메뉴 건너뛰기




Volumn 111, Issue 32, 2014, Pages 11762-11767

Network-level architecture and the evolutionary potential of underground metabolism

Author keywords

Enzyme promiscuity; Evolutionary innovation; Molecular evolution; Network evolution; Phenotype microarray

Indexed keywords

CARBON;

EID: 84905969902     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1406102111     Document Type: Article
Times cited : (98)

References (35)
  • 1
    • 0017272554 scopus 로고
    • Enzyme recruitment in evolution of new function
    • Jensen RA (1976) Enzyme recruitment in evolution of new function. Annu Rev Microbiol 30:409-425
    • (1976) Annu Rev Microbiol , vol.30 , pp. 409-425
    • Jensen, R.A.1
  • 3
    • 0036306663 scopus 로고    scopus 로고
    • Homology, pathway distance and chromosomal localization of the small molecule metabolism enzymes in Escherichia coli
    • Rison SC, Teichmann SA, Thornton JM (2002) Homology, pathway distance and chromosomal localization of the small molecule metabolism enzymes in Escherichia coli. J Mol Biol 318(3):911-932
    • (2002) J Mol Biol , vol.318 , Issue.3 , pp. 911-932
    • Rison, S.C.1    Teichmann, S.A.2    Thornton, J.M.3
  • 4
    • 77953623874 scopus 로고    scopus 로고
    • Enzyme promiscuity: A mechanistic and evolutionary perspective
    • Khersonsky O, Tawfik DS (2010) Enzyme promiscuity: A mechanistic and evolutionary perspective. Annu Rev Biochem 79:471-505
    • (2010) Annu Rev Biochem , vol.79 , pp. 471-505
    • Khersonsky, O.1    Tawfik, D.S.2
  • 5
    • 0032005335 scopus 로고    scopus 로고
    • Underground metabolism
    • D'Ari R, Casadesús J (1998) Underground metabolism. BioEssays 20(2):181-186
    • (1998) Bio Essays , vol.20 , Issue.2 , pp. 181-186
    • D'Ari, R.1    Casadesús, J.2
  • 6
    • 33846023053 scopus 로고    scopus 로고
    • Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family
    • Kuznetsova E, et al. (2006) Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family. J Biol Chem 281(47): 36149-36161
    • (2006) J Biol Chem , vol.281 , Issue.47 , pp. 36149-36161
    • Kuznetsova, E.1
  • 7
    • 84857374810 scopus 로고    scopus 로고
    • Enzyme functional evolution through improved catalysis of ancestrally nonpreferred substrates
    • Huang R, et al. (2012) Enzyme functional evolution through improved catalysis of ancestrally nonpreferred substrates. Proc Natl Acad Sci USA 109(8):2966-2971
    • (2012) Proc Natl Acad Sci USA , vol.109 , Issue.8 , pp. 2966-2971
    • Huang, R.1
  • 8
    • 3543002852 scopus 로고    scopus 로고
    • Ligand selectivity and competition between enzymes in silico
    • Macchiarulo A, Nobeli I, Thornton JM (2004) Ligand selectivity and competition between enzymes in silico. Nat Biotechnol 22(8):1039-1045
    • (2004) Nat Biotechnol , vol.22 , Issue.8 , pp. 1039-1045
    • Macchiarulo, A.1    Nobeli, I.2    Thornton, J.M.3
  • 9
    • 11244281311 scopus 로고    scopus 로고
    • The ?evolvability' of promiscuous protein functions
    • Aharoni A, et al. (2005) The ?evolvability' of promiscuous protein functions. Nat Genet 37(1):73-76
    • (2005) Nat Genet , vol.37 , Issue.1 , pp. 73-76
    • Aharoni, A.1
  • 10
    • 78651330012 scopus 로고    scopus 로고
    • BRENDA, the enzyme information system in 2011
    • Database issue
    • ScheerM, et al. (2011) BRENDA, the enzyme information system in 2011. Nucleic Acids Res 39(Database issue):D670-D676
    • (2011) Nucleic Acids Res , vol.39
    • Scheer, M.1
  • 11
    • 34347332311 scopus 로고    scopus 로고
    • A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
    • Feist AM, et al. (2007) A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol 3:121
    • (2007) Mol Syst Biol , vol.3 , pp. 121
    • Feist, A.M.1
  • 12
    • 84865571240 scopus 로고    scopus 로고
    • Network context and selection in the evolution to enzyme specificity
    • Nam H, et al. (2012) Network context and selection in the evolution to enzyme specificity. Science 337(6098):1101-1104
    • (2012) Science , vol.337 , Issue.6098 , pp. 1101-1104
    • Nam, H.1
  • 13
    • 84876571447 scopus 로고    scopus 로고
    • ECMDB: The E. Coli metabolome database
    • Database issue
    • Guo AC, et al. (2013) ECMDB: The E. coli Metabolome Database. Nucleic Acids Res 41(Database issue):D625-D630
    • (2013) Nucleic Acids Res , vol.41
    • Guo, A.C.1
  • 14
    • 79953166401 scopus 로고    scopus 로고
    • Role of chemistry versus substrate binding in recruiting promiscuous enzyme functions
    • Khersonsky O, Malitsky S, Rogachev I, Tawfik DS (2011) Role of chemistry versus substrate binding in recruiting promiscuous enzyme functions. Biochemistry 50(13): 2683-2690
    • (2011) Biochemistry , vol.50 , Issue.13 , pp. 2683-2690
    • Khersonsky, O.1    Malitsky, S.2    Rogachev, I.3    Tawfik, D.S.4
  • 15
    • 0034064689 scopus 로고    scopus 로고
    • A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks
    • Schuster S, Fell DA, Dandekar T (2000) A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat Biotechnol 18(3):326-332
    • (2000) Nat Biotechnol , vol.18 , Issue.3 , pp. 326-332
    • Schuster, S.1    Fell, D.A.2    Dandekar, T.3
  • 16
    • 84867651617 scopus 로고    scopus 로고
    • Real-time evolution of new genes by innovation, amplification, and divergence
    • Näsvall J, Sun L, Roth JR, Andersson DI (2012) Real-time evolution of new genes by innovation, amplification, and divergence. Science 338(6105):384-387
    • (2012) Science , vol.338 , Issue.6105 , pp. 384-387
    • Näsvall, J.1    Sun, L.2    Roth, J.R.3    Andersson, D.I.4
  • 17
    • 84867660750 scopus 로고    scopus 로고
    • Inhibitory cross-talk upon introduction of a new metabolic pathway into an existing metabolic network
    • Kim J, Copley SD (2012) Inhibitory cross-talk upon introduction of a new metabolic pathway into an existing metabolic network. Proc Natl Acad Sci USA 109(42): E2856-E2864
    • (2012) Proc Natl Acad Sci USA , vol.109 , Issue.42
    • Kim, J.1    Copley, S.D.2
  • 18
    • 84855946759 scopus 로고    scopus 로고
    • Compound toxicity screening and structure-activity relationship modeling in Escherichia coli
    • Planson AG, Carbonell P, Paillard E, Pollet N, Faulon JL (2012) Compound toxicity screening and structure-activity relationship modeling in Escherichia coli. Biotechnol Bioeng 109(3):846-850
    • (2012) Biotechnol Bioeng , vol.109 , Issue.3 , pp. 846-850
    • Planson, A.G.1    Carbonell, P.2    Paillard, E.3    Pollet, N.4    Faulon, J.L.5
  • 19
    • 84888122057 scopus 로고    scopus 로고
    • Computational evaluation of cellular metabolic costs successfully predicts genes whose expression is deleterious
    • Wagner A, et al. (2013) Computational evaluation of cellular metabolic costs successfully predicts genes whose expression is deleterious. Proc Natl Acad Sci USA 110(47):19166-19171
    • (2013) Proc Natl Acad Sci USA , vol.110 , Issue.47 , pp. 19166-19171
    • Wagner, A.1
  • 20
    • 9544253891 scopus 로고    scopus 로고
    • Genome-scale models of microbial cells: Evaluating the consequences of constraints
    • Price ND, Reed JL, Palsson BO (2004) Genome-scale models of microbial cells: Evaluating the consequences of constraints. Nat Rev Microbiol 2(11):886-897
    • (2004) Nat Rev Microbiol , vol.2 , Issue.11 , pp. 886-897
    • Price, N.D.1    Reed, J.L.2    Palsson, B.O.3
  • 23
    • 78649857195 scopus 로고    scopus 로고
    • Three serendipitous pathways in E. Coli can bypass a block in pyridoxal-5'-phosphate synthesis
    • Kim J, Kershner JP, Novikov Y, Shoemaker RK, Copley SD (2010) Three serendipitous pathways in E. coli can bypass a block in pyridoxal-5'-phosphate synthesis. Mol Syst Biol 6:436
    • (2010) Mol Syst Biol , vol.6 , pp. 436
    • Kim, J.1    Kershner, J.P.2    Novikov, Y.3    Shoemaker, R.K.4    Copley, S.D.5
  • 24
    • 79952166228 scopus 로고    scopus 로고
    • Artificial gene amplification reveals an abundance of promiscuous resistance determinants in Escherichia coli
    • Soo VW, Hanson-Manful P, Patrick WM (2011) Artificial gene amplification reveals an abundance of promiscuous resistance determinants in Escherichia coli. Proc Natl Acad Sci USA 108(4):1484-1489
    • (2011) Proc Natl Acad Sci USA , vol.108 , Issue.4 , pp. 1484-1489
    • Soo, V.W.1    Hanson-Manful, P.2    Patrick, W.M.3
  • 25
    • 33646568438 scopus 로고    scopus 로고
    • Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. Coli K-12 ORF archive): Unique resources for biological research
    • Kitagawa M, et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): Unique resources for biological research. DNA Res 12(5):291-299
    • (2005) DNA Res , vol.12 , Issue.5 , pp. 291-299
    • Kitagawa, M.1
  • 26
    • 4544321006 scopus 로고    scopus 로고
    • Production of natural and rare pentoses using microorganisms and their enzymes
    • Ahmed Z (2001) Production of natural and rare pentoses using microorganisms and their enzymes. Electron J Biotechnol 4(2):1-16
    • (2001) Electron J Biotechnol , vol.4 , Issue.2 , pp. 1-16
    • Ahmed, Z.1
  • 27
    • 80054069179 scopus 로고    scopus 로고
    • A comprehensive genome-scale reconstruction of Escherichia coli metabolism-2011
    • Orth JD, et al. (2011) A comprehensive genome-scale reconstruction of Escherichia coli metabolism-2011. Mol Syst Biol 7:535
    • (2011) Mol Syst Biol , vol.7 , pp. 535
    • Orth, J.D.1
  • 28
    • 28444475529 scopus 로고    scopus 로고
    • Adaptive evolution of bacterial metabolic networks by horizontal gene transfer
    • Pál C, Papp B, Lercher MJ (2005) Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat Genet 37(12):1372-1375
    • (2005) Nat Genet , vol.37 , Issue.12 , pp. 1372-1375
    • Pál, C.1    Papp, B.2    Lercher, M.J.3
  • 29
    • 0035823264 scopus 로고    scopus 로고
    • The small world inside large metabolic networks
    • Wagner A, Fell DA (2001) The small world inside large metabolic networks. Proc Biol Sci 268(1478):1803-1810
    • (2001) Proc Biol Sci , vol.268 , Issue.1478 , pp. 1803-1810
    • Wagner, A.1    Fell, D.A.2
  • 30
    • 84862996527 scopus 로고    scopus 로고
    • The rise of chemodiversity in plants
    • Weng JK, Philippe RN, Noel JP (2012) The rise of chemodiversity in plants. Science 336(6089):1667-1670
    • (2012) Science , vol.336 , Issue.6089 , pp. 1667-1670
    • Weng, J.K.1    Philippe, R.N.2    Noel, J.P.3
  • 31
    • 80052031934 scopus 로고    scopus 로고
    • Systems-biology approaches for predicting genomic evolution
    • Papp B, Notebaart RA, Pál C (2011) Systems-biology approaches for predicting genomic evolution. Nat Rev Genet 12(9):591-602
    • (2011) Nat Rev Genet , vol.12 , Issue.9 , pp. 591-602
    • Papp, B.1    Notebaart, R.A.2    Pál, C.3
  • 32
    • 84879377643 scopus 로고    scopus 로고
    • Predicting C4 photosynthesis evolution: Modular, individually adaptive steps on a Mount Fuji fitness landscape
    • Heckmann D, et al. (2013) Predicting C4 photosynthesis evolution: Modular, individually adaptive steps on a Mount Fuji fitness landscape. Cell 153(7):1579-1588
    • (2013) Cell , vol.153 , Issue.7 , pp. 1579-1588
    • Heckmann, D.1
  • 33
    • 72049125350 scopus 로고    scopus 로고
    • Cancer-associated IDH1 mutations produce 2-hydroxyglutarate
    • Dang L, et al. (2009) Cancer-associated IDH1 mutations produce 2-hydroxyglutarate. Nature 462(7274):739-744
    • (2009) Nature , vol.462 , Issue.7274 , pp. 739-744
    • Dang, L.1
  • 35
    • 84859982600 scopus 로고    scopus 로고
    • Visualization and curveparameter estimation strategies for efficient exploration of phenotype microarray kinetics
    • Vaas LA, Sikorski J, Michael V, Göker M, Klenk HP (2012) Visualization and curveparameter estimation strategies for efficient exploration of phenotype microarray kinetics. PLoS ONE 7(4):e34846.
    • (2012) PLoS ONE , vol.7 , Issue.4
    • Vaas, L.A.1    Sikorski, J.2    Michael, V.3    Göker, M.4    Klenk, H.P.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.