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Volumn 84, Issue 19, 2018, Pages

Multiple optimal phenotypes overcome redox and glycolytic intermediate metabolite imbalances in Escherichia coli pgi knockout evolutions

Author keywords

Adaptive laboratory evolution; Escherichia coli; Multi omics analysis; Mutation analysis; Pgi gene knockout; Systems biology

Indexed keywords

ESCHERICHIA COLI PROTEIN; GLUCOSE 6 PHOSPHATE ISOMERASE; PGI PROTEIN, E COLI;

EID: 85053445003     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.00823-18     Document Type: Article
Times cited : (23)

References (86)
  • 1
    • 84862497417 scopus 로고    scopus 로고
    • Investigating the effects of perturbations to pgi and eno gene expression on central carbon metabolism in Escherichia coli using 13C metabolic flux analysis
    • Usui Y, Hirasawa T, Furusawa C, Shirai T, Yamamoto N, Mori H, Shimizu H. 2012. Investigating the effects of perturbations to pgi and eno gene expression on central carbon metabolism in Escherichia coli using 13C metabolic flux analysis. Microb Cell Fact 11:87. https://doi.org/10.1186/ 1475-2859-11-87
    • (2012) Microb Cell Fact , vol.11 , pp. 87
    • Usui, Y.1    Hirasawa, T.2    Furusawa, C.3    Shirai, T.4    Yamamoto, N.5    Mori, H.6    Shimizu, H.7
  • 2
    • 80053462862 scopus 로고    scopus 로고
    • NADPH-dependent pgi-gene knockout Escherichia coli metabolism producing shikimate on different carbon sources
    • Ahn J, Chung BKS, Lee D-Y, Park M, Karimi IA, Jung J-K, Lee H. 2011. NADPH-dependent pgi-gene knockout Escherichia coli metabolism producing shikimate on different carbon sources. FEMS Microbiol Lett 324:10-16. https://doi.org/10.1111/j.1574-6968.2011.02378.x
    • (2011) FEMS Microbiol Lett , vol.324 , pp. 10-16
    • Ahn, J.1    Chung, B.K.S.2    Lee, D.-Y.3    Park, M.4    Karimi, I.A.5    Jung, J.-K.6    Lee, H.7
  • 4
    • 33646362289 scopus 로고    scopus 로고
    • Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes
    • Fong SS, Nanchen A, Palsson BO, Sauer U. 2006. Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes. J Biol Chem 281:8024-8033. https:// doi.org/10.1074/jbc.M510016200
    • (2006) J Biol Chem , vol.281 , pp. 8024-8033
    • Fong, S.S.1    Nanchen, A.2    Palsson, B.O.3    Sauer, U.4
  • 6
    • 84886013496 scopus 로고    scopus 로고
    • Depletion of glycolytic intermediates plays a key role in glucose-phosphate stress in Escherichia coli
    • Richards GR, Patel MV, Lloyd CR, Vanderpool CK. 2013. Depletion of glycolytic intermediates plays a key role in glucose-phosphate stress in Escherichia coli. J Bacteriol 195:4816-4825. https://doi.org/10.1128/JB.00705-13
    • (2013) J Bacteriol , vol.195 , pp. 4816-4825
    • Richards, G.R.1    Patel, M.V.2    Lloyd, C.R.3    Vanderpool, C.K.4
  • 7
    • 8544271637 scopus 로고    scopus 로고
    • Involvement of a novel transcriptional activator and small RNA in post-transcriptional regulation of the glucose phosphoenolpyruvate phosphotransferase system
    • Vanderpool CK, Gottesman S. 2004. Involvement of a novel transcriptional activator and small RNA in post-transcriptional regulation of the glucose phosphoenolpyruvate phosphotransferase system. Mol Microbiol 54:1076-1089. https://doi.org/10.1111/j.1365-2958.2004.04348.x
    • (2004) Mol Microbiol , vol.54 , pp. 1076-1089
    • Vanderpool, C.K.1    Gottesman, S.2
  • 8
    • 33947139094 scopus 로고    scopus 로고
    • The novel transcription factor SgrR coordinates the response to glucose-phosphate stress
    • Vanderpool CK, Gottesman S. 2007. The novel transcription factor SgrR coordinates the response to glucose-phosphate stress. J Bacteriol 189: 2238-2248. https://doi.org/10.1128/JB.01689-06
    • (2007) J Bacteriol , vol.189 , pp. 2238-2248
    • Vanderpool, C.K.1    Gottesman, S.2
  • 9
    • 2042476756 scopus 로고
    • Hydrogen donor system for Escherichia coli ribonucleoside-diphosphate reductase dependent upon glutathione
    • Holmgren A. 1976. Hydrogen donor system for Escherichia coli ribonucleoside-diphosphate reductase dependent upon glutathione. Proc Natl Acad Sci U S A 73:2275-2279
    • (1976) Proc Natl Acad Sci U S A , vol.73 , pp. 2275-2279
    • Holmgren, A.1
  • 10
    • 84923925548 scopus 로고    scopus 로고
    • Metabolic engineering of Escherichia coli for the production of riboflavin
    • Lin Z, Xu Z, Li Y, Wang Z, Chen T, Zhao X. 2014. Metabolic engineering of Escherichia coli for the production of riboflavin. Microb Cell Fact 13:104. https://doi.org/10.1186/s12934-014-0104-5
    • (2014) Microb Cell Fact , vol.13 , pp. 104
    • Lin, Z.1    Xu, Z.2    Li, Y.3    Wang, Z.4    Chen, T.5    Zhao, X.6
  • 13
    • 84879489028 scopus 로고    scopus 로고
    • Adaptive laboratory evolution-principles and applications for biotechnology
    • Dragosits M, Mattanovich D. 2013. Adaptive laboratory evolution-principles and applications for biotechnology. Microb Cell Fact 12:64. https://doi.org/ 10.1186/1475-2859-12-64
    • (2013) Microb Cell Fact , vol.12 , pp. 64
    • Dragosits, M.1    Mattanovich, D.2
  • 14
    • 84924408551 scopus 로고    scopus 로고
    • Transhydrogenase promotes the robustness and evolvability of E. coli deficient in NADPH production
    • Chou H-H, Marx CJ, Sauer U. 2015. Transhydrogenase promotes the robustness and evolvability of E. coli deficient in NADPH production. PLoS Genet 11:e1005007. https://doi.org/10.1371/journal.pgen.1005007
    • (2015) PLoS Genet , vol.11
    • Chou, H.-H.1    Marx, C.J.2    Sauer, U.3
  • 15
    • 70349306551 scopus 로고    scopus 로고
    • Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism
    • Nakahigashi K, Toya Y, Ishii N, Soga T, Hasegawa M, Watanabe H, Takai Y, Honma M, Mori H, Tomita M. 2009. Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism. Mol Syst Biol 5:306. https://doi.org/10.1038/ msb.2009.65
    • (2009) Mol Syst Biol , vol.5 , pp. 306
    • Nakahigashi, K.1    Toya, Y.2    Ishii, N.3    Soga, T.4    Hasegawa, M.5    Watanabe, H.6    Takai, Y.7    Honma, M.8    Mori, H.9    Tomita, M.10
  • 18
    • 84963796141 scopus 로고    scopus 로고
    • Modeling method for increased precision and scope of directly measurable fluxes at a genome-scale
    • McCloskey D, Young JD, Xu S, Palsson BO, Feist AM. 2016. Modeling method for increased precision and scope of directly measurable fluxes at a genome-scale. Anal Chem 88:3844-3852. https://doi.org/10.1021/ acs.analchem.5b04914
    • (2016) Anal Chem , vol.88 , pp. 3844-3852
    • McCloskey, D.1    Young, J.D.2    Xu, S.3    Palsson, B.O.4    Feist, A.M.5
  • 19
    • 84944340025 scopus 로고    scopus 로고
    • Identification of novel sRNAs involved in biofilm formation, motility, and fimbriae formation in Escherichia coli
    • Bak G, Lee J, Suk S, Kim D, Young Lee J, Kim K-S, Choi B-S, Lee Y. 2015. Identification of novel sRNAs involved in biofilm formation, motility, and fimbriae formation in Escherichia coli. Sci Rep 5:15287. https://doi.org/ 10.1038/srep15287
    • (2015) Sci Rep , vol.5 , pp. 15287
    • Bak, G.1    Lee, J.2    Suk, S.3    Kim, D.4    Young Lee, J.5    Kim, K.-S.6    Choi, B.-S.7    Lee, Y.8
  • 20
    • 0035796390 scopus 로고    scopus 로고
    • Expression of the glucose transporter gene, ptsG, is regulated at the mRNA degradation step in response to glycolytic flux in Escherichia coli
    • Kimata K, Tanaka Y, Inada T, Aiba H. 2001. Expression of the glucose transporter gene, ptsG, is regulated at the mRNA degradation step in response to glycolytic flux in Escherichia coli. EMBO J 20:3587-3595. https://doi.org/10.1093/emboj/20.13.3587
    • (2001) EMBO J , vol.20 , pp. 3587-3595
    • Kimata, K.1    Tanaka, Y.2    Inada, T.3    Aiba, H.4
  • 21
    • 34247104624 scopus 로고    scopus 로고
    • Physiological consequences of small RNAmediated regulation of glucose-phosphate stress
    • Vanderpool CK. 2007. Physiological consequences of small RNAmediated regulation of glucose-phosphate stress. Curr Opin Microbiol 10:146-151. https://doi.org/10.1016/j.mib.2007.03.011
    • (2007) Curr Opin Microbiol , vol.10 , pp. 146-151
    • Vanderpool, C.K.1
  • 23
    • 84941746034 scopus 로고    scopus 로고
    • The architecture of ArgR-DNA complexes at the genome-scale in Escherichia coli
    • Cho S, Cho Y-B, Kang TJ, Kim SC, Palsson B, Cho B-K. 2015. The architecture of ArgR-DNA complexes at the genome-scale in Escherichia coli. Nucleic Acids Res 43:3079-3088. https://doi.org/10.1093/nar/gkv150
    • (2015) Nucleic Acids Res , vol.43 , pp. 3079-3088
    • Cho, S.1    Cho, Y.-B.2    Kang, T.J.3    Kim, S.C.4    Palsson, B.5    Cho, B.-K.6
  • 25
    • 84866160409 scopus 로고    scopus 로고
    • Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling
    • Kim D, Hong JS-J, Qiu Y, Nagarajan H, Seo J-H, Cho B-K, Tsai S-F, Palsson BØ. 2012. Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling. PLoS Genet 8:e1002867. https://doi.org/10.1371/ journal.pgen.1002867
    • (2012) PLoS Genet , vol.8
    • Kim, D.1    Hong, J.S.-J.2    Qiu, Y.3    Nagarajan, H.4    Seo, J.-H.5    Cho, B.-K.6    Tsai, S.-F.7    Palsson, BØ.8
  • 26
    • 83655163675 scopus 로고    scopus 로고
    • Deciphering the transcriptional regulatory logic of amino acid metabolism
    • Cho B-K, Federowicz S, Park Y-S, Zengler K, Palsson BØ. 2011. Deciphering the transcriptional regulatory logic of amino acid metabolism. Nat Chem Biol 8:65-71. https://doi.org/10.1038/nchembio.710
    • (2011) Nat Chem Biol , vol.8 , pp. 65-71
    • Cho, B.-K.1    Federowicz, S.2    Park, Y.-S.3    Zengler, K.4    Palsson, BØ.5
  • 27
    • 0026660358 scopus 로고
    • Interaction at a distance between multiple operators controls the adjacent, divergently transcribed glpTQ-glpACB operons of Escherichia coli K-12
    • Larson TJ, Cantwell JS, van Loo-Bhattacharya AT. 1992. Interaction at a distance between multiple operators controls the adjacent, divergently transcribed glpTQ-glpACB operons of Escherichia coli K-12. J Biol Chem 267:6114-6121
    • (1992) J Biol Chem , vol.267 , pp. 6114-6121
    • Larson, T.J.1    Cantwell, J.S.2    van Loo-Bhattacharya, A.T.3
  • 28
    • 0023812828 scopus 로고
    • Role of uhp genes in expression of the Escherichia coli sugar-phosphate transport system
    • Weston LA, Kadner RJ. 1988. Role of uhp genes in expression of the Escherichia coli sugar-phosphate transport system. J Bacteriol 170: 3375-3383. https://doi.org/10.1128/jb.170.8.3375-3383.1988
    • (1988) J Bacteriol , vol.170 , pp. 3375-3383
    • Weston, L.A.1    Kadner, R.J.2
  • 29
    • 0031020834 scopus 로고    scopus 로고
    • Protein phosphorylation affects binding of the Escherichia coli transcription activator UhpA to the uhpT promoter
    • Dahl JL, Wei BY, Kadner RJ. 1997. Protein phosphorylation affects binding of the Escherichia coli transcription activator UhpA to the uhpT promoter. J Biol Chem 272:1910-1919. https://doi.org/10.1074/jbc.272.3.1910
    • (1997) J Biol Chem , vol.272 , pp. 1910-1919
    • Dahl, J.L.1    Wei, B.Y.2    Kadner, R.J.3
  • 31
  • 32
    • 51649128997 scopus 로고    scopus 로고
    • Leakage of adenylates during cold methanol/glycerol quenching of Escherichia coli
    • Link H, Anselment B, Weuster-Botz D. 2008. Leakage of adenylates during cold methanol/glycerol quenching of Escherichia coli. Metabolomics 4:240-247. https://doi.org/10.1007/s11306-008-0114-6
    • (2008) Metabolomics , vol.4 , pp. 240-247
    • Link, H.1    Anselment, B.2    Weuster-Botz, D.3
  • 33
    • 45149128433 scopus 로고    scopus 로고
    • The cost of expression of Escherichia coli lac operon proteins is in the process, not in the products
    • Stoebel DM, Dean AM, Dykhuizen DE. 2008. The cost of expression of Escherichia coli lac operon proteins is in the process, not in the products. Genetics 178:1653-1660. https://doi.org/10.1534/genetics.107.085399
    • (2008) Genetics , vol.178 , pp. 1653-1660
    • Stoebel, D.M.1    Dean, A.M.2    Dykhuizen, D.E.3
  • 34
    • 84883810552 scopus 로고    scopus 로고
    • Metabolic costs of amino acid and protein production in Escherichia coli
    • Kaleta C, Schäuble S, Rinas U, Schuster S. 2013. Metabolic costs of amino acid and protein production in Escherichia coli. Biotechnol J 8:1105-1114. https://doi.org/10.1002/biot.201200267
    • (2013) Biotechnol J , vol.8 , pp. 1105-1114
    • Kaleta, C.1    Schäuble, S.2    Rinas, U.3    Schuster, S.4
  • 35
    • 33144488588 scopus 로고    scopus 로고
    • Guanosine 3=, 5=-bispyrophosphate coordinates global gene expression during glucoselactose diauxie in Escherichia coli
    • Traxler MF, Chang D-E, Conway T. 2006. Guanosine 3=, 5=-bispyrophosphate coordinates global gene expression during glucoselactose diauxie in Escherichia coli. Proc Natl Acad Sci U S A 103: 2374-2379. https://doi.org/10.1073/pnas.0510995103
    • (2006) Proc Natl Acad Sci U S A , vol.103 , pp. 2374-2379
    • Traxler, M.F.1    Chang, D.-E.2    Conway, T.3
  • 36
    • 0032693327 scopus 로고    scopus 로고
    • Functional genomics: expression analysis of Escherichia coli growing on minimal and rich media
    • Tao H, Bausch C, Richmond C, Blattner FR, Conway T. 1999. Functional genomics: expression analysis of Escherichia coli growing on minimal and rich media. J Bacteriol 181:6425-6440
    • (1999) J Bacteriol , vol.181 , pp. 6425-6440
    • Tao, H.1    Bausch, C.2    Richmond, C.3    Blattner, F.R.4    Conway, T.5
  • 37
    • 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 U S A 99:3695-3700. https://doi.org/10.1073/pnas.062526999
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 3695-3700
    • Akashi, H.1    Gojobori, T.2
  • 38
    • 0027429065 scopus 로고
    • The galactose regulon of Escherichia coli
    • Weickert MJ, Adhya S. 1993. The galactose regulon of Escherichia coli. Mol Microbiol 10:245-251. https://doi.org/10.1111/j.1365-2958.1993.tb01950.x
    • (1993) Mol Microbiol , vol.10 , pp. 245-251
    • Weickert, M.J.1    Adhya, S.2
  • 40
    • 84890119228 scopus 로고    scopus 로고
    • A dual role for the inducer in signalling by MalT, a signal transduction ATPase with numerous domains (STAND)
    • Liu P, Danot O, Richet E. 2013. A dual role for the inducer in signalling by MalT, a signal transduction ATPase with numerous domains (STAND). Mol Microbiol 90:1309-1323. https://doi.org/10.1111/mmi.12434
    • (2013) Mol Microbiol , vol.90 , pp. 1309-1323
    • Liu, P.1    Danot, O.2    Richet, E.3
  • 41
    • 77954852400 scopus 로고    scopus 로고
    • The inducer maltotriose binds in the central cavity of the tetratricopeptide-like sensor domain of MalT, a bacterial STAND transcription factor
    • Danot O. 2010. The inducer maltotriose binds in the central cavity of the tetratricopeptide-like sensor domain of MalT, a bacterial STAND transcription factor. Mol Microbiol 77:628-641. https://doi.org/10.1111/j.1365-2958.2010.07237.x
    • (2010) Mol Microbiol , vol.77 , pp. 628-641
    • Danot, O.1
  • 42
    • 84941023887 scopus 로고    scopus 로고
    • A pH and solvent optimized reverse-phase ion-paring-LC-MS/MS method that leverages multiple scan-types for targeted absolute quantification of intracellular metabolites
    • McCloskey D, Gangoiti JA, Palsson BO, Feist AM. 2015. A pH and solvent optimized reverse-phase ion-paring-LC-MS/MS method that leverages multiple scan-types for targeted absolute quantification of intracellular metabolites. Metabolomics 11:1338-1350. https://doi.org/10.1007/s11306-015-0790-y
    • (2015) Metabolomics , vol.11 , pp. 1338-1350
    • McCloskey, D.1    Gangoiti, J.A.2    Palsson, B.O.3    Feist, A.M.4
  • 43
    • 0029790760 scopus 로고    scopus 로고
    • SoxR, a [2Fe-2S] transcription factor, is active only in its oxidized form
    • Gaudu P, Weiss B. 1996. SoxR, a [2Fe-2S] transcription factor, is active only in its oxidized form. Proc Natl Acad Sci U S A 93:10094-10098
    • (1996) Proc Natl Acad Sci U S A , vol.93 , pp. 10094-10098
    • Gaudu, P.1    Weiss, B.2
  • 44
    • 0030844766 scopus 로고    scopus 로고
    • Cysteineto-alanine replacements in the Escherichia coli SoxR protein and the role of the [2Fe-2S] centers in transcriptional activation
    • Bradley TM, Hidalgo E, Leautaud V, Ding H, Demple B. 1997. Cysteineto-alanine replacements in the Escherichia coli SoxR protein and the role of the [2Fe-2S] centers in transcriptional activation. Nucleic Acids Res 25:1469-1475. https://doi.org/10.1093/nar/25.8.1469
    • (1997) Nucleic Acids Res , vol.25 , pp. 1469-1475
    • Bradley, T.M.1    Hidalgo, E.2    Leautaud, V.3    Ding, H.4    Demple, B.5
  • 45
    • 0035152663 scopus 로고    scopus 로고
    • Oxygen-and growth rate-dependent regulation of Escherichia coli fumarase (FumA, FumB, and FumC) activity
    • Tseng C-P, Yu C-C, Lin H-H, Chang C-Y, Kuo J-T. 2001. Oxygen-and growth rate-dependent regulation of Escherichia coli fumarase (FumA, FumB, and FumC) activity. J Bacteriol 183:461-467. https://doi.org/10.1128/JB.183.2.461-467.2001
    • (2001) J Bacteriol , vol.183 , pp. 461-467
    • Tseng, C.-P.1    Yu, C.-C.2    Lin, H.-H.3    Chang, C.-Y.4    Kuo, J.-T.5
  • 47
    • 0035856579 scopus 로고    scopus 로고
    • Metabolic flux response to phosphoglucose isomerase knock-out in Escherichia coli and impact of overexpression of the soluble transhydrogenase UdhA
    • Canonaco F, Hess TA, Heri S, Wang T, Szyperski T, Sauer U. 2001. Metabolic flux response to phosphoglucose isomerase knock-out in Escherichia coli and impact of overexpression of the soluble transhydrogenase UdhA. FEMS Microbiol Lett 204:247-252. https://doi.org/10.1111/j.1574-6968.2001.tb1 0892.x
    • (2001) FEMS Microbiol Lett , vol.204 , pp. 247-252
    • Canonaco, F.1    Hess, T.A.2    Heri, S.3    Wang, T.4    Szyperski, T.5    Sauer, U.6
  • 48
    • 1342325419 scopus 로고    scopus 로고
    • The soluble and membrane-bound transhydrogenases UdhA and PntAB have divergent functions in NADPH metabolism of Escherichia coli
    • Sauer U, Canonaco F, Heri S, Perrenoud A, Fischer E. 2004. The soluble and membrane-bound transhydrogenases UdhA and PntAB have divergent functions in NADPH metabolism of Escherichia coli. J Biol Chem 279:6613-6619. https://doi.org/10.1074/jbc.M311657200
    • (2004) J Biol Chem , vol.279 , pp. 6613-6619
    • Sauer, U.1    Canonaco, F.2    Heri, S.3    Perrenoud, A.4    Fischer, E.5
  • 49
    • 0021801376 scopus 로고
    • Branch point control by the phosphorylation state of isocitrate dehydrogenase. A quantitative examination of fluxes during a regulatory transition
    • Walsh K, Koshland DE, Jr. 1985. Branch point control by the phosphorylation state of isocitrate dehydrogenase. A quantitative examination of fluxes during a regulatory transition. J Biol Chem 260:8430-8437
    • (1985) J Biol Chem , vol.260 , pp. 8430-8437
    • Walsh, K.1    Koshland, D.E.2
  • 50
    • 0024320578 scopus 로고
    • Evidence for an arginine residue at the coenzyme-binding site of Escherichia coli isocitrate dehydrogenase
    • McKee JS, Nimmo HG. 1989. Evidence for an arginine residue at the coenzyme-binding site of Escherichia coli isocitrate dehydrogenase. Biochem J 261:301-304. https://doi.org/10.1042/bj2610301
    • (1989) Biochem J , vol.261 , pp. 301-304
    • McKee, J.S.1    Nimmo, H.G.2
  • 51
    • 0021741048 scopus 로고
    • The branch point effect. Ultrasensitivity and subsensitivity to metabolic control
    • LaPorte DC, Walsh K, Koshland DE, Jr. 1984. The branch point effect. Ultrasensitivity and subsensitivity to metabolic control. J Biol Chem 259:14068-14075
    • (1984) J Biol Chem , vol.259 , pp. 14068-14075
    • LaPorte, D.C.1    Walsh, K.2    Koshland, D.E.3
  • 52
    • 14544286855 scopus 로고    scopus 로고
    • The selective cause of an ancient adaptation
    • Zhu G, Golding GB, Dean AM. 2005. The selective cause of an ancient adaptation. Science 307:1279-1282. https://doi.org/10.1126/science.1106974
    • (2005) Science , vol.307 , pp. 1279-1282
    • Zhu, G.1    Golding, G.B.2    Dean, A.M.3
  • 53
    • 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 U S A 97:6640-6645. https://doi.org/10.1073/pnas.120163297
    • (2000) Proc Natl Acad Sci U S A , vol.97 , pp. 6640-6645
    • Datsenko, K.A.1    Wanner, B.L.2
  • 56
  • 57
    • 65549092780 scopus 로고    scopus 로고
    • Use of randomized sampling for analysis of metabolic networks
    • Schellenberger J, Palsson BØ. 2009. Use of randomized sampling for analysis of metabolic networks. J Biol Chem 284:5457-5461. https://doi.org/10.1074/jbc.R800048200
    • (2009) J Biol Chem , vol.284 , pp. 5457-5461
    • Schellenberger, J.1    Palsson, BØ.2
  • 58
    • 84955504676 scopus 로고    scopus 로고
    • MID Max: LC-MS/MS method for measuring the precursor and product mass isotopomer distributions of metabolic intermediates and cofactors for metabolic flux analysis applications
    • McCloskey D, Young JD, Xu S, Palsson BO, Feist AM. 2016. MID Max: LC-MS/MS method for measuring the precursor and product mass isotopomer distributions of metabolic intermediates and cofactors for metabolic flux analysis applications. Anal Chem 88:1362-1370. https:// doi.org/10.1021/acs.analchem.5b03887
    • (2016) Anal Chem , vol.88 , pp. 1362-1370
    • McCloskey, D.1    Young, J.D.2    Xu, S.3    Palsson, B.O.4    Feist, A.M.5
  • 59
    • 84894231008 scopus 로고    scopus 로고
    • A model-driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K-12 MG1655 that is biochemically and thermodynamically consistent
    • McCloskey D, Gangoiti JA, King ZA, Naviaux RK, Barshop BA, Palsson BO, Feist AM. 2014. A model-driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K-12 MG1655 that is biochemically and thermodynamically consistent. Biotechnol Bioeng 111: 803-815. https://doi.org/10.1002/bit.25133
    • (2014) Biotechnol Bioeng , vol.111 , pp. 803-815
    • McCloskey, D.1    Gangoiti, J.A.2    King, Z.A.3    Naviaux, R.K.4    Barshop, B.A.5    Palsson, B.O.6    Feist, A.M.7
  • 60
    • 84939880056 scopus 로고    scopus 로고
    • Fast Swinnex filtration (FSF): a fast and robust sampling and extraction method suitable for metabolomics analysis of cultures grown in complex media
    • McCloskey D, Utrilla J, Naviaux RK, Palsson BO, Feist AM. 2014. Fast Swinnex filtration (FSF): a fast and robust sampling and extraction method suitable for metabolomics analysis of cultures grown in complex media. Metabolomics 11:198-209. https://doi.org/10.1007/s11306-014-0686-2
    • (2014) Metabolomics , vol.11 , pp. 198-209
    • McCloskey, D.1    Utrilla, J.2    Naviaux, R.K.3    Palsson, B.O.4    Feist, A.M.5
  • 61
  • 62
    • 85054273496 scopus 로고    scopus 로고
    • LMGene software for data transformation and identification of differentially expressed genes in gene expression arrays
    • Rocke D, Tillinghast J, Durbin-Johnson B, Wu SL. 2013. LMGene software for data transformation and identification of differentially expressed genes in gene expression arrays. R package version 2.4.0
    • (2013) R package version 2.4.0
    • Rocke, D.1    Tillinghast, J.2    Durbin-Johnson, B.3    Wu, S.L.4
  • 63
    • 84899511589 scopus 로고    scopus 로고
    • INCA: a computational platform for isotopically nonstationary metabolic flux analysis
    • Young JD. 2014. INCA: a computational platform for isotopically nonstationary metabolic flux analysis. Bioinformatics 30:1333-1335. https:// doi.org/10.1093/bioinformatics/btu015
    • (2014) Bioinformatics , vol.30 , pp. 1333-1335
    • Young, J.D.1
  • 64
    • 84895896805 scopus 로고    scopus 로고
    • optGpSampler: an improved tool for uniformly sampling the solution-space of genomescale metabolic networks
    • Megchelenbrink W, Huynen M, Marchiori E. 2014. optGpSampler: an improved tool for uniformly sampling the solution-space of genomescale metabolic networks. PLoS One 9:e86587. https://doi.org/10.1371/ journal.pone.0086587
    • (2014) PLoS One , vol.9
    • Megchelenbrink, W.1    Huynen, M.2    Marchiori, E.3
  • 65
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast memoryefficient short read aligner
    • Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast memoryefficient short read aligner. Genome Biol 10:R25. https://doi.org/10.1186/ gb-2009-10-3-r25
    • (2009) Genome Biol , vol.10 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 66
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28:511-515. https://doi.org/10.1038/nbt.1621
    • (2010) Nat Biotechnol , vol.28 , pp. 511-515
    • Trapnell, C.1    Williams, B.A.2    Pertea, G.3    Mortazavi, A.4    Kwan, G.5    van Baren, M.J.6    Salzberg, S.L.7    Wold, B.J.8    Pachter, L.9
  • 67
    • 84917686994 scopus 로고    scopus 로고
    • Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq
    • Deatherage DE, Barrick JE. 2014. Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. Methods Mol Biol 1151:165-188. https://doi.org/10.1007/978-1-4939-0554-6_12
    • (2014) Methods Mol Biol , vol.1151 , pp. 165-188
    • Deatherage, D.E.1    Barrick, J.E.2
  • 69
    • 0345059376 scopus 로고    scopus 로고
    • Announcing the worldwide Protein Data Bank
    • Berman H, Henrick K, Nakamura H. 2003. Announcing the worldwide Protein Data Bank. Nat Struct Biol 10:980. https://doi.org/10.1038/ nsb1203-980
    • (2003) Nat Struct Biol , vol.10 , pp. 980
    • Berman, H.1    Henrick, K.2    Nakamura, H.3
  • 70
    • 84902905303 scopus 로고    scopus 로고
    • Ab initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment
    • Xu D, Zhang Y. 2013. Ab initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment. Sci Rep 3:1895. https://doi.org/10.1038/srep01895
    • (2013) Sci Rep , vol.3 , pp. 1895
    • Xu, D.1    Zhang, Y.2
  • 71
    • 34249869832 scopus 로고    scopus 로고
    • Ab initio modeling of small proteins by iterative TASSER simulations
    • Wu S, Skolnick J, Zhang Y. 2007. Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol 5:17. https://doi.org/10.1186/ 1741-7007-5-17
    • (2007) BMC Biol , vol.5 , pp. 17
    • Wu, S.1    Skolnick, J.2    Zhang, Y.3
  • 73
    • 0029878720 scopus 로고    scopus 로고
    • VMD: visual molecular dynamics
    • Humphrey W, Dalke A, Schulten K. 1996. VMD: visual molecular dynamics. J Mol Graph 14:33-38. https://doi.org/10.1016/0263-7855(96)00018-5
    • (1996) J Mol Graph , vol.14 , pp. 33-38
    • Humphrey, W.1    Dalke, A.2    Schulten, K.3
  • 74
    • 84886004932 scopus 로고    scopus 로고
    • Physiological consequences of multipletarget regulation by the small RNA SgrS in Escherichia coli
    • Sun Y, Vanderpool CK. 2013. Physiological consequences of multipletarget regulation by the small RNA SgrS in Escherichia coli. J Bacteriol 195:4804-4815. https://doi.org/10.1128/JB.00722-13
    • (2013) J Bacteriol , vol.195 , pp. 4804-4815
    • Sun, Y.1    Vanderpool, C.K.2
  • 75
    • 84955350699 scopus 로고    scopus 로고
    • Diverse mechanisms of posttranscriptional repression by the small RNA regulator of glucose-phosphate stress
    • Bobrovskyy M, Vanderpool CK. 2016. Diverse mechanisms of posttranscriptional repression by the small RNA regulator of glucose-phosphate stress. Mol Microbiol 99:254-273. https://doi.org/10.1111/mmi.13230
    • (2016) Mol Microbiol , vol.99 , pp. 254-273
    • Bobrovskyy, M.1    Vanderpool, C.K.2
  • 76
    • 0031026282 scopus 로고    scopus 로고
    • Functional characterization of roles of GalR and GalS as regulators of the gal regulon
    • Geanacopoulos M, Adhya S. 1997. Functional characterization of roles of GalR and GalS as regulators of the gal regulon. J Bacteriol 179:228-234. https://doi.org/10.1128/jb.179.1.228-234.1997
    • (1997) J Bacteriol , vol.179 , pp. 228-234
    • Geanacopoulos, M.1    Adhya, S.2
  • 77
    • 0030928287 scopus 로고    scopus 로고
    • Repressor induced site-specific binding of HU for transcriptional regulation
    • Aki T, Adhya S. 1997. Repressor induced site-specific binding of HU for transcriptional regulation. EMBO J 16:3666-3674. https://doi.org/10.1093/ emboj/16.12.3666
    • (1997) EMBO J , vol.16 , pp. 3666-3674
    • Aki, T.1    Adhya, S.2
  • 78
    • 34447341173 scopus 로고    scopus 로고
    • Signal integration in the galactose network of Escherichia coli
    • Semsey S, Krishna S, Sneppen K, Adhya S. 2007. Signal integration in the galactose network of Escherichia coli. Mol Microbiol 65:465-476. https:// doi.org/10.1111/j.1365-2958.2007.05798.x
    • (2007) Mol Microbiol , vol.65 , pp. 465-476
    • Semsey, S.1    Krishna, S.2    Sneppen, K.3    Adhya, S.4
  • 79
    • 79956148584 scopus 로고    scopus 로고
    • Is superoxide able to induce SoxRS?
    • Liochev SI, Fridovich I. 2011. Is superoxide able to induce SoxRS? Free Radic Biol Med 50:1813. https://doi.org/10.1016/j.freeradbiomed.2011.03.029
    • (2011) Free Radic Biol Med , vol.50 , pp. 1813
    • Liochev, S.I.1    Fridovich, I.2
  • 80
    • 84863143443 scopus 로고    scopus 로고
    • The metal core structures in the recombinant Escherichia coli transcriptional factor SoxR
    • Lo F-C, Lee J-F, Liaw W-F, Hsu I-J, Tsai Y-F, Chan SI, Yu SS-F. 2012. The metal core structures in the recombinant Escherichia coli transcriptional factor SoxR. Chemistry 18:2565-2577. https://doi.org/10.1002/chem.201100838
    • (2012) Chemistry , vol.18 , pp. 2565-2577
    • Lo, F.-C.1    Lee, J.-F.2    Liaw, W.-F.3    Hsu, I.-J.4    Tsai, Y.-F.5    Chan, S.I.6    Yu, S.S.-F.7
  • 81
    • 85025112078 scopus 로고    scopus 로고
    • Sensing mechanisms in the redox-regulated, [2Fe-2S] cluster-containing, bacterial transcriptional factor SoxR
    • Kobayashi K. 2017. Sensing mechanisms in the redox-regulated, [2Fe-2S] cluster-containing, bacterial transcriptional factor SoxR. Acc Chem Res 50:1672-1678. https://doi.org/10.1021/acs.accounts.7b00137
    • (2017) Acc Chem Res , vol.50 , pp. 1672-1678
    • Kobayashi, K.1
  • 82
    • 0029796248 scopus 로고    scopus 로고
    • Glutathione-mediated destabilization in vitro of [2Fe-2S] centers in the SoxR regulatory protein
    • Ding H, Demple B. 1996. Glutathione-mediated destabilization in vitro of [2Fe-2S] centers in the SoxR regulatory protein. Proc Natl Acad Sci U S A 93:9449-9453
    • (1996) Proc Natl Acad Sci U S A , vol.93 , pp. 9449-9453
    • Ding, H.1    Demple, B.2
  • 83
    • 0028049068 scopus 로고
    • An iron-sulfur center essential for transcriptional activation by the redox-sensing SoxR protein
    • Hidalgo E, Demple B. 1994. An iron-sulfur center essential for transcriptional activation by the redox-sensing SoxR protein. EMBO J 13:138-146
    • (1994) EMBO J , vol.13 , pp. 138-146
    • Hidalgo, E.1    Demple, B.2
  • 84
    • 0029152251 scopus 로고
    • Binuclear [2Fe-2S] clusters in the Escherichia coli SoxR protein and role of the metal centers in transcription
    • Hidalgo E, Bollinger JM, Jr, Bradley TM, Walsh CT, Demple B. 1995. Binuclear [2Fe-2S] clusters in the Escherichia coli SoxR protein and role of the metal centers in transcription. J Biol Chem 270:20908-20914. https://doi.org/10.1074/jbc.270.36.20908
    • (1995) J Biol Chem , vol.270 , pp. 20908-20914
    • Hidalgo, E.1    Bollinger, J.M.2    Bradley, T.M.3    Walsh, C.T.4    Demple, B.5
  • 85
    • 0029993477 scopus 로고    scopus 로고
    • Activation of SoxR-dependent transcription in vitro by noncatalytic or NifS-mediated assembly of [2Fe-2S] clusters into apo-SoxR
    • Hidalgo E, Demple B. 1996. Activation of SoxR-dependent transcription in vitro by noncatalytic or NifS-mediated assembly of [2Fe-2S] clusters into apo-SoxR. J Biol Chem 271:7269-7272. https://doi.org/10.1074/jbc.271.13.7269
    • (1996) J Biol Chem , vol.271 , pp. 7269-7272
    • Hidalgo, E.1    Demple, B.2
  • 86
    • 41949137280 scopus 로고    scopus 로고
    • Crystal structure of the [2Fe-2S] oxidative-stress sensor SoxR bound to DNA
    • Watanabe S, Kita A, Kobayashi K, Miki K. 2008. Crystal structure of the [2Fe-2S] oxidative-stress sensor SoxR bound to DNA. Proc Natl Acad Sci U S A 105:4121-4126. https://doi.org/10.1073/pnas.0709188105
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 4121-4126
    • Watanabe, S.1    Kita, A.2    Kobayashi, K.3    Miki, K.4


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