Romano AH, Conway T. Evolution of carbohydrate metabolic pathways. Res Microbiol. 1996;147:448–55.
Article
CAS
Google Scholar
Eisenberg RC, Dobrogosz WJ. Gluconate metabolism in Escherichia coli. J Bacteriol. 1967;93:941–9.
CAS
Google Scholar
Flamholz A, Noor E, Bar-Even A, Liebermeister W, Milo R. Glycolytic strategy as a tradeoff between energy yield and protein cost. Proc Natl Acad Sci. 2013;110:10039–44.
Article
CAS
Google Scholar
Ng CY, Farasat I, Maranas CD, Salis HM. Rational design of a synthetic Entner–Doudoroff pathway for improved and controllable NADPH regeneration. Metab Eng. 2015;29:86–96.
Article
CAS
Google Scholar
Li C, Ying L-Q, Zhang S-S, Chen N, Liu W-F, Tao Y. Modification of targets related to the Entner–Doudoroff/pentose phosphate pathway route for methyl-d-erythritol 4-phosphate-dependent carotenoid biosynthesis in Escherichia coli. Microb Cell Fact. 2015;14:1–12.
Article
Google Scholar
Liu H, Wang Y, Tang Q, Kong W, Chung W-J, Lu T. MEP pathway-mediated isopentenol production in metabolically engineered Escherichia coli. Microb Cell Factor. 2014;13:1–8.
Article
Google Scholar
Chavarría M, Nikel PI, Pérez-Pantoja D, de Lorenzo V. The Entner–Doudoroff pathway empowers Pseudomonas putida KT2440 with a high tolerance to oxidative stress. Environ Microbiol. 2013;15:1772–85.
Article
Google Scholar
Klingner A, Bartsch A, Dogs M, Wagner-Dobler I, Jahn D, Simon M, Brinkhoff T, Becker J, Wittmann C. Large-scale 13C-flux profiling reveals conservation of the Entner-Doudoroff pathway as a glycolytic strategy among marine bacteria that use glucose. Appl Environ Microbiol. 2015;81:2408–22.
Article
CAS
Google Scholar
He L, Xiao Y, Gebreselassie N, Zhang F, Antoniewicz MR, Tang YJ, Peng L. Central metabolic responses to the overproduction of fatty acids in Escherichia coli based on 13C-metabolic flux analysis. Biotechnol Bioeng. 2014;111:575–85.
Article
CAS
Google Scholar
Toya Y, Ishii N, Nakahigashi K, Hirasawa T, Soga T, Tomita M, Shimizu K. 13C-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;26:975–92.
CAS
Google Scholar
Seol E, Sekar BS, Raj SM, Park S. Co-production of hydrogen and ethanol from glucose by modification of glycolytic pathways in Escherichia coli—from Embden-Meyerhof-Parnas pathway to pentose phosphate pathway. Biotechnol J. 2016;11:249–56.
Article
CAS
Google Scholar
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;281:8024–33.
Article
CAS
Google Scholar
Hollinshead WD, Henson WR, Abernathy M, Moon TS, Tang YJ. Rapid metabolic analysis of Rhodococcus opacus PD630 via parallel 13C-metabolite fingerprinting. Biotechnol Bioeng. 2016;113:91–100.
Article
CAS
Google Scholar
Shearer G, Lee JC, Koo JA, Kohl DH. Quantitative estimation of channeling from early glycolytic intermediates to CO2 in intact Escherichia coli. FEBS J. 2005;272:3260–9.
Article
CAS
Google Scholar
Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol. 2006.
Fraenkel DG. Mutants in glucose metabolism. Annu Rev Biochem. 1986;55:317–37.
Article
CAS
Google Scholar
Seol E, Ainala SK, Sekar BS, Park S. Metabolic engineering of Escherichia coli strains for co-production of hydrogen and ethanol from glucose. Int J Hydrogen Energy. 2014;39(33):19323–30.
Article
CAS
Google Scholar
Koirala S, Wang X, Rao CV. Reciprocal regulation of l-arabinose and d-xylose metabolism in Escherichia coli. J Bacteriol. 2016;198:386–93.
Article
CAS
Google Scholar
Beisel CL, Afroz T. Rethinking the hierarchy of sugar utilization in bacteria. J Bacteriol. 2016;198:374–6.
Article
CAS
Google Scholar
Zhao J, Shimizu K. Metabolic flux analysis of Escherichia coli K12 grown on 13C-labeled acetate and glucose using GC–MS and powerful flux calculation method. J Biotechnol. 2003;101:101–17.
Article
CAS
Google Scholar
Xiao Y, Ruan Z, Liu Z, Wu SG, Varman AM, Liu Y, Tang YJ. Engineering Escherichia coli to convert acetic acid to free fatty acids. Biochem Eng J. 2013;76:60–9.
Article
CAS
Google Scholar
Luli GW, Strohl WR. Comparison of growth, acetate production, and acetate inhibition of Escherichia coli strains in batch and fed-batch fermentations. Appl Environ Microbiol. 1990;56:1004–11.
CAS
Google Scholar
Nöh K, Grönke K, Luo B, Takors R, Oldiges M, Wiechert W. Metabolic flux analysis at ultra short time scale: isotopically non-stationary 13C labeling experiments. J Biotechnol. 2007;129:249–67.
Article
Google Scholar
Williams TCR, Sweetlove LJ, Ratcliffe RG. Capturing metabolite channeling in metabolic flux phenotypes. Plant Physiol. 2011;157:981–4.
Article
CAS
Google Scholar
Malaisse WJ, Zhang Y, Sener A. Enzyme-to-enzyme channeling in the early steps of glycolysis in rat pancreatic islets. Endocrine. 2004;24:105–9.
Article
CAS
Google Scholar
Debnam PM, Shearer G, Blackwood L, Kohl DH. Evidence for channeling of intermediates in the oxidative pentose phosphate pathway by soybean and pea nodule extracts, yeast extracts, and purified yeast enzymes. Eur J Biochem. 1997;246:283–90.
Article
CAS
Google Scholar
Long CP, Gonzalez JE, Sandoval NR, Antoniewicz MR. Characterization of physiological responses to 22 gene knockouts in Escherichia coli central carbon metabolism. Metab Eng. 2016;37:102–13.
Article
CAS
Google Scholar
Burgard AP, Maranas CD. Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions. Biotechnol Bioeng. 2001;74:364–75.
Article
CAS
Google Scholar
Kim J-H, Block DE, Mills DA. Simultaneous consumption of pentose and hexose sugars: an optimal microbial phenotype for efficient fermentation of lignocellulosic biomass. Appl Microbiol Biotechnol. 2010;88:1077–85.
Article
CAS
Google Scholar
Nieves LM, Panyon LA, Wang X. Engineering sugar utilization and microbial tolerance toward lignocellulose conversion. Front Bioeng Biotechnol. 2015;3:17.
Article
Google Scholar
Gorke B, Stulke J. Carbon catabolite repression in bacteria: many ways to make the most out of nutrients. Nat Rev Microbiol. 2008;6:613–24.
Article
Google Scholar
Lu H, Zhao X, Wang Y, Ding X, Wang J, Garza E, Manow R, Iverson A, Zhou S. Enhancement of d-lactic acid production from a mixed glucose and xylose substrate by the Escherichia coli strain JH15 devoid of the glucose effect. BMC Biotechnol. 2016;16:1–10.
Article
Google Scholar
Su B, Wu M, Zhang Z, Lin J, Yang L. Efficient production of xylitol from hemicellulosic hydrolysate using engineered Escherichia coli. Metab Eng. 2015;31:112–22.
Article
CAS
Google Scholar
Jung I-Y, Lee J-W, Min W-K, Park Y-C, Seo J-H. Simultaneous conversion of glucose and xylose to 3-hydroxypropionic acid in engineered Escherichia coli by modulation of sugar transport and glycerol synthesis. Bioresour Technol. 2015;198:709–16.
Article
CAS
Google Scholar
Chiang C-J, Lee HM, Guo HJ, Wang ZW, Lin L-J, Chao Y-P. Systematic approach to engineer Escherichia coli pathways for co-utilization of a glucose–xylose mixture. J Agric Food Chem. 2013;61:7583–90.
Article
CAS
Google Scholar
Chassagnole C, Noisommit-Rizzi N, Schmid JW, Mauch K, Reuss M. Dynamic modeling of the central carbon metabolism of Escherichia coli. Biotechnol Bioeng. 2002;79:53–73.
Article
CAS
Google Scholar
Morita T, El-Kazzaz W, Tanaka Y, Inada T, Aiba H. Accumulation of glucose 6-phosphate or fructose 6-phosphate is responsible for destabilization of glucose transporter mRNA in Escherichia coli. J Biol Chem. 2003;278:15608–14.
Article
CAS
Google Scholar
Ding J, Holzwarth G, Penner MH, Patton-Vogt J, Bakalinsky AT. Overexpression of acetyl-CoA synthetase in Saccharomyces cerevisiae increases acetic acid tolerance. FEMS Microbiol Lett. 2015;362:1–7.
Article
Google Scholar
Repaske DR, Adler J. Change in intracellular pH of Escherichia coli mediates the chemotactic response to certain attractants and repellents. J Bacteriol. 1981;145:1196–208.
CAS
Google Scholar
Zhang YHP. Substrate channeling and enzyme complexes for biotechnological applications. Biotechnol Adv. 2011;29:715–25.
Article
CAS
Google Scholar
Wheeldon I, Minteer SD, Banta S, Barton SC, Atanassov P, Sigman M. Substrate channelling as an approach to cascade reactions. Nat Chem. 2016;8:299–309.
Article
CAS
Google Scholar
Janßen HJ, Steinbüchel A. Fatty acid synthesis in Escherichia coli and its applications towards the production of fatty acid based biofuels. Biotechnol Biofuels. 2014;7:7.
Article
Google Scholar
Noor E, Bar-Even A, Flamholz A, Reznik E, Liebermeister W, Milo R. Pathway thermodynamics highlights kinetic obstacles in central metabolism. PLoS Comput Biol. 2014;10:e1003483.
Article
Google Scholar
Link H, Kochanowski K, Sauer U. Systematic identification of allosteric protein-metabolite interactions that control enzyme activity in vivo. Nat Biotechnol. 2013;31:357–61.
Article
CAS
Google Scholar
Millard P, Massou S, Wittmann C, Portais J-C, Létisse F. Sampling of intracellular metabolites for stationary and non-stationary 13C metabolic flux analysis in Escherichia coli. Anal Biochem. 2014;465:38–49.
Article
CAS
Google Scholar
Sarria S, Wong B, Martín HG, Keasling JD, Peralta-Yahya P. Microbial synthesis of pinene. ACS Synth Biol. 2014;3:466–75.
Article
CAS
Google Scholar
Yao R, Xiong D, Hu H, Wakayama M, Yu W, Zhang X, Shimizu K. Elucidation of the co-metabolism of glycerol and glucose in Escherichia coli by genetic engineering, transcription profiling, and 13C metabolic flux analysis. Biotechnol Biofuels. 2016;9:175.
Article
Google Scholar
Lee TS, Krupa RA, Zhang F, Hajimorad M, Holtz WJ, Prasad N, Lee SK, Keasling JD. BglBrick vectors and datasheets: a synthetic biology platform for gene expression. J Biol Eng. 2011;5:12–3.
Article
CAS
Google Scholar
Ham TS, Dmytriv Z, Plahar H, Chen J, Hillson NJ, Keasling JD. Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools. Nucleic Acids Res. 2012;40:e141.
Article
Google Scholar
Fu Y, Yoon JM, Jarboe L, Shanks JV. Metabolic flux analysis of Escherichia coli MG1655 under octanoic acid (C8) stress. Appl Microbiol Biotechnol. 2015;99:4397–408.
Article
CAS
Google Scholar
Rodriguez S, Denby CM, Van Vu T, Baidoo EEK, Wang G, Keasling JD. ATP citrate lyase mediated cytosolic acetyl-CoA biosynthesis increases mevalonate production in Saccharomyces cerevisiae. Microb Cell Fact. 2016;15:48.
Article
Google Scholar
You L, Page L, Feng X, Berla B, Pakrasi HB, Tang YJ. Metabolic pathway confirmation and discovery through 13C-labeling of proteinogenic amino acids. J Vis Exp. 2012;59:e3583.
Google Scholar
Wahl SA, Dauner M, Wiechert W. New tools for mass isotopomer data evaluation in 13C flux analysis: mass isotope correction, data consistency checking, and precursor relationships. Biotechnol Bioeng. 2004;85:259–68.
Article
CAS
Google Scholar
Borodina I, Schöller C, Eliasson A, Nielsen J. Metabolic network analysis of Streptomyces tenebrarius, a streptomyces species with an active entner–doudoroff pathway. Appl Environ Microbiol. 2005;71:2294–302.
Article
CAS
Google Scholar
Bennett BD, Yuan J, Kimball EH, Rabinowitz JD. Absolute quantitation of intracellular metabolite concentrations by an isotope ratio-based approach. Nat Protoc. 2008;3:1299–311.
Article
CAS
Google Scholar
Orth JD, Conrad TM, Na J, Lerman JA, Nam H, Feist AM, Palsson BØ. A comprehensive genome-scale reconstruction of Escherichia coli metabolism—2011. Mol Syst Biol. 2011;7(1):535.
Article
Google Scholar