메뉴 건너뛰기




Volumn 283, Issue 11, 2016, Pages 2149-2163

Metabolic network architecture and carbon source determine metabolite production costs

Author keywords

amino acid auxotrophies; biosynthetic cost; Escherichia coli; flux balance analysis; metabolic trade off; resource allocation problem

Indexed keywords

AMINO ACID METABOLISM; ARTICLE; AUXOTROPHY; CARBON SOURCE; CONTROLLED STUDY; ENERGY EXPENDITURE; ESCHERICHIA COLI; GLUCONEOGENESIS; GLYCOLYSIS; GROWTH RATE; METABOLITE; NONHUMAN; PRIORITY JOURNAL; BIOTECHNOLOGY; GENETICS; METABOLISM;

EID: 84965025835     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/febs.13727     Document Type: Article
Times cited : (43)

References (43)
  • 4
    • 0025825078 scopus 로고
    • Growth rate of Escherichia coli
    • Marr AG (1991) Growth rate of Escherichia coli. Microbiol Rev 55, 316–333.
    • (1991) Microbiol Rev , vol.55 , pp. 316-333
    • Marr, A.G.1
  • 5
    • 0031426064 scopus 로고    scopus 로고
    • Microbial physiology and ecology of slow growth
    • Koch AL (1997) Microbial physiology and ecology of slow growth. Microbiol Mol Biol Rev 61, 305–318.
    • (1997) Microbiol Mol Biol Rev , vol.61 , pp. 305-318
    • Koch, A.L.1
  • 6
    • 80052076284 scopus 로고    scopus 로고
    • Bacterial growth rate reflects a bottleneck in resource allocation
    • Goelzer A & Fromion V (2011) Bacterial growth rate reflects a bottleneck in resource allocation. Biochim Biophys Acta 1810, 978–988.
    • (2011) Biochim Biophys Acta , vol.1810 , pp. 978-988
    • Goelzer, A.1    Fromion, V.2
  • 7
    • 0037422210 scopus 로고    scopus 로고
    • Metabolic flux analysis of Escherichia coli K12 grown on 13 C-labeled acetate and glucose using GC-MS and powerful flux calculation method
    • Zhao J & Shimizu K (2003) Metabolic flux analysis of Escherichia coli K12 grown on 13 C-labeled acetate and glucose using GC-MS and powerful flux calculation method. J Biotechnol 101, 101–117.
    • (2003) J Biotechnol , vol.101 , pp. 101-117
    • Zhao, J.1    Shimizu, K.2
  • 9
    • 0014944566 scopus 로고
    • Non-Darwinian evolution: a critique
    • Richmond RC (1970) Non-Darwinian evolution: a critique. Nature 225, 1025–1028.
    • (1970) Nature , vol.225 , pp. 1025-1028
    • Richmond, R.C.1
  • 10
    • 0037133671 scopus 로고    scopus 로고
    • Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis
    • Akashi H & Gojobori T (2002) Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. Proc Natl Acad Sci USA 99, 3695–3700.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 3695-3700
    • Akashi, H.1    Gojobori, T.2
  • 12
    • 0037391699 scopus 로고    scopus 로고
    • Global metabolic regulation analysis for Escherichia coli K12 based on protein expression by 2-dimensional electrophoresis and enzyme activity measurement
    • Peng L & Shimizu K (2003) Global metabolic regulation analysis for Escherichia coli K12 based on protein expression by 2-dimensional electrophoresis and enzyme activity measurement. Appl Microbiol Biotechnol 61, 163–178.
    • (2003) Appl Microbiol Biotechnol , vol.61 , pp. 163-178
    • Peng, L.1    Shimizu, K.2
  • 13
    • 34248157233 scopus 로고    scopus 로고
    • Selection on synthesis cost affects interprotein amino acid usage in all three domains of life
    • Swire J (2007) Selection on synthesis cost affects interprotein amino acid usage in all three domains of life. J Mol Evol 64, 558–571.
    • (2007) J Mol Evol , vol.64 , pp. 558-571
    • Swire, J.1
  • 14
    • 0020891851 scopus 로고
    • Escherichia coli habitats, cell types, and molecular mechanisms of gene control
    • Savageau MA (1983) Escherichia coli habitats, cell types, and molecular mechanisms of gene control. Am Nat 122, 732–744.
    • (1983) Am Nat , vol.122 , pp. 732-744
    • Savageau, M.A.1
  • 15
    • 78149408759 scopus 로고    scopus 로고
    • Survival of Escherichia coli in the environment: fundamental and public health aspects
    • van Elsas JD, Semenov AV, Costa R & Trevors JT (2011) Survival of Escherichia coli in the environment: fundamental and public health aspects. ISME J 5, 173–183.
    • (2011) ISME J , vol.5 , pp. 173-183
    • van Elsas, J.D.1    Semenov, A.V.2    Costa, R.3    Trevors, J.T.4
  • 16
    • 84908147262 scopus 로고    scopus 로고
    • Biosynthesis of the aromatic amino acids
    • Pittard J & Yang J (2008) Biosynthesis of the aromatic amino acids. EcoSal Plus 3, doi: 10.1128/ecosalplus.3.6.1.8.
    • (2008) EcoSal Plus , vol.3
    • Pittard, J.1    Yang, J.2
  • 17
    • 0015136024 scopus 로고
    • Phenylalanine and tyrosine biosynthesis in Escherichia coli K-12: mutants derepressed for 3-deoxy-d-arabinoheptulosonic acid 7-phosphate synthetase (phe), 3-deoxy-d-arabinoheptulosonic acid 7-phosphate synthetase (tyr), chorismate mutase T-prephenate dehydrogenase, and transaminase A
    • Im SWK, Davidson H & Pittard J (1971) Phenylalanine and tyrosine biosynthesis in Escherichia coli K-12: mutants derepressed for 3-deoxy-d-arabinoheptulosonic acid 7-phosphate synthetase (phe), 3-deoxy-d-arabinoheptulosonic acid 7-phosphate synthetase (tyr), chorismate mutase T-prephenate dehydrogenase, and transaminase A. J Bacteriol 108, 400–409.
    • (1971) J Bacteriol , vol.108 , pp. 400-409
    • Im, S.W.K.1    Davidson, H.2    Pittard, J.3
  • 18
    • 23144432213 scopus 로고    scopus 로고
    • Optimality and evolutionary tuning of the expression level of a protein
    • Dekel E & Alon U (2005) Optimality and evolutionary tuning of the expression level of a protein. Nature 436, 588–592.
    • (2005) Nature , vol.436 , pp. 588-592
    • Dekel, E.1    Alon, U.2
  • 19
    • 0345739833 scopus 로고    scopus 로고
    • Differential proteome analysis: two-dimensional nano-LC/MS of E. coli proteome grown on different carbon sources
    • Vollmer M, Nägele E & Hörth P (2003) Differential proteome analysis: two-dimensional nano-LC/MS of E. coli proteome grown on different carbon sources. J Biomol Tech 14, 128–135.
    • (2003) J Biomol Tech , vol.14 , pp. 128-135
    • Vollmer, M.1    Nägele, E.2    Hörth, P.3
  • 20
    • 33644943635 scopus 로고    scopus 로고
    • Analysis of the proteome of Pseudomonas putida KT2440 grown on different sources of carbon and energy
    • Kurbatov L, Albrecht D, Herrmann H & Petruschka L (2006) Analysis of the proteome of Pseudomonas putida KT2440 grown on different sources of carbon and energy. Environ Microbiol 8, 466–478.
    • (2006) Environ Microbiol , vol.8 , pp. 466-478
    • Kurbatov, L.1    Albrecht, D.2    Herrmann, H.3    Petruschka, L.4
  • 21
    • 84864063600 scopus 로고    scopus 로고
    • Design and characterization of auxotrophy-based amino acid biosensors
    • Bertels F, Merker H & Kost C (2012) Design and characterization of auxotrophy-based amino acid biosensors. PLoS One 7, e41349.
    • (2012) PLoS One , vol.7
    • Bertels, F.1    Merker, H.2    Kost, C.3
  • 22
    • 84929377154 scopus 로고    scopus 로고
    • Plasticity and epistasis strongly affect bacterial fitness after losing multiple metabolic genes
    • D'Souza G, Waschina S, Kaleta C & Kost C (2015) Plasticity and epistasis strongly affect bacterial fitness after losing multiple metabolic genes. Evolution 69, 1244–1254.
    • (2015) Evolution , vol.69 , pp. 1244-1254
    • D'Souza, G.1    Waschina, S.2    Kaleta, C.3    Kost, C.4
  • 23
    • 84907962466 scopus 로고    scopus 로고
    • Less is more: selective advantages can explain the prevalent loss of biosynthetic genes in bacteria
    • D'Souza G, Waschina S, Pande S, Bohl K, Kaleta C & Kost C (2014) Less is more: selective advantages can explain the prevalent loss of biosynthetic genes in bacteria. Evolution 68, 2559–2570.
    • (2014) Evolution , vol.68 , pp. 2559-2570
    • D'Souza, G.1    Waschina, S.2    Pande, S.3    Bohl, K.4    Kaleta, C.5    Kost, C.6
  • 24
    • 84925014516 scopus 로고    scopus 로고
    • Proteome reallocation in Escherichia coli with increasing specific growth rate
    • Peebo K, Valgepea K, Maser A, Nahku R, Adamberg K & Vilu R (2015) Proteome reallocation in Escherichia coli with increasing specific growth rate. Mol BioSyst 11, 1184–1193.
    • (2015) Mol BioSyst , vol.11 , pp. 1184-1193
    • Peebo, K.1    Valgepea, K.2    Maser, A.3    Nahku, R.4    Adamberg, K.5    Vilu, R.6
  • 25
    • 84867746452 scopus 로고    scopus 로고
    • Metabolic specialization and the assembly of microbial communities
    • Johnson DR, Goldschmidt F, Lilja EE & Ackermann M (2012) Metabolic specialization and the assembly of microbial communities. ISME J 6, 1985–1991.
    • (2012) ISME J , vol.6 , pp. 1985-1991
    • Johnson, D.R.1    Goldschmidt, F.2    Lilja, E.E.3    Ackermann, M.4
  • 27
    • 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.
    • (1998) Mol Biol Evol , vol.15 , pp. 789-797
    • Treves, D.S.1    Manning, S.2    Adams, J.3
  • 28
    • 45849093668 scopus 로고    scopus 로고
    • Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli
    • Blount ZD, Borland CZ & Lenski RE (2008) Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proc Natl Acad Sci USA 105, 7899–7906.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 7899-7906
    • Blount, Z.D.1    Borland, C.Z.2    Lenski, R.E.3
  • 29
    • 34547162359 scopus 로고    scopus 로고
    • Metabolic characterization of Escherichia coli strains adapted to growth on lactate
    • Hua Q, Joyce AR, Palsson BØ & Fong SS (2007) Metabolic characterization of Escherichia coli strains adapted to growth on lactate. Appl Environ Microbiol 73, 4639–4647.
    • (2007) Appl Environ Microbiol , vol.73 , pp. 4639-4647
    • Hua, Q.1    Joyce, A.R.2    Palsson, B.Ø.3    Fong, S.S.4
  • 31
    • 0025895183 scopus 로고
    • Toward a science of metabolic engineering
    • Bailey JE (1991) Toward a science of metabolic engineering. Science 252, 1668–1675.
    • (1991) Science , vol.252 , pp. 1668-1675
    • Bailey, J.E.1
  • 32
    • 38449117858 scopus 로고    scopus 로고
    • Nutritional and engineering aspects of microbial process development
    • In, (Peteren F, &, Amstutz R, eds), Birkhäuser Basel, Basel, Switzerland
    • Masurekar PS (2008) Nutritional and engineering aspects of microbial process development. In Natural Compounds as Drugs, Vol. 65 (Peteren F & Amstutz R, eds), pp. 291-328. Birkhäuser Basel, Basel, Switzerland.
    • (2008) Natural Compounds as Drugs , vol.65 , pp. 291-328
    • Masurekar, P.S.1
  • 35
    • 0034612342 scopus 로고    scopus 로고
    • One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products
    • Datsenko KA & Wanner BL (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci 97, 6640–6645.
    • (2000) Proc Natl Acad Sci , vol.97 , pp. 6640-6645
    • Datsenko, K.A.1    Wanner, B.L.2
  • 36
    • 0023096283 scopus 로고
    • Transposon mutagenesis of Azospirillum brasilense and Azospirillum lipoferum: physical analysis of Tn5 and Tn5-Mob insertion mutants
    • Vanstockem M, Michiels K, Vanderleyden J & Van Gool AP (1987) Transposon mutagenesis of Azospirillum brasilense and Azospirillum lipoferum: physical analysis of Tn5 and Tn5-Mob insertion mutants. Appl Environ Microbiol 53, 410–415.
    • (1987) Appl Environ Microbiol , vol.53 , pp. 410-415
    • Vanstockem, M.1    Michiels, K.2    Vanderleyden, J.3    Van Gool, A.P.4
  • 37
    • 84864584520 scopus 로고    scopus 로고
    • Prediction of microbial growth rate versus biomass yield by a metabolic network with kinetic parameters
    • Adadi R, Volkmer B, Milo R, Heinemann M & Shlomi T (2012) Prediction of microbial growth rate versus biomass yield by a metabolic network with kinetic parameters. PLoS Comput Biol 8, e1002575.
    • (2012) PLoS Comput Biol , vol.8
    • Adadi, R.1    Volkmer, B.2    Milo, R.3    Heinemann, M.4    Shlomi, T.5
  • 38
    • 0016418469 scopus 로고
    • Tryptophanase: Structure, Catalytic Activities, and Mechanism of Action
    • In, Meister A, ed.), John Wiley & Sons Inc, Hoboken, NJ
    • Snell EE (1975) Tryptophanase: Structure, Catalytic Activities, and Mechanism of Action. In Advances in Enzymology and Related Areas of Molecular Biology (Meister A, ed.), pp. 287–333. John Wiley & Sons Inc, Hoboken, NJ.
    • (1975) Advances in Enzymology and Related Areas of Molecular Biology , pp. 287-333
    • Snell, E.E.1
  • 42
    • 84966600544 scopus 로고
    • Algorithm AS 136: a K-means clustering algorithm
    • Hartigan JA & Wong MA (1979) Algorithm AS 136: a K-means clustering algorithm. Appl Stat 28, 100.
    • (1979) Appl Stat , vol.28 , pp. 100
    • Hartigan, J.A.1    Wong, M.A.2
  • 43
    • 33746197428 scopus 로고    scopus 로고
    • Adaptive linear step-up procedures that control the false discovery rate
    • Benjamini Y, Krieger AM & Yekutieli D (2006) Adaptive linear step-up procedures that control the false discovery rate. Biometrika 93, 491–507.
    • (2006) Biometrika , vol.93 , pp. 491-507
    • Benjamini, Y.1    Krieger, A.M.2    Yekutieli, D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.