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Volumn 11, Issue , 2012, Pages

Investigating the effects of perturbations to pgi and eno gene expression on central carbon metabolism in Escherichia coli using 13 C metabolic flux analysis

Author keywords

13 C Metabolic flux analysis; Eno; Escherichia coli; Gene expression perturbations; Metabolic sensitivity analysis; Pgi

Indexed keywords

CARBON 13; ENOLASE; GLUCOSE 6 PHOSPHATE DEHYDROGENASE; GLUCOSE 6 PHOSPHATE ISOMERASE; GLYOXYLIC ACID; ISOCITRATE DEHYDROGENASE; PENTOSE PHOSPHATE; PHOSPHOENOLPYRUVATE CARBOXYKINASE (ATP); TRICARBOXYLIC ACID;

EID: 84862497417     PISSN: None     EISSN: 14752859     Source Type: Journal    
DOI: 10.1186/1475-2859-11-87     Document Type: Article
Times cited : (48)

References (31)
  • 1
    • 0036500993 scopus 로고    scopus 로고
    • Systems biology: a brief overview
    • 10.1126/science.1069492, 11872829
    • Kitano H. Systems biology: a brief overview. Science 2002, 295:1662-1664. 10.1126/science.1069492, 11872829.
    • (2002) Science , vol.295 , pp. 1662-1664
    • Kitano, H.1
  • 2
    • 20644467467 scopus 로고    scopus 로고
    • Systems biotechnology for strain improvement
    • 10.1016/j.tibtech.2005.05.003, 15923052
    • Lee SY, Lee DY, Kim TY. Systems biotechnology for strain improvement. Trends Biotechnol 2005, 23:349-358. 10.1016/j.tibtech.2005.05.003, 15923052.
    • (2005) Trends Biotechnol , vol.23 , pp. 349-358
    • Lee, S.Y.1    Lee, D.Y.2    Kim, T.Y.3
  • 3
    • 78149407462 scopus 로고    scopus 로고
    • Metabolic fluxes and beyond-systems biology understanding and engineering of microbial metabolism
    • 10.1007/s00253-010-2854-2, 20821203
    • Kohlstedt M, Becker J, Wittmann C. Metabolic fluxes and beyond-systems biology understanding and engineering of microbial metabolism. Appl Microbiol Biotechnol 2010, 88:1065-1075. 10.1007/s00253-010-2854-2, 20821203.
    • (2010) Appl Microbiol Biotechnol , vol.88 , pp. 1065-1075
    • Kohlstedt, M.1    Becker, J.2    Wittmann, C.3
  • 5
    • 0032485569 scopus 로고    scopus 로고
    • 13 C tracer experiments and metabolite balancing for metabolic flux analysis: comparing two approaches
    • 10.1002/(SICI)1097-0290(19980420)58:2/3<254::AID-BIT19>3.0.CO;2-C, 10191397
    • Schmidt K, Marx A, de Graaf AA, Wiechert W, Sahm H, Nielsen J, Villadsen J. 13 C tracer experiments and metabolite balancing for metabolic flux analysis: comparing two approaches. Biotechnol Bioeng 1998, 58:254-257. 10.1002/(SICI)1097-0290(19980420)58:2/3<254::AID-BIT19>3.0.CO;2-C, 10191397.
    • (1998) Biotechnol Bioeng , vol.58 , pp. 254-257
    • Schmidt, K.1    Marx, A.2    de Graaf, A.A.3    Wiechert, W.4    Sahm, H.5    Nielsen, J.6    Villadsen, J.7
  • 6
    • 0036365460 scopus 로고    scopus 로고
    • Metabolic flux analysis using mass spectrometry
    • Wittmann C. Metabolic flux analysis using mass spectrometry. Adv Biochem Eng Biotechnol 2002, 74:39-64.
    • (2002) Adv Biochem Eng Biotechnol , vol.74 , pp. 39-64
    • Wittmann, C.1
  • 7
    • 1542265814 scopus 로고    scopus 로고
    • Metabolic flux analysis of pykF gene knockout Escherichia coli based on 13 C-labeling experiments together with measurements of enzyme activities and intracellular metabolite concentrations
    • 10.1007/s00253-003-1357-9, 12802531
    • Al Zaid Siddiquee K, Arauzo-Bravo MJ, Shimizu K. Metabolic flux analysis of pykF gene knockout Escherichia coli based on 13 C-labeling experiments together with measurements of enzyme activities and intracellular metabolite concentrations. Appl Microbiol Biotechnol 2004, 63:407-417. 10.1007/s00253-003-1357-9, 12802531.
    • (2004) Appl Microbiol Biotechnol , vol.63 , pp. 407-417
    • Al Zaid Siddiquee, K.1    Arauzo-Bravo, M.J.2    Shimizu, K.3
  • 8
    • 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
    • 10.1111/j.1574-6968.2004.tb09563.x, 15158258
    • Siddiquee KA, Arauzo-Bravo MJ, Shimizu K. Effect of a pyruvate kinase (pykF-gene) knockout mutation on the control of gene expression and metabolic fluxes in Escherichia coli. FEMS Microbiol Lett 2004, 235:25-33. 10.1111/j.1574-6968.2004.tb09563.x, 15158258.
    • (2004) FEMS Microbiol Lett , vol.235 , pp. 25-33
    • Siddiquee, K.A.1    Arauzo-Bravo, M.J.2    Shimizu, K.3
  • 9
    • 77956969126 scopus 로고    scopus 로고
    • 13 C-Metabolic flux analysis for batch culture of Escherichia coli and its pyk and pgi gene knockout mutants based on mass isotopomer distribution of intracellular metabolites
    • Toya Y, Ishii N, Nakahigashi K, Hirasawa T, Soga T, Tomita M, Shimizu K. 13 C-Metabolic flux analysis for batch culture of Escherichia coli and its pyk and pgi gene knockout mutants based on mass isotopomer distribution of intracellular metabolites. Biotechnol Prog 2010, 26:975-992.
    • (2010) Biotechnol Prog , vol.26 , pp. 975-992
    • Toya, Y.1    Ishii, N.2    Nakahigashi, K.3    Hirasawa, T.4    Soga, T.5    Tomita, M.6    Shimizu, K.7
  • 10
    • 0345529074 scopus 로고    scopus 로고
    • Responses of the central metabolism in Escherichia coli to phosphoglucose isomerase and glucose-6-phosphate dehydrogenase knockouts
    • 10.1128/JB.185.24.7053-7067.2003, 296241, 14645264
    • Hua Q, Yang C, Baba T, Mori H, Shimizu K. Responses of the central metabolism in Escherichia coli to phosphoglucose isomerase and glucose-6-phosphate dehydrogenase knockouts. J Bacteriol 2003, 185:7053-7067. 10.1128/JB.185.24.7053-7067.2003, 296241, 14645264.
    • (2003) J Bacteriol , vol.185 , pp. 7053-7067
    • Hua, Q.1    Yang, C.2    Baba, T.3    Mori, H.4    Shimizu, K.5
  • 11
    • 80051498516 scopus 로고    scopus 로고
    • Catabolic regulation analysis of Escherichia coli and its crp, mlc, mgsA, pgi and ptsG mutants
    • 10.1186/1475-2859-10-67, 3169459, 21831320
    • Yao R, Hirose Y, Sarkar D, Nakahigashi K, Ye Q, Shimizu K. Catabolic regulation analysis of Escherichia coli and its crp, mlc, mgsA, pgi and ptsG mutants. Microb Cell Fact 2011, 10:67. 10.1186/1475-2859-10-67, 3169459, 21831320.
    • (2011) Microb Cell Fact , vol.10 , pp. 67
    • Yao, R.1    Hirose, Y.2    Sarkar, D.3    Nakahigashi, K.4    Ye, Q.5    Shimizu, K.6
  • 13
    • 34548623183 scopus 로고    scopus 로고
    • Response of the central metabolism of Escherichia coli to modified expression of the gene encoding the glucose-6-phosphate dehydrogenase
    • 10.1016/j.febslet.2007.06.066, 17631881
    • Nicolas C, Kiefer P, Letisse F, Krömer J, Massou S, Soucaille P, Wittmann C, Lindley ND, Portais JC. Response of the central metabolism of Escherichia coli to modified expression of the gene encoding the glucose-6-phosphate dehydrogenase. FEBS Lett 2007, 581:3771-3776. 10.1016/j.febslet.2007.06.066, 17631881.
    • (2007) FEBS Lett , vol.581 , pp. 3771-3776
    • Nicolas, C.1    Kiefer, P.2    Letisse, F.3    Krömer, J.4    Massou, S.5    Soucaille, P.6    Wittmann, C.7    Lindley, N.D.8    Portais, J.C.9
  • 14
    • 0024311484 scopus 로고
    • Isolation and characterization of the phosphoglucose isomerase gene from Escherichia coli
    • 10.1007/BF00330951, 2549364
    • Froman BE, Tait RC, Gottlieb LD. Isolation and characterization of the phosphoglucose isomerase gene from Escherichia coli. Mol Gen Genet 1989, 217:126-131. 10.1007/BF00330951, 2549364.
    • (1989) Mol Gen Genet , vol.217 , pp. 126-131
    • Froman, B.E.1    Tait, R.C.2    Gottlieb, L.D.3
  • 15
    • 0030485527 scopus 로고    scopus 로고
    • Cloning, nucleotide sequence, and functional expression of the Escherichia coli enolase (eno) gene in a temperature-sensitive eno mutant strain
    • Klein M, Sprenger GA, Freudl R. Cloning, nucleotide sequence, and functional expression of the Escherichia coli enolase (eno) gene in a temperature-sensitive eno mutant strain. DNA Seq 1996, 6:351-355.
    • (1996) DNA Seq , vol.6 , pp. 351-355
    • Klein, M.1    Sprenger, G.A.2    Freudl, R.3
  • 17
    • 55549133238 scopus 로고    scopus 로고
    • Construction of Escherichia coli gene expression level perturbation collection
    • 10.1016/j.ymben.2008.08.002, 18790072
    • Kashiwagi A, Sakurai T, Tsuru S, Ying BW, Mori K, Yomo T. Construction of Escherichia coli gene expression level perturbation collection. Metab Eng 2009, 11:56-63. 10.1016/j.ymben.2008.08.002, 18790072.
    • (2009) Metab Eng , vol.11 , pp. 56-63
    • Kashiwagi, A.1    Sakurai, T.2    Tsuru, S.3    Ying, B.W.4    Mori, K.5    Yomo, T.6
  • 18
    • 0018722217 scopus 로고
    • Evidence suggesting that the NADPH/NADP ratio modulates the splitting of the isocitrate flux between the glyoxylic and tricarboxylic acid cycles, in Escherichia coli
    • 10.1016/0014-5793(79)80642-0, 39785
    • Bautista J, Satrústegui J, Machado A. Evidence suggesting that the NADPH/NADP ratio modulates the splitting of the isocitrate flux between the glyoxylic and tricarboxylic acid cycles, in Escherichia coli. FEBS Lett 1979, 105:333-336. 10.1016/0014-5793(79)80642-0, 39785.
    • (1979) FEBS Lett , vol.105 , pp. 333-336
    • Bautista, J.1    Satrústegui, J.2    Machado, A.3
  • 19
    • 80955142256 scopus 로고    scopus 로고
    • Biochemical properties and physiological roles of NADP-dependent malic enzyme in Escherichia coli
    • 10.1007/s12275-011-0487-5, 22068497
    • Wang B, Wang P, Zheng E, Chen X, Zhao H, Song P, Su R, Li X, Zhu G. Biochemical properties and physiological roles of NADP-dependent malic enzyme in Escherichia coli. J Microbiol 2011, 49:797-802. 10.1007/s12275-011-0487-5, 22068497.
    • (2011) J Microbiol , vol.49 , pp. 797-802
    • Wang, B.1    Wang, P.2    Zheng, E.3    Chen, X.4    Zhao, H.5    Song, P.6    Su, R.7    Li, X.8    Zhu, G.9
  • 20
    • 0023703923 scopus 로고
    • Glyoxylate bypass operon of Escherichia coli: cloning and determination of the functional map
    • 210654, 2826399
    • Chung T, Klumpp DJ, LaPorte DC. Glyoxylate bypass operon of Escherichia coli: cloning and determination of the functional map. J Bacteriol 1988, 170:386-392. 210654, 2826399.
    • (1988) J Bacteriol , vol.170 , pp. 386-392
    • Chung, T.1    Klumpp, D.J.2    LaPorte, D.C.3
  • 21
    • 0022212761 scopus 로고
    • Compensatory phosphorylation of isocitrate dehydrogenase. A mechanism for adaptation to the intracellular environment
    • LaPorte DC, Thorsness PE, Koshland DE. Compensatory phosphorylation of isocitrate dehydrogenase. A mechanism for adaptation to the intracellular environment. J Biol Chem 1985, 260:10563-10568.
    • (1985) J Biol Chem , vol.260 , pp. 10563-10568
    • LaPorte, D.C.1    Thorsness, P.E.2    Koshland, D.E.3
  • 22
    • 33646362289 scopus 로고    scopus 로고
    • Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes
    • 10.1074/jbc.M510016200, 16319065
    • Fong SS, Nanchen A, Palsson BO, Sauer U. Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes. J Biol Chem 2006, 281:8024-8033. 10.1074/jbc.M510016200, 16319065.
    • (2006) J Biol Chem , vol.281 , pp. 8024-8033
    • Fong, S.S.1    Nanchen, A.2    Palsson, B.O.3    Sauer, U.4
  • 23
    • 78649694766 scopus 로고    scopus 로고
    • Genetic basis of growth adaptation of Escherichia coli after deletion of pgi, a major metabolic gene
    • 10.1371/journal.pgen.1001186, 2973815, 21079674
    • Charusanti P, Conrad TM, Knight EM, Venkataraman K, Fong NL, Xie B, Gao Y, Palsson BO. Genetic basis of growth adaptation of Escherichia coli after deletion of pgi, a major metabolic gene. PLoS Genet 2010, 6:e1001186. 10.1371/journal.pgen.1001186, 2973815, 21079674.
    • (2010) PLoS Genet , vol.6
    • Charusanti, P.1    Conrad, T.M.2    Knight, E.M.3    Venkataraman, K.4    Fong, N.L.5    Xie, B.6    Gao, Y.7    Palsson, B.O.8
  • 24
    • 80855123905 scopus 로고    scopus 로고
    • Evaluating 13 C enrichment data of free amino acids for precise metabolic flux analysis
    • 10.1002/biot.201000446, 22069095
    • Mori E, Furusawa C, Kajihata S, Shirai T, Shimizu H. Evaluating 13 C enrichment data of free amino acids for precise metabolic flux analysis. Biotechnol J 2011, 6:1377-1387. 10.1002/biot.201000446, 22069095.
    • (2011) Biotechnol J , vol.6 , pp. 1377-1387
    • Mori, E.1    Furusawa, C.2    Kajihata, S.3    Shirai, T.4    Shimizu, H.5
  • 26
    • 0017759929 scopus 로고
    • The enzymic interconversion of acetate and acetyl-coenzyme A in Escherichia coli
    • 10.1099/00221287-102-2-327, 21941
    • Brown TD, Jones-Mortimer MC, Kornberg HL. The enzymic interconversion of acetate and acetyl-coenzyme A in Escherichia coli. J Gen Microbiol 1977, 102:327-336. 10.1099/00221287-102-2-327, 21941.
    • (1977) J Gen Microbiol , vol.102 , pp. 327-336
    • Brown, T.D.1    Jones-Mortimer, M.C.2    Kornberg, H.L.3
  • 27
    • 0028138812 scopus 로고
    • Identification and characterization of the ackA (acetate kinase A)-pta (phosphotransacetylase) operon and complementation analysis of acetate utilization by an ackA-pta deletion mutant of Escherichia coli
    • Kakuda H, Hosono K, Shiroishi K, Ichihara S. Identification and characterization of the ackA (acetate kinase A)-pta (phosphotransacetylase) operon and complementation analysis of acetate utilization by an ackA-pta deletion mutant of Escherichia coli. J Biochem (Tokyo) 1994, 116:916-922.
    • (1994) J Biochem (Tokyo) , vol.116 , pp. 916-922
    • Kakuda, H.1    Hosono, K.2    Shiroishi, K.3    Ichihara, S.4
  • 28
    • 23344450789 scopus 로고    scopus 로고
    • Characterization of the acetate-producing pathways in Escherichia coli
    • Dittrich CR, Bennett GN, San KY. Characterization of the acetate-producing pathways in Escherichia coli. Biotechnol Prog 2005, 21:1062-1067.
    • (2005) Biotechnol Prog , vol.21 , pp. 1062-1067
    • Dittrich, C.R.1    Bennett, G.N.2    San, K.Y.3
  • 29
    • 0021677273 scopus 로고
    • Molecular cloning of the gene (poxB) encoding the pyruvate oxidase of Escherichia coli, a lipid-activated enzyme
    • 215823, 6209262
    • Grabau C, Cronan JE. Molecular cloning of the gene (poxB) encoding the pyruvate oxidase of Escherichia coli, a lipid-activated enzyme. J Bacteriol 1984, 160:1088-1092. 215823, 6209262.
    • (1984) J Bacteriol , vol.160 , pp. 1088-1092
    • Grabau, C.1    Cronan, J.E.2
  • 30
    • 33644558689 scopus 로고    scopus 로고
    • Effect of lpdA gene knockout on the metabolism in Escherichia coli based on enzyme activities, intracellular metabolite concentrations and metabolic flux analysis by 13 C-labeling experiments
    • 10.1016/j.jbiotec.2005.09.016, 16310273
    • Li M, Ho PY, Yao S, Shimizu K. Effect of lpdA gene knockout on the metabolism in Escherichia coli based on enzyme activities, intracellular metabolite concentrations and metabolic flux analysis by 13 C-labeling experiments. J Biotechnol 2006, 122:254-266. 10.1016/j.jbiotec.2005.09.016, 16310273.
    • (2006) J Biotechnol , vol.122 , pp. 254-266
    • Li, M.1    Ho, P.Y.2    Yao, S.3    Shimizu, K.4
  • 31
    • 84863304598 scopus 로고    scopus 로고
    • R Foundation for Statistical Computing, Vienna, R Development Core Team
    • R Development Core Team R: A language and environment for statistical computing 2012, R Foundation for Statistical Computing, Vienna, R Development Core Team.
    • (2012) R: A language and environment for statistical computing


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