메뉴 건너뛰기




Volumn 6, Issue 6, 2010, Pages 1-12

The carbon assimilation network in Escherichia coli is densely connected and largely sign-determined by directions of metabolic fluxes

Author keywords

[No Author keywords available]

Indexed keywords

CARBON; GENES; METABOLISM;

EID: 77955499190     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000812     Document Type: Article
Times cited : (48)

References (52)
  • 1
    • 33846400424 scopus 로고    scopus 로고
    • Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
    • Faith J, Hayete B, Thaden J, Mogno I, Wierzbowski J, et al. (2007) Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol 5: 0054-0066.
    • (2007) PLoS Biol , vol.5 , pp. 0054-0066
    • Faith, J.1    Hayete, B.2    Thaden, J.3    Mogno, I.4    Wierzbowski, J.5
  • 2
    • 0037066717 scopus 로고    scopus 로고
    • Global expression profiling of acetategrown Escherichia coli
    • Oh M, Rohlin L, Kao K, Liao J (2002) Global expression profiling of acetategrown Escherichia coli. J Biol Chem 277: 13175-13183.
    • (2002) J Biol Chem , vol.277 , pp. 13175-13183
    • Oh, M.1    Rohlin, L.2    Kao, K.3    Liao, J.4
  • 3
    • 22744432208 scopus 로고    scopus 로고
    • Precise temporal modulation in the response of the SOS DNA repair network in individual bacteria
    • Friedman N, Vardi S, Ronen M, Alon U, Stavans J (2005) Precise temporal modulation in the response of the SOS DNA repair network in individual bacteria. PLoS Biol 3: e238.
    • (2005) PLoS Biol , vol.3
    • Friedman, N.1    Vardi, S.2    Ronen, M.3    Alon, U.4    Stavans, J.5
  • 4
  • 5
    • 34347396784 scopus 로고    scopus 로고
    • Identification of regulatory network topological units coordinating the genome-wide transcriptional response to glucose in Escherichia coli
    • Gutierrez-Ros R, Freyre-Gonzalez J, Resendis O, Collado-Vides J, Saier M, et al. (2007) Identification of regulatory network topological units coordinating the genome-wide transcriptional response to glucose in Escherichia coli. BMC Microbiol 7: 53.
    • (2007) BMC Microbiol , vol.7 , pp. 53
    • Gutierrez-Ros, R.1    Freyre-Gonzalez, J.2    Resendis, O.3    Collado-Vides, J.4    Saier, M.5
  • 6
    • 41549140156 scopus 로고    scopus 로고
    • Cyclic AMP-dependent catabolite repression is the dominant control mechanism of metabolic fluxes under glucose limitation in Escherichia coli
    • Nanchen A, Schicker A, Revelles O, Sauer U (2008) Cyclic AMP-dependent catabolite repression is the dominant control mechanism of metabolic fluxes under glucose limitation in Escherichia coli. J Bacteriol 190: 2323-2330.
    • (2008) J Bacteriol , vol.190 , pp. 2323-2330
    • Nanchen, A.1    Schicker, A.2    Revelles, O.3    Sauer, U.4
  • 7
    • 0036953237 scopus 로고    scopus 로고
    • DNA topology-mediated control of global gene expression in Escherichia coli
    • Hatfield G, Benham C (2002) DNA topology-mediated control of global gene expression in Escherichia coli. Annu Rev Genet 36: 175-203.
    • (2002) Annu Rev Genet , vol.36 , pp. 175-203
    • Hatfield, G.1    Benham, C.2
  • 8
    • 35748932045 scopus 로고    scopus 로고
    • Topology of the global regulatory network of carbon limitation in Escherichia coli
    • Hardiman T, Lemuth K, Keller MA, Reuss M, Siemann-Herzberg M (2007) Topology of the global regulatory network of carbon limitation in Escherichia coli. J Biotechnol 132: 359-374.
    • (2007) J Biotechnol , vol.132 , pp. 359-374
    • Hardiman, T.1    Lemuth, K.2    Keller, M.A.3    Reuss, M.4    Siemann-Herzberg, M.5
  • 9
    • 33646570920 scopus 로고    scopus 로고
    • In vitro reconstitution of catabolite repression in Escherichia coli
    • Park YH, Lee B, Seok YJ, Peterkofsky A (2006) In vitro reconstitution of catabolite repression in Escherichia coli. J Biol Chem 281: 6448-6454.
    • (2006) J Biol Chem , vol.281 , pp. 6448-6454
    • Park, Y.H.1    Lee, B.2    Seok, Y.J.3    Peterkofsky, A.4
  • 10
    • 0000973692 scopus 로고    scopus 로고
    • Regulation of carbon utilization
    • In: Neidhardt F, Curtiss III R, Ingraham J, Lin E, Low K, et al, eds., Washington D.C.: ASM Press
    • Saier MJ, Ramseier T, J R (1996) Regulation of carbon utilization. In: Neidhardt F, Curtiss III R, Ingraham J, Lin E, Low K, et al, eds. Escherichia coli and Salmonella: Cellular and Molecular Biology. Washington D.C.: ASM Press. pp 1325-1343.
    • (1996) Escherichia Coli and Salmonella: Cellular and Molecular Biology , pp. 1325-1343
    • Saier, M.J.1    Ramseier Jr., T.2
  • 11
    • 42949164125 scopus 로고    scopus 로고
    • Formulating genome-scale kinetic models in the post-genome era
    • Jamshidi N, Palsson BO (2008) Formulating genome-scale kinetic models in the post-genome era. Mol Syst Biol 4: 171.
    • (2008) Mol Syst Biol , vol.4 , pp. 171
    • Jamshidi, N.1    Palsson, B.O.2
  • 13
    • 0032025439 scopus 로고    scopus 로고
    • Simplification of mathematical models of chemical reaction systems
    • Okino M, Mavrovouniotis M (1998) Simplification of mathematical models of chemical reaction systems. Chem Rev 98: 391-408.
    • (1998) Chem Rev , vol.98 , pp. 391-408
    • Okino, M.1    Mavrovouniotis, M.2
  • 14
    • 0026000298 scopus 로고
    • Control theory of regulatory cascades
    • Kahn D, Westerhoff H (1991) Control theory of regulatory cascades. J Theor Biol 153: 255-285.
    • (1991) J Theor Biol , vol.153 , pp. 255-285
    • Kahn, D.1    Westerhoff, H.2
  • 16
    • 0023709196 scopus 로고
    • Metabolic control theory: A structural approach
    • Reder C (1988) Metabolic control theory: a structural approach. J Theor Biol 135: 175-201.
    • (1988) J Theor Biol , vol.135 , pp. 175-201
    • Reder, C.1
  • 17
    • 34247612307 scopus 로고    scopus 로고
    • Multiple highthroughput analyses monitor the response of E. coli to perturbations
    • Ishii N, Nakahigashi K, Baba T, Robert M, Soga T, et al. (2007) Multiple highthroughput analyses monitor the response of E. coli to perturbations. Science 316: 593-597.
    • (2007) Science , vol.316 , pp. 593-597
    • Ishii, N.1    Nakahigashi, K.2    Baba, T.3    Robert, M.4    Soga, T.5
  • 18
    • 0038048325 scopus 로고    scopus 로고
    • Inferring genetic networks and identifying compound mode of action via expression profiling
    • Gardner T, di Bernardo D, Lorenz D, Collins J (2003) Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301: 102-105.
    • (2003) Science , vol.301 , pp. 102-105
    • Gardner, T.1    di Bernardo, D.2    Lorenz, D.3    Collins, J.4
  • 19
    • 0030574086 scopus 로고    scopus 로고
    • On the sign pattern of metabolic control coefficients
    • Sen AK (1996) On the sign pattern of metabolic control coefficients. J Theor Biol 182: 269-275.
    • (1996) J Theor Biol , vol.182 , pp. 269-275
    • Sen, A.K.1
  • 21
    • 0026528726 scopus 로고
    • Cloning and nucleotide sequence of the Escherichia coli K-12 ppsA gene, encoding PEP synthase
    • Niersbach M, Kreuzaler F, Geerse RH, Postma PW, Hirsch HJ (1992) Cloning and nucleotide sequence of the Escherichia coli K-12 ppsA gene, encoding PEP synthase. Mol Gen Genet 231: 332-336.
    • (1992) Mol Gen Genet , vol.231 , pp. 332-336
    • Niersbach, M.1    Kreuzaler, F.2    Geerse, R.H.3    Postma, P.W.4    Hirsch, H.J.5
  • 22
    • 0029610838 scopus 로고
    • Cloning of the two pyruvate kinase isoenzyme structural genes from Escherichia coli: The relative roles of these enzymes in pyruvate biosynthesis
    • Ponce E, Flores N, Martinez A, Valle F, Boĺvar F (1995) Cloning of the two pyruvate kinase isoenzyme structural genes from Escherichia coli: the relative roles of these enzymes in pyruvate biosynthesis. J Bacteriol 177: 5719-5722.
    • (1995) J Bacteriol , vol.177 , pp. 5719-5722
    • Ponce, E.1    Flores, N.2    Martinez, A.3    Valle, F.4    Boĺvar, F.5
  • 23
    • 0029147255 scopus 로고
    • The global regulatory protein FruR modulates the direction of carbon flow in Escherichia coli
    • Ramseier TM, Bledig S, Michotey V, Feghali R, Saier MH (1995) The global regulatory protein FruR modulates the direction of carbon flow in Escherichia coli. Mol Microbiol 16: 1157-1169.
    • (1995) Mol Microbiol , vol.16 , pp. 1157-1169
    • Ramseier, T.M.1    Bledig, S.2    Michotey, V.3    Feghali, R.4    Saier, M.H.5
  • 24
    • 0030029512 scopus 로고    scopus 로고
    • FruR mediates catabolite activation of pyruvate kinase (PykF) gene expression in Escherichia coli
    • Bledig S, Ramseier T, Saier JMH (1996) FruR mediates catabolite activation of pyruvate kinase (PykF) gene expression in Escherichia coli. J Bacteriol 178: 280-283.
    • (1996) J Bacteriol , vol.178 , pp. 280-283
    • Bledig, S.1    Ramseier, T.2    Saier, J.M.H.3
  • 25
    • 2442655332 scopus 로고    scopus 로고
    • Transcriptome analysis of CRP-dependent catabolite control of gene expression in Escherichia coli
    • Gosset G, Zhang Z, Nayyar S, Cuevas W, Saier Jr. M (2004) Transcriptome analysis of CRP-dependent catabolite control of gene expression in Escherichia coli. J Bacteriol 186: 3516-3524.
    • (2004) J Bacteriol , vol.186 , pp. 3516-3524
    • Gosset, G.1    Zhang, Z.2    Nayyar, S.3    Cuevas, W.4    Saier, M.5
  • 26
    • 7444245668 scopus 로고    scopus 로고
    • Identification of the CRP regulon using in vitro and in vivo transcriptional profiling
    • Zheng D, Constantinidou C, Hobman J, Minchin S (2004) Identification of the CRP regulon using in vitro and in vivo transcriptional profiling. Nucleic Acids Res 32: 5874-5893.
    • (2004) Nucleic Acids Res , vol.32 , pp. 5874-5893
    • Zheng, D.1    Constantinidou, C.2    Hobman, J.3    Minchin, S.4
  • 27
    • 33646352736 scopus 로고    scopus 로고
    • A quantitative approach to catabolite repression in Escherichia coli
    • Bettenbrock K, Fischer S, Kremling A, Jahreis K, Sauter T, et al. (2005) A quantitative approach to catabolite repression in Escherichia coli. J Biol Chem 281: 2578-2584.
    • (2005) J Biol Chem , vol.281 , pp. 2578-2584
    • Bettenbrock, K.1    Fischer, S.2    Kremling, A.3    Jahreis, K.4    Sauter, T.5
  • 29
    • 33646377419 scopus 로고    scopus 로고
    • Qualitative simulation of the carbon starvation response in Escherichia coli
    • Ropers D, de Jong H, Page M, Schneider D, Geiselmann J (2006) Qualitative simulation of the carbon starvation response in Escherichia coli. Biosystems 84: 124-152.
    • (2006) Biosystems , vol.84 , pp. 124-152
    • Ropers, D.1    de Jong, H.2    Page, M.3    Schneider, D.4    Geiselmann, J.5
  • 30
    • 40049093544 scopus 로고    scopus 로고
    • A feed-forward loop guarantees robust behavior in Escherichia coli carbohydrate uptake
    • Kremling A, Bettenbrock K, Gilles ED (2008) A feed-forward loop guarantees robust behavior in Escherichia coli carbohydrate uptake. Bioinformatics 24: 704-710.
    • (2008) Bioinformatics , vol.24 , pp. 704-710
    • Kremling, A.1    Bettenbrock, K.2    Gilles, E.D.3
  • 31
    • 0017286403 scopus 로고
    • The control of pyruvate kinase of Escherichia coli. Binding of substrate and allosteric effectors to the enzyme activated by fructose 1,6-bisphosphate
    • Waygood EB, Mort JS, Sanwal BD (1976) The control of pyruvate kinase of Escherichia coli. Binding of substrate and allosteric effectors to the enzyme activated by fructose 1,6-bisphosphate. Biochemistry 15: 277-282.
    • (1976) Biochemistry , vol.15 , pp. 277-282
    • Waygood, E.B.1    Mort, J.S.2    Sanwal, B.D.3
  • 32
    • 0027272139 scopus 로고
    • Glucose metabolism in Escherichia coli and the effect of increased amount of aldolase
    • Babul J, Clifton D, Kretschmer M, Fraenkel DG (1993) Glucose metabolism in Escherichia coli and the effect of increased amount of aldolase. Biochemistry 32: 4685-4692.
    • (1993) Biochemistry , vol.32 , pp. 4685-4692
    • Babul, J.1    Clifton, D.2    Kretschmer, M.3    Fraenkel, D.G.4
  • 33
    • 0032077377 scopus 로고    scopus 로고
    • From specific gene regulation to genomic networks: A global analysis of transcriptional regulation in Escherichia coli
    • Thieffry D, Huerta AM, Pérez-Rueda E, Collado-Vides J (1998) From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli. Bioessays 20: 433-440.
    • (1998) Bioessays , vol.20 , pp. 433-440
    • Thieffry, D.1    Huerta, A.M.2    Pérez-Rueda, E.3    Collado-Vides, J.4
  • 34
    • 0036578654 scopus 로고    scopus 로고
    • Topological and causal structure of the yeast transcriptional regulatory network
    • Guelzim N, Bottani S, Bourgine P, Képès F (2002) Topological and causal structure of the yeast transcriptional regulatory network. Nat Genet 31: 60-63.
    • (2002) Nat Genet , vol.31 , pp. 60-63
    • Guelzim, N.1    Bottani, S.2    Bourgine, P.3    Képès, F.4
  • 35
    • 0036578795 scopus 로고    scopus 로고
    • Network motifs in the transcriptional regulation network of Escherichia coli
    • Shen-Orr S, Milo R, Mangan S, Alon U (2002) Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 31: 64-68.
    • (2002) Nat Genet , vol.31 , pp. 64-68
    • Shen-Orr, S.1    Milo, R.2    Mangan, S.3    Alon, U.4
  • 36
    • 13544269611 scopus 로고    scopus 로고
    • An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs
    • Ma HW, Kumar B, Ditges U, Gunzer F, Buer J, et al. (2004) An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs. Nucl Acids Res 32: 6643-6649.
    • (2004) Nucl Acids Res , vol.32 , pp. 6643-6649
    • Ma, H.W.1    Kumar, B.2    Ditges, U.3    Gunzer, F.4    Buer, J.5
  • 37
    • 55449084318 scopus 로고    scopus 로고
    • Effect of cra gene knockout together with edd and iclR genes knockout on the metabolism in Escherichia coli
    • Sarkar D, Siddiquee K, Araúzo-Bravo M, Oba T, Shimizu K (2008) Effect of cra gene knockout together with edd and iclR genes knockout on the metabolism in Escherichia coli. Arch Microbiol 190: 558-571.
    • (2008) Arch Microbiol , vol.190 , pp. 558-571
    • Sarkar, D.1    Siddiquee, K.2    Araúzo-Bravo, M.3    Oba, T.4    Shimizu, K.5
  • 38
    • 0001389945 scopus 로고
    • Enzyme induction as an all-or-none phenomenon
    • Novick A, Weiner M (1957) Enzyme induction as an all-or-none phenomenon. Proc Natl Acad Sci U S A 43: 553-566.
    • (1957) Proc Natl Acad Sci U S A , vol.43 , pp. 553-566
    • Novick, A.1    Weiner, M.2
  • 43
    • 2342648924 scopus 로고    scopus 로고
    • Integrating highthroughput and computational data elucidates bacterial networks
    • Covert M, Knight E, Reed J, Herrgard M, Palsson B (2004) Integrating highthroughput and computational data elucidates bacterial networks. Nature 429: 92-100.
    • (2004) Nature , vol.429 , pp. 92-100
    • Covert, M.1    Knight, E.2    Reed, J.3    Herrgard, M.4    Palsson, B.5
  • 44
    • 51749113592 scopus 로고    scopus 로고
    • Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli
    • Covert MW, Xiao N, Chen TJ, Karr JR (2008) Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli. Bioinformatics 24: 2044-2050.
    • (2008) Bioinformatics , vol.24 , pp. 2044-2050
    • Covert, M.W.1    Xiao, N.2    Chen, T.J.3    Karr, J.R.4
  • 45
    • 34247183123 scopus 로고    scopus 로고
    • A genome-scale computational study of the interplay between transcriptional regulation and metabolism
    • Shlomi T, Eisenberg Y, Sharan R, Ruppin E (2007) A genome-scale computational study of the interplay between transcriptional regulation and metabolism. Mol Syst Biol 3: 101-101.
    • (2007) Mol Syst Biol , vol.3 , pp. 101-101
    • Shlomi, T.1    Eisenberg, Y.2    Sharan, R.3    Ruppin, E.4
  • 46
    • 2442675518 scopus 로고    scopus 로고
    • Effect of a pyruvate kinase (pykF gene) knockout mutation on the control of gene expression and metabolic fluxes in Escherichia coli
    • Siddiquee K, Araúzo-Bravo, Shimizu MK (2004) Effect of a pyruvate kinase (pykF gene) knockout mutation on the control of gene expression and metabolic fluxes in Escherichia coli. FEMS Microbiol Lett 235: 25-33.
    • (2004) FEMS Microbiol Lett , vol.235 , pp. 25-33
    • Siddiquee, K.1    Araúzo-Bravo2    Shimizu, M.K.3
  • 47
    • 27744573112 scopus 로고    scopus 로고
    • A global regulatory role of gluconeogenic genes in Escherichia coli revealed by transcriptome network analysis
    • Kao KC, Tran LM, Liao JC (2005) A global regulatory role of gluconeogenic genes in Escherichia coli revealed by transcriptome network analysis. J Biol Chem 280: 36079-36087.
    • (2005) J Biol Chem , vol.280 , pp. 36079-36087
    • Kao, K.C.1    Tran, L.M.2    Liao, J.C.3
  • 48
    • 0037626593 scopus 로고    scopus 로고
    • Qualitative stability and ambiguity in model ecosystems
    • Dambacher JM, Luh H, Li HW, Rossignol PA (2003) Qualitative stability and ambiguity in model ecosystems. Am Nat 161: 876-888.
    • (2003) Am Nat , vol.161 , pp. 876-888
    • Dambacher, J.M.1    Luh, H.2    Li, H.W.3    Rossignol, P.A.4
  • 50
    • 0031231891 scopus 로고    scopus 로고
    • Qualitative comparative statics
    • Quirck J (1997) Qualitative comparative statics. J Math Econ 28: 127-154.
    • (1997) J Math Econ , vol.28 , pp. 127-154
    • Quirck, J.1
  • 52
    • 0038027881 scopus 로고    scopus 로고
    • Molecular interaction maps as information organizers and simulation guides
    • Kohn K (2001) Molecular interaction maps as information organizers and simulation guides. Chaos 11: 84-97.
    • (2001) Chaos , vol.11 , pp. 84-97
    • Kohn, K.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.