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Volumn 112, Issue 3, 2015, Pages 929-934

Model-driven discovery of underground metabolic functions in Escherichia coli

Author keywords

Genome scale modeling; Isozyme discovery; Substrate promiscuity; Systems biology; Underground metabolism

Indexed keywords

AMINOTRANSFERASE; BACTERIAL ENZYME; CITRATE SYNTHASE; ISOENZYME;

EID: 84921340441     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1414218112     Document Type: Article
Times cited : (73)

References (40)
  • 1
    • 84902670142 scopus 로고    scopus 로고
    • Accuracy-rate tradeoffs: How do enzymes meet demands of selectivity and catalytic efficiency?
    • Tawfik DS (2014) Accuracy-rate tradeoffs: How do enzymes meet demands of selectivity and catalytic efficiency? Curr Opin Chem Biol 21:73-80.
    • (2014) Curr Opin Chem Biol , vol.21 , pp. 73-80
    • Tawfik, D.S.1
  • 2
    • 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
    • 0029905462 scopus 로고    scopus 로고
    • The origin and early evolution of life: Prebiotic chemistry, the pre-RNA world, and time
    • Lazcano A, Miller SL (1996) The origin and early evolution of life: Prebiotic chemistry, the pre-RNA world, and time. Cell 85(6):793-798.
    • (1996) Cell , vol.85 , Issue.6 , pp. 793-798
    • Lazcano, A.1    Miller, S.L.2
  • 4
    • 0036600740 scopus 로고    scopus 로고
    • Pathway evolution, structurally speaking
    • Rison SCG, Thornton JM (2002) Pathway evolution, structurally speaking. Curr Opin Struct Biol 12(3):374-382.
    • (2002) Curr Opin Struct Biol , vol.12 , Issue.3 , pp. 374-382
    • Rison, S.C.G.1    Thornton, J.M.2
  • 5
    • 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
  • 6
    • 0032005335 scopus 로고    scopus 로고
    • Underground metabolism
    • D' Ari R, Casadesús J (1998) Underground metabolism. BioEssays 20(2):181-186.
    • (1998) BioEssays , vol.20 , Issue.2 , pp. 181-186
    • D'Ari, R.1    Casadesús, J.2
  • 7
    • 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
  • 8
    • 84905969902 scopus 로고    scopus 로고
    • Network-level architecture and the evolutionary potential of underground metabolism
    • Notebaart RA, et al. (2014) Network-level architecture and the evolutionary potential of underground metabolism. Proc Natl Acad Sci USA 111(32):11762-11767.
    • (2014) Proc Natl Acad Sci USA , vol.111 , Issue.32 , pp. 11762-11767
    • Notebaart, R.A.1
  • 9
    • 84867747152 scopus 로고    scopus 로고
    • Current challenges in genome annotation through structural biology and bioinformatics
    • Furnham N, de Beer TAP, Thornton JM (2012) Current challenges in genome annotation through structural biology and bioinformatics. Curr Opin Struct Biol 22(5): 594-601.
    • (2012) Curr Opin Struct Biol , vol.22 , Issue.5 , pp. 594-601
    • Furnham, N.1    De Beer, T.A.P.2    Thornton, J.M.3
  • 10
    • 77649239492 scopus 로고    scopus 로고
    • An efficient, multiply promiscuous hydrolase in the alkaline phosphatase superfamily
    • van Loo B, et al. (2010) An efficient, multiply promiscuous hydrolase in the alkaline phosphatase superfamily. Proc Natl Acad Sci USA 107(7):2740-2745.
    • (2010) Proc Natl Acad Sci USA , vol.107 , Issue.7 , pp. 2740-2745
    • Van Loo, B.1
  • 11
    • 70350195337 scopus 로고    scopus 로고
    • Gene amplification and adaptive evolution in bacteria
    • Andersson DI, Hughes D (2009) Gene amplification and adaptive evolution in bacteria. Annu Rev Genet 43:167-195.
    • (2009) Annu Rev Genet , vol.43 , pp. 167-195
    • Andersson, D.I.1    Hughes, D.2
  • 12
    • 84879002382 scopus 로고    scopus 로고
    • Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli
    • McCloskey D, Palsson BO, Feist AM (2013) Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli. Mol Syst Biol 9:661.
    • (2013) Mol Syst Biol , vol.9 , pp. 661
    • McCloskey, D.1    Palsson, B.O.2    Feist, A.M.3
  • 13
    • 84892788440 scopus 로고    scopus 로고
    • Constraint-based models predict metabolic and associated cellular functions
    • Bordbar A, Monk JM, King ZA, Palsson BO (2014) Constraint-based models predict metabolic and associated cellular functions. Nat Rev Genet 15(2):107-120.
    • (2014) Nat Rev Genet , vol.15 , Issue.2 , pp. 107-120
    • Bordbar, A.1    Monk, J.M.2    King, Z.A.3    Palsson, B.O.4
  • 14
    • 84862159261 scopus 로고    scopus 로고
    • Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions
    • Orth JD, Palsson B (2012) Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions. BMC Syst Biol 6:30.
    • (2012) BMC Syst Biol , vol.6 , pp. 30
    • Orth, J.D.1    Palsson, B.2
  • 15
    • 33751226921 scopus 로고    scopus 로고
    • Systems approach to refining genome annotation
    • Reed JL, et al. (2006) Systems approach to refining genome annotation. Proc Natl Acad Sci USA 103(46):17480-17484.
    • (2006) Proc Natl Acad Sci USA , vol.103 , Issue.46 , pp. 17480-17484
    • Reed, J.L.1
  • 16
    • 63549108441 scopus 로고    scopus 로고
    • GrowMatch: An automated method for reconciling in silico/in vivo growth predictions
    • Kumar VS, Maranas CD (2009) GrowMatch: An automated method for reconciling in silico/in vivo growth predictions. PLOS Comput Biol 5(3):e1000308.
    • (2009) PLOS Comput Biol , vol.5 , Issue.3 , pp. e1000308
    • Kumar, V.S.1    Maranas, C.D.2
  • 17
    • 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
  • 19
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul SF, et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25(17):3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , Issue.17 , pp. 3389-3402
    • Altschul, S.F.1
  • 20
    • 0022550466 scopus 로고
    • The cloning and sequence analysis of the aspC and tyrB genes from Escherichia coli K12. Comparison of the primary structures of the aspartate aminotransferase and aromatic aminotransferase of E. Coli with those of the pig aspartate aminotransferase isoenzymes
    • Fotheringham I.G., et al. (1986) The cloning and sequence analysis of the aspC and tyrB genes from Escherichia coli K12. Comparison of the primary structures of the aspartate aminotransferase and aromatic aminotransferase of E. coli with those of the pig aspartate aminotransferase isoenzymes. Biochem J 234(3):593-604.
    • (1986) Biochem J , vol.234 , Issue.3 , pp. 593-604
    • Fotheringham, I.G.1
  • 21
    • 0017359090 scopus 로고
    • Escherichia coli mutants deficient in the aspartate and aromatic amino acid aminotransferases
    • Gelfand DH, Steinberg RA (1977) Escherichia coli mutants deficient in the aspartate and aromatic amino acid aminotransferases. J Bacteriol 130(1):429-440.
    • (1977) J Bacteriol , vol.130 , Issue.1 , pp. 429-440
    • Gelfand, D.H.1    Steinberg, R.A.2
  • 22
    • 0018087744 scopus 로고
    • Role of the Escherichia coli aromatic amino acid aminotransferase in leucine biosynthesis
    • Powell JT, Morrison JF (1978) Role of the Escherichia coli aromatic amino acid aminotransferase in leucine biosynthesis. J Bacteriol 136(1):1-4.
    • (1978) J Bacteriol , vol.136 , Issue.1 , pp. 1-4
    • Powell, J.T.1    Morrison, J.F.2
  • 23
    • 0018357196 scopus 로고
    • Transaminase B from Escherichia coli: Quaternary structure, amino-terminal sequence, substrate specificity, and absence of a separate valine-alpha-ketoglutarate activity
    • Lee-Peng FC, Hermodson MA, Kohlhaw GB (1979) Transaminase B from Escherichia coli: Quaternary structure, amino-terminal sequence, substrate specificity, and absence of a separate valine-alpha-ketoglutarate activity. J Bacteriol 139(2):339-345.
    • (1979) J Bacteriol , vol.139 , Issue.2 , pp. 339-345
    • Lee-Peng, F.C.1    Hermodson, M.A.2    Kohlhaw, G.B.3
  • 24
    • 31544450286 scopus 로고    scopus 로고
    • Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: The Keio collection
    • Baba T, et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: The Keio collection. Mol Syst Biol 2:0008.
    • (2006) Mol Syst Biol , vol.2 , pp. 0008
    • Baba, T.1
  • 25
    • 70350641005 scopus 로고    scopus 로고
    • Genome evolution and adaptation in a long-term experiment with Escherichia coli
    • Barrick JE, et al. (2009) Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461(7268):1243-1247.
    • (2009) Nature , vol.461 , Issue.7268 , pp. 1243-1247
    • Barrick, J.E.1
  • 26
    • 0033537677 scopus 로고    scopus 로고
    • The dual biosynthetic capability of N-acetylornithine aminotransferase in arginine and lysine biosynthesis
    • Ledwidge R, Blanchard JS (1999) The dual biosynthetic capability of N-acetylornithine aminotransferase in arginine and lysine biosynthesis. Biochemistry 38(10):3019-3024.
    • (1999) Biochemistry , vol.38 , Issue.10 , pp. 3019-3024
    • Ledwidge, R.1    Blanchard, J.S.2
  • 27
    • 84874615902 scopus 로고    scopus 로고
    • Determination of the structure of the catabolic N-succinylornithine transaminase (AstC) from Escherichia coli
    • Newman J, et al. (2013) Determination of the structure of the catabolic N-succinylornithine transaminase (AstC) from Escherichia coli. PLoS ONE 8(3):e58298.
    • (2013) PLoS ONE , vol.8 , Issue.3 , pp. e58298
    • Newman, J.1
  • 28
    • 84864022425 scopus 로고    scopus 로고
    • Mechanism for regulation of the putrescine utilization pathway by the transcription factor PuuR in Escherichia coli K-12
    • Nemoto N, et al. (2012) Mechanism for regulation of the putrescine utilization pathway by the transcription factor PuuR in Escherichia coli K-12. J Bacteriol 194(13): 3437-3447.
    • (2012) J Bacteriol , vol.194 , Issue.13 , pp. 3437-3447
    • Nemoto, N.1
  • 29
    • 77954065271 scopus 로고    scopus 로고
    • I-TASSER: A unified platform for automated protein structure and function prediction
    • Roy A, Kucukural A, Zhang Y (2010) I-TASSER: A unified platform for automated protein structure and function prediction. Nat Protoc 5(4):725-738.
    • (2010) Nat Protoc , vol.5 , Issue.4 , pp. 725-738
    • Roy, A.1    Kucukural, A.2    Zhang, Y.3
  • 30
    • 74249104499 scopus 로고    scopus 로고
    • Fast and accurate automatic structure prediction with HHpred
    • Hildebrand A, Remmert M, Biegert A, Söding J (2009) Fast and accurate automatic structure prediction with HHpred. Proteins 77(Suppl 9):128-132.
    • (2009) Proteins , vol.77 , pp. 128-132
    • Hildebrand, A.1    Remmert, M.2    Biegert, A.3    Söding, J.4
  • 31
    • 63849246525 scopus 로고    scopus 로고
    • Protein structure prediction on the Web: A case study using the Phyre server
    • Kelley LA, Sternberg MJ (2009) Protein structure prediction on the Web: A case study using the Phyre server. Nat Protoc 4(3):363-371.
    • (2009) Nat Protoc , vol.4 , Issue.3 , pp. 363-371
    • Kelley, L.A.1    Sternberg, M.J.2
  • 32
    • 78650475398 scopus 로고    scopus 로고
    • Phenotypic landscape of a bacterial cell
    • Nichols RJ, et al. (2011) Phenotypic landscape of a bacterial cell. Cell 144(1):143-156.
    • (2011) Cell , vol.144 , Issue.1 , pp. 143-156
    • Nichols, R.J.1
  • 33
    • 0141504252 scopus 로고    scopus 로고
    • Experimental determination and system level analysis of essential genes in Escherichia coli MG1655
    • Gerdes SY, et al. (2003) Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J Bacteriol 185(19):5673-5684.
    • (2003) J Bacteriol , vol.185 , Issue.19 , pp. 5673-5684
    • Gerdes, S.Y.1
  • 34
    • 31544474634 scopus 로고    scopus 로고
    • Long-term survival during stationary phase: Evolution and the GASP phenotype
    • Finkel SE (2006) Long-term survival during stationary phase: Evolution and the GASP phenotype. Nat Rev Microbiol 4(2):113-120.
    • (2006) Nat Rev Microbiol , vol.4 , Issue.2 , pp. 113-120
    • Finkel, S.E.1
  • 35
    • 0027310402 scopus 로고
    • Does Escherichia coli possess a second citrate synthase gene?
    • Patton AJ, Hough DW, Towner P, Danson MJ (1993) Does Escherichia coli possess a second citrate synthase gene? Eur J Biochem 214(1):75-81.
    • (1993) Eur J Biochem , vol.214 , Issue.1 , pp. 75-81
    • Patton, A.J.1    Hough, D.W.2    Towner, P.3    Danson, M.J.4
  • 36
    • 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(13):4158-4168.
    • (2010) Appl Environ Microbiol , vol.76 , Issue.13 , pp. 4158-4168
    • Lee, D.H.1    Palsson, B.O.2
  • 37
    • 0002153005 scopus 로고
    • Correlation of citrate utilization by members of the colon-aerogenes group with other differential characteristics and with habitat
    • Koser SA (1924) Correlation of citrate utilization by members of the colon-aerogenes group with other differential characteristics and with habitat. J Bacteriol 9(1):59-77.
    • (1924) J Bacteriol , vol.9 , Issue.1 , pp. 59-77
    • Koser, S.A.1
  • 39
    • 84890290025 scopus 로고    scopus 로고
    • Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments
    • Monk JM, et al. (2013) Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments. Proc Natl Acad Sci USA 110(50):20338-20343.
    • (2013) Proc Natl Acad Sci USA , vol.110 , Issue.50 , pp. 20338-20343
    • Monk, J.M.1
  • 40
    • 84867881743 scopus 로고    scopus 로고
    • Structure-based prediction of protein-protein interactions on a genome-wide scale
    • Zhang QC, et al. (2012) Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature 490(7421):556-560.
    • (2012) Nature , vol.490 , Issue.7421 , pp. 556-560
    • Zhang, Q.C.1


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