from cellulosic materials and water catalyzed by enzyme cocktails. ChemSusChem. 2009;2:149-52.
    • (2009) ChemSusChem , vol.2 , pp. 149-152
    • Ye, X.1    Wang, Y.2    Hopkins, R.C.3    Adams, M.W.W.4    Evans, B.R.5    Mielenz, J.R.6
  • 52
    • 84906317195 scopus 로고    scopus 로고
    • Recent advances in genomic DNA sequencing of microbial species from single cells
    • Lasken RS, McLean JS. Recent advances in genomic DNA sequencing of microbial species from single cells. Nat Rev Genet. 2014;15:577-84.
    • (2014) Nat Rev Genet , vol.15 , pp. 577-584
    • Lasken, R.S.1    McLean, J.S.2
  • 53
    • 84899969499 scopus 로고    scopus 로고
    • 13C-MFA delineates the photomixotrophic metabolism of Synechocystis sp. PCC 6803 under light- and carbon-sufficient conditions
    • 13C-MFA delineates the photomixotrophic metabolism of Synechocystis sp. PCC 6803 under light- and carbon-sufficient conditions. Biotechnol J. 2014;9:684-92.
    • (2014) Biotechnol J , vol.9 , pp. 684-692
    • You, L.1    Berla, B.2    He, L.3    Pakrasi, H.B.4    Tang, Y.J.5


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