Shimizu K (2014) Microbial production of biofuels and biochemicals from biomass. NOVA publ, Co, New York
Google Scholar
Kitano H (2002) Systems biology: a brief overview. Science 295:1662–1664
Article
CAS
Google Scholar
Kitano H (2002) Computational systems biology. Nature 420:206–210
Article
CAS
Google Scholar
Stelling J (2004) Mathematical models in microbial systems biology. Curr Opin Microbiol 7:513–518
Article
Google Scholar
Kotte O, Zaugg JB, Heinemann M (2010) Bacterial adaptation through distributed sensing of metabolic fluxes. Mol Sys Biol 6:355
Google Scholar
Vemuri GN, Aristidou A (2005) Metabolic engineering in the -omics era: elucidating and modulating regulatory networks. Microbiol Mol Biol Rev 69:197–216
Article
CAS
Google Scholar
Shimizu K (2014) Regulation systems of bacteria such as Escherichia coli in response to nutrient limitation and environmental stresses. Metabolites 4:1–35
Article
CAS
Google Scholar
Matsuoka Y, Shimizu K (2011) Metabolic regulation in Escherichia coli in response to culture environments via global regulators. Biotechnol J 6:1330–1341
Article
CAS
Google Scholar
Chuvukov V, Gerosa L, Kochanowski K, Sauer U (2014) Coordination of microbial metabolism. Nat Rev 12:327–340
Google Scholar
Selinger DW, Wright MA, Church GM (2003) On the complete determination of biological systems. Trends Biotechnol 21:251–254
Article
CAS
Google Scholar
Machado D, Costa R, Rocha M, Ferreira E, Tidor B, Rocha I (2011) Modeling formalisms in systems biology. AMP Expre 1:1–34
Article
CAS
Google Scholar
Almquist J, Cvijovic M, Hatzimanikatis V, Nielsen J, Jirstrand M (2014) Kinetic models in industrial biotechnology-improving cell factory performance. Metabolic Eng 24:38–60
Article
CAS
Google Scholar
Costa RS, Machado D, Rocha I, Pereira EC (2011) Critical perspective on the consequences of the limited availability of kinetic data in metabolic dynamic modeling. IET Syst Biol 5:157–163
Article
CAS
Google Scholar
Ashyraliyev M, Fomekong-Nanfack Y, Kaandorp JA, Blom JG (2009) Systems biology: parameter estimation for biochemical models. FEBS J 276:886–902
Article
CAS
Google Scholar
Cvijovic M, Bordel S, Nielsen J (2011) Mathematical models of cell factories: moving towards the core of industrial biotechnology. Microb Biotechnol 4:572–584
Article
CAS
Google Scholar
Sauer U (2006) Metabolic networks in motion: 13C-based flux analysis. Mol Syst Anal 2:62
Google Scholar
Long CP, Antoniewicz MR (2014) Metabolic flux analysis of Escherichia coli knockouts: lessons from the Keio collection and future outlook. Curr Opin Biotechnol 28:127–133
Article
CAS
Google Scholar
Quek LE, Nielsen LK (2014) Steady-State 13C Fluxomics Using OpenFLUX. In: Krömer JO, Nielsen LK, Blank LM (eds) Metabolic flux analysis: methods and protocols, vol. 1191, Springer, New York, 209-224
Shimizu K (2004) Metabolic flux analysis based on 13C-labeling experiments and integration of the information with gene and protein expression patterns. Adv Biochem Eng Biotechnol 91:1–49
CAS
Google Scholar
Shimizu K (2013) Bacterial cellular metabolic systems. Woodhead Publ Ltd., Oxford
Book
Google Scholar
Matsuoka Y, Shimizu K (2014) 13C-Metabolic flux analysis for Escherichia coli. In: Krömer JO, Nielsen LK, Blank LM (eds) Metabolic flux analysis: methods and protocols, vol. 1191, Springer, New York, 261-289
Shimizu K (2009) Toward systematic metabolic engineering based on the analysis of metabolic regulation by the integration of different levels of information. Biochem Eng J 46:235–251
Article
CAS
Google Scholar
Wittman C (2007) Fluxome analysis using GC-MS. Microb Cell Fact 6:6
Article
CAS
Google Scholar
Herrgard MJ, Lee B-S, Portnoy V, Palsson BO (2006) Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae. Genome Res 16:627–635
Article
CAS
Google Scholar
O'Brien EJ, Lerman JA, Chang RL, Hyduke DR, Palsson BO (2013) Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction. Mol Sys Biol 9:693
Article
CAS
Google Scholar
Schuetz R, Kuepfer SU (2007) Systematic evaluation of objective functions forpredicting intracellular fluxes in Escherichia coli. Mol Syst Biol 3:119
Article
CAS
Google Scholar
Schuetz R, Zamboni N, Zampieri M, Heinemann M, Sauer U (2012) Multidimensional optimality of microbial metabolism. Science 336:601–604
Article
CAS
Google Scholar
Burgard AP, Pharkya P, Maranas CD (2003) Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng 84:647–657
Article
CAS
Google Scholar
Pharkya P, Maranas CD (2006) An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems. Metab Eng 8:1–13
Article
CAS
Google Scholar
Ranganathan S, Suthers PF, Maranas CD (2010) OptForce: an optimization procedure for identifying all genetic manipulations leading to targeted overproductions. Plos Comput Biol 6:e1000744
Article
CAS
Google Scholar
Rocha I, Maia P, Evangelista P, Vilaca P, Soares S, Pinto JP, Nielsen J, Patil KR, Ferreira EC, Rocha M (2010) OptFlux: an open-source software platform for in silico metabolic engineering. BMC Syst Biol 4:45
Article
CAS
Google Scholar
Choon YW, Mohamad MS, Deris S, Illias RM, Chong CK, Chai LE, Omatu S, Corchado JM (2014) Differential bees flux balance analysis with OptKnock for in silico microbial strains optimization. PLoS One 9:e102744
Article
CAS
Google Scholar
Pharkya P, Burgard AP, Maranas CD (2014) OptStrain: a computational framework for redesign of microbial production systems. Genom Res 14:2367–2376
Article
CAS
Google Scholar
Yang L, Cluett WR, Mahadevan R (2011) EMILiO: a fast algorithm for genome-scale strain design. Metab Eng 13:272–281
Article
CAS
Google Scholar
Cotten C, Reed JL (2013) Constraint-based strain design using continuous modifications (CosMos) of flux bounds finds new strategies for metabolic engineering. Biotechnol J 8:595–604
Article
CAS
Google Scholar
Ibarra RU, Edwards JS, Palsson BO (2002) Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 420:186–189
Article
CAS
Google Scholar
Segrè D, Vitkup D, Church GM (2002) Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci U S A 99:15112–15117
Article
CAS
Google Scholar
Rark JM, Kim TY, Lee SY (2009) Constraints-based genome-scale metabolic simulation for systems metabolic engineering. Biotechnol Adv 27:979–988
Article
Google Scholar
Zomorrodi AR, Suthers PF, Ranganathan S, Maranas CD (2012) Mathematical optimization applications in metabolic networks. Metab Eng 14:672–686
Article
CAS
Google Scholar
Covert MW, Xiao N, Chen TJ, Karr JR (2008) Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli. Bioinformatics 24:2044–2050
Article
CAS
Google Scholar
Meadows AL, Karnik R, Lam H, Forestell S, Snedecor B (2010) Application of dynamic flux balance analysis to an industrial Escherichia coli fermentation. Metab Eng 12:150–160
Article
CAS
Google Scholar
Feng X, Xu Y, Chen Y, Tang YJ (2012) MicrobesFlux: a web platform for drafting metabolic models from the KEGG database. BMC Syst Biol 6:94
Article
Google Scholar
Zhuang K, Izallalen M, Mouser P, Richter H, Risso C, Mahadevan R, Lovley DR (2011) Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments. Isme J 5:305–316
Article
Google Scholar
Salimi F, Zhuang K, Mahadevan R (2010) Genome-scale metabolic modeling of a clostridial co-culture for consolidated bioprocessing. Biotechnol J 5:726–738
Article
CAS
Google Scholar
Jamshidi N, Palsson BØ (2008) Formulating genome-scale kinetic models in the post-genome era. Mol Syst Biol 4:171
Article
Google Scholar
Jamshidi N, Palsson BØ (2010) Mass action stoichiometric simulation models: incorporating kinetics and regulation into stoichiometric models. Biophys J 98:175–185
Article
CAS
Google Scholar
Smallbone K, Simeonidis E, Broomhead DS, Kell DB (2007) Something from nothing - bridging the gap between constraint-based and kinetic modelling. FEBS J 274:5576–5585
Article
CAS
Google Scholar
Smallbone K, Simeonidis E, Swainston N, Mendes P (2010) Towards a genome-scale kinetic model of cellular metabolism. BMC Syst Biol 4:6
Article
CAS
Google Scholar
Fleming RM, Thiele I, Provan G, Nasheuer HP (2010) Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism. J Theor Biol 264:683–692
Article
CAS
Google Scholar
Antoniewicz MR (2013) Dynamic metabolic flux analysis-tools for probing transient states of metabolic networks. Curr Opin Biotechnol 24:973–978
Article
CAS
Google Scholar
Hoffner K, Harwood SM, Barton PI (2013) A reliable simulator for dynamic flux balance analysis. Biotechnol Bioeng 110:792–802
Article
CAS
Google Scholar
Mahadevan R, Edwards JS, Doyle FJ (2002) Dynamic flux balance analysis of diauxic growth in Escherichia coli. Biophys J 83:1331–1340
Article
CAS
Google Scholar
Hanly TJ, Henson MA (2011) Dynamic flux balance modeling of microbial co-cultures for efficient batch fermentation of glucose and xylose mixtures. Biotechnol Bioeng 108:376–385
Article
CAS
Google Scholar
Hanly TJ, Urello M, Henson MA (2012) Dynamic flux balance modeling of S. cerevisiae and E. coli co-cultures for efficient consumption of glucose/xylose mixtures. Appl Microbiol Biotechnol 93:2529–2541
Article
CAS
Google Scholar
Hanly TJ, Henson MA (2013) Dynamic metabolic modeling of a microaerobic yeast co-culture: predicting and optimizing ethanol production from glucose/xylose mixtures. Biotechnol Biofuels 6:44
Article
CAS
Google Scholar
Chowdhury A, Zomorrodi AR, Maranas CD (2014) k-OptForce: integrating kinetics with flux balance analysis for strain design. PLoS Comput Biol 10:e1003487
Article
CAS
Google Scholar
Klumpp S, Hwa T (2008) Growth-rate dependent partitioning of RNA polymerases in bacteria. PNAS USA 105:20245–20250
Article
CAS
Google Scholar
Klumpp S, Zhang Z, Hwa T (2009) Growth-rate dependent global effects on gene expression in bacteria. Cell 139:1366–1375
Article
Google Scholar
Valgepea K, Adamberg K, Seiman A, Vilu R (2013) Escherichia coli achieves faster growth by increasing catalytic and translational rates of proteins. Mol Biosyst 9:2344–2358
Article
CAS
Google Scholar
Harcomb WR, Delaney NF, Leiby N, Klitgord N, Marx CJ (2013) The ability of flux balance analysis to predict evolution of central metabolism scales with the initial distance to the optimum. PLoS Comput Biol 9:e1003091
Article
CAS
Google Scholar
Edwards JS, Covert MW, Palsson BØ (2002) Metabolic modelling of microbes: the flux-balance approach. Environ Microbiol 4:133–140
Article
Google Scholar
Karr JR, Sanghvi JC, Macklin DN, Gutschow MW, Jacobs JM, Bolival B Jr, Assad-Garcia N, Glass JI, Covert MW (2012) A whole-cell computational model predicts phenotype from genotype. Cell 150:389–401
Article
CAS
Google Scholar
Gunawardera J (2012) Silicon dreams of cells into symbols. Nature 30:838–840
Google Scholar
Freddolino PL, Tavazoie S (2012) The dawn of virtual cell biology. Cell 150:248–250
Article
CAS
Google Scholar
Tomita M (2001) Whole-cell simulation: a grand challenge of the 21st century. Trends in Biotech 19:205–210
Article
CAS
Google Scholar
Heinrich R, Rapoport TA (1974) A linear steady-state treatment of enzymatic chains. General properties, control and effector strength. Eur J Biochem 42:89–95
Article
CAS
Google Scholar
van Riel NA (2006) Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments. Brief Bioinform 7:364–374
Article
Google Scholar
Heijnen JJ (2005) Approximative kinetic formats used in metabolic network modeling. Biotechnol Bioeng 91:534–545
Article
CAS
Google Scholar
Wu L, Wang WM, van Winden WA, van Gulik WM, Heijnen JJ (2004) A new framework for the estimation of control parameters in metabolic pathways using lin-log kinetics. Eur J Biochem 271:3348–3359
Article
CAS
Google Scholar
del Rosario RCH, Mendoza E, Voit EO (2008) Challenges in lin-log modelling of glycolysis in Lactococcus lactis. Iet Syst Biol 2:136–149
Article
Google Scholar
Hatzimanikatis V, Emmerling M, Sauer U, Bailey JE (1998) Application of mathematical tools for metabolic design of microbial ethanol production. Biotechnol Bioeng 58:154–161
Article
CAS
Google Scholar
Wang L, Hatzimanikatis V (2006) Metabolic engineering under uncertainty-II: analysis of yeast metabolism. Metab Eng 8:142–159
Article
CAS
Google Scholar
Pozo C, Marín-Sanguino A, Alves R, Guillén-Gosálbez G, Jiménez L, Sorribas A (2011) Steady-state global optimization of metabolic non-linear dynamic models through recasting into power-law canonical models. BMC Syst Biol 5:137
Article
Google Scholar
Sorribas A, Hernandez-Bermejo B, Vilaprinyo E, Alves R (2007) Cooperativity and saturation in biochemical networks: a saturable formalism using Taylor series approximations. Biotechnol Bioeng 97:1259–1277
Article
CAS
Google Scholar
Liebermeister W, Klipp E (2006) Bringing metabolic networks to life: convenience rate law and thermodynamic constraints. Theor Biol Med Model 3:41
Article
CAS
Google Scholar
Kim JI, Song HS, Sunkara SR, Lali A, Ramkrishna D (2012) Exacting predictions by cybernetic model confirmed experimentally: steady state multiplicity in the chemostat. Biotechnol Prog 28:1160–1166
Article
CAS
Google Scholar
Covert MW, Palsson BØ (2002) Transcriptional regulation in constraints-based metabolic models of Escherichia coli. J Biol Chem 277:28058–28064
Article
CAS
Google Scholar
Covert MW, Palsson BØ (2003) Constraints-based models: regulation of gene expression reduces the steady-state solution space. J Theor Biol 221:309–325
Article
CAS
Google Scholar
Covert MW, Schilling CH, Famili I, Edwards JS, Goryanin II, Selkov E, Palsson BØ (2001) Metabolic modeling of microbial strains in silico. Trends Biochem Sci 26:179–186
Article
CAS
Google Scholar
Herrgård MJ, Fong SS, Palsson BØ (2006) Identification of genome-scale metabolic network models using experimentally measured flux profiles. Plos Comput Biol 2:676–686
Google Scholar
Song HS, Morgan JA, Ramkrishna D (2009) Systematic development of hybrid cybernetic models: application to recombinant yeast co-consuming glucose and xylose. Biotechnol Bioeng 103:984–1002
Article
CAS
Google Scholar
Ramkrishna D, Kompala DS, Tsao GT (1987) Are microbes optimal strategists. Biotechnol Progr 3:121–126
Article
Google Scholar
Varner J, Ramkrishna D (1999) Metabolic engineering from a cybernetic perspective. 1. Theoretical preliminaries. Biotechnol Prog 15:407–425
Article
CAS
Google Scholar
Young JD (2005) A system-level mathematical description of metabolic regulation combining aspects of elementary mode analysis with cybernetic control laws. PhD thesis, Purdue University
Young JD, Henne KL, Morgan JA, Konopka AE, Ramkrishna D (2008) Integrating cybernetic modeling with pathway analysis provides a dynamic, systems-level description of metabolic control. Biotechnol Bioeng 100:542–559
Article
CAS
Google Scholar
Schuster S, Fell DA, Dandekar T (2000) A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat Biotechnol 18:326–332
Article
CAS
Google Scholar
Kim JW, Dang CV (2005) Multifaceted roles of glycolytic enzymes. Trends Biocem Sci 30:142–150
Article
CAS
Google Scholar
Kim JI, Varner JD, Ramkrishna D (2008) A hybrid model of anaerobic E. coli GJT001: combination of elementary flux modes and cybernetic variables. Biotechnol Prog 24:993–1006
Article
CAS
Google Scholar
Teusink B, Passarge J, Reijenga CA, Esgalhado E, van der Weijden CC, Schepper M, Walsh MC, Bakker BM, van Dam K, Westerhoff HV, Snoep JL (2000) Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry. Eur J Biochem 267:5313–5329
Article
CAS
Google Scholar
Chakrabarti A, Miskovic L, Soh KC, Hatzimanikatis V (2013) Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints. Biotechnol J 8:1043–1057
Article
CAS
Google Scholar
Hatzimanikatis V, Bailey JE (1996) MCA has more to say. J Theor Biol 182:233–242
Article
CAS
Google Scholar
Smallbone K, Messiha HL, Carroll KM, Winder CL, Malys N, Dunn WB, Murabito E, Swainston N, Dada JO, Khan F, Pir P, Simeonidis E, Spasić I, Wishart J, Weichart D, Hayes NW, Jameson D, Broomhead DS, Oliver SG, Gaskell SJ, McCarthy JE, Paton NW, Westerhoff HV, Kell DB, Mendes P (2013) A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes. FEBS Lett 587:2832–2841
Article
CAS
Google Scholar
Stanford NJ, Lubitz T, Smallbone K, Klipp E, Mendes P, Liebermeister W (2013) Systematic construction of kinetic models from genome-scale metabolic networks. PLoS One 8:e79195
Article
CAS
Google Scholar
Savageau MA (1970) Biochemical systems analysis. 3. Dynamic solutions using a power-law approximation. J Theor Biol 26:215–226
Article
CAS
Google Scholar
Voit Eberhard O (2013) Biochemical systems theory: a review. ISRN Biomathematics 2013:897658
Google Scholar
Dräger A, Kronfeld M, Ziller MJ, Supper J, Planatscher H, Magnus JB, Oldiges M, Kohlbacher O, Zell A (2009) Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies. BMC Syst Biol 3:5
Article
Google Scholar
Costa RS, Machado D, Rocha I, Ferreira EC (2010) Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis-Menten and approximate kinetic equations. Biosystems 100:150–157
Article
CAS
Google Scholar
Rizk ML, Liao JC (2009) Ensemble modeling for aromatic production in Escherichia coli. PLoS One 4:e6903
Article
CAS
Google Scholar
Tan YK, Liao JC (2012) Metabolic ensemble modeling for strain engineers. Biotechnol J 7:343–353
Article
CAS
Google Scholar
Contador CA, Rizk ML, Asenjo JA, Liao JC (2009) Ensemble modeling for strain development of L-lysine-producing Escherichia coli. Metab Eng 11(4–5):221–233
Article
CAS
Google Scholar
Dean JT, Rizk ML, TanY DKM, Liao JC (2010) Ensemble modeling of hepatic fatty acid metabolism with a synthetic glyoxylate shunt. Biophys J 98:1385–1395
Article
CAS
Google Scholar
Lee Y, Lafontaine Rivera JG, Liao JC (2014) Ensemble modeling for robustness analysis in engineering non-native metabolic pathways. Metab Eng 25:63–71
Article
CAS
Google Scholar
Khazaei T, McGuigan A, Mahadevan R (2012) Ensemble modeling of cancer metabolism. Front Physiol 3:135
Article
Google Scholar
Khodayari A, Zomorrodi AR, Liao JC, Maranas CD (2014) A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data. Metab Eng 25:50–62
Article
CAS
Google Scholar
Ishii N, Nakahigashi K, Baba T, Robert M, Soga T, Kanai A, Hirasawa T, Naba M, Hirai K, Hoque A, Ho PY, Kakazu Y, Sugawara K, Igarashi S, Harada S, Masuda T, Sugiyama N, Togashi T, Hasegawa M, Takai Y, Yugi K, Arakawa K, Iwata N, Toya Y, Nakayama Y, Nishioka T, Shimizu K, Mori H, Tomita M (2007) Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science 316:593–597
Article
CAS
Google Scholar
Rizzi M, Baltes M, Theobald U, Reuss M (1997) In vivo analysis of metabolic dynamic in Saccharomyces cerevisiae: II. Mathematical model. Biotechnol Bioeng 55:592–608
Article
CAS
Google Scholar
Theobald U, Mailinger W, Baltes M, Rizzi M, Reuss M (1997) In vivo analysis of metabolic dynamic in Saccharomyces cerevisiae: I. Experimental observations. Biotechnol Bioeng 55:305–316
Article
CAS
Google Scholar
Chassagnole C, Noisommit-Rizzi N, Schmid JW, Mauch K, Reuss M (2002) Dynamic modeling of the central carbon metabolism of Escherichia coli. Biotechnol Bioeng 79:53–73
Article
CAS
Google Scholar
Kadir TA, Mannan AA, Kierzek AM, McFadden J, Shimizu K (2010) Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification. Microb Cell Fact 9:88
Article
CAS
Google Scholar
Peskov K, Mogilevskaya E, Demin O (2012) Kinetic modelling of central carbon metabolism in Escherichia coli. FEBS J 279:3374–3385
Article
CAS
Google Scholar
Usuda Y, Nishio Y, Iwatani S, Van Dien SJ, Imaizumi A, Shimbo K, Kageyama N, Iwahata D, Miyano H, Matsui K (2010) Dynamic modeling of Escherichia coli metabolic and regulatory systems for amino-acid production. J Biotechnol 147:17–30
Article
CAS
Google Scholar
Matsuoka Y, Shimizu K (2013) Catabolite regulation analysis of Escherichia coli for acetate overflow mechanism and co-consumption of multiple sugars based on systems biology approach using computer simulation. J Biotechnol 168:155–173
Article
CAS
Google Scholar
Yao R, Hirose Y, Sarkar D, Nakahigashi K, Ye Q, Shimizu K (2011) Catabolic regulation analysis of Escherichia coli and its crp, mlc, mgsA, pgi and ptsG mutants. Microb Cell Fact 10:67
Article
CAS
Google Scholar
Toya Y, Ishii N, Nakahigashi K, Hirasawa T, Soga T, Tomita T, Shimizu K (2010) 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 26:975–992
CAS
Google Scholar
Toya Y, Nakahigashi K, Tomita M, Shimizu K (2012) Metabolic regulation analysis of wild-type and arcA mutant Escherichia coli under nitrate conditions using different levels of omics data. Mol Biosyst 8:2593–2604
Article
CAS
Google Scholar
Hasona A, Kim Y, Healy FG, Ingram LO, Shanmugam KT (2004) Pyruvate formate lyase and acetate kinase are essential for anaerobic growth of Escherichia coli on xylose. J Bacteriol 186:7593–7600
Article
CAS
Google Scholar
Kremling A, Bettenbrock K, Gilles ED (2008) A feed-forward loop guarantees robust behavior in Escherichia coli carbohydrate uptake. Bioinformatics 24:704–710
Article
CAS
Google Scholar
Kochanowski K, Volkmer B, Gerosa L, Haverkorn van Rijsewijk BR, Schmidt A, Heinemann M (2013) Functioning of a metabolic flux sensor in Escherichia coli. Proc Natl Acad Sci U S A 110:1130–1135
Article
CAS
Google Scholar
Huberts DH, Niebel B, Heinemann M (2012) A flux-sensing mechanism could regulate the switch between respiration and fermentation. FEMS Yeast Res 12:118–128
Article
CAS
Google Scholar
Christen S, Sauer U (2011) Intracellular characterization of aerobic glucose metabolism in seven yeast species by 13C flux analysis and metabolomics. FEMS Yeast Res 11:263–272
Article
CAS
Google Scholar
Boels E, Hollenberg CP (1997) The molecular genetics of hexose transport in yeasts. FEMS Microbiol Rev 21:85–111
Article
Google Scholar
Ricci JCD (1996) Influence of phosphenolpyruvate on the dynamic behavior of phosphofructokinase of Escherichia coli. J Theor Biol 178:145–150
Article
Google Scholar
Yang C, Hua Q, Baba T, Mori H, Shimizu K (2003) Analysis of Escherichia coli anaprelotic metabolism and its regulation mechanisms from the metabolic responses to altered dilution rates and phosphoenolpyruvate carboxykinase knockout. Biotechnol Bioeng 84:129–144
Article
CAS
Google Scholar
Lee B, Yen J, Yang L, Liao JC (1999) Incorporating qualitative knowledge in enzyme kinetic models using fuzzy logic. Biotechnol Bioeng 63:722–729
Article
Google Scholar
Nizam SA, Zhu JF, Ho PY, Shimizu K (2009) Effects of arcA and arcB genes knockout on the metabolism in Escherichia coli under aerobic condition. Biochem Eng J 44:240–250
Article
CAS
Google Scholar
Vemuri GN, Eiteman MA, Altman E (2006) Increased recombinant protein production in Escherichia coli strains with overexpressed water-forming NADH oxidase and a deleted ArcA regulatory protein. Biotechnol Bioeng 94:538–542
Article
CAS
Google Scholar
Vemuri GN, Altman E, Sangurdekar DP, Khodursky AB, Eiteman MA (2006) Overflow metabolism in Escherichia coli during steady-state growth: transcriptional regulation and effect of the redox ratio. Appl Environ Microbiol 72:3653–3661
Article
CAS
Google Scholar
Wolfe AJ (2005) The acetate switch. Microbiol Mol Biol Rev 69:12–50
Article
CAS
Google Scholar
Xu YF, Amador-Noguez D, Reaves ML, Feng XJ, Rabinowitz JD (2012) Ultrasensitive regulation of anapleurosis via allosteric activation of PEP carboxylase. Nat Chem Biol 8:562–568
Article
CAS
Google Scholar
Voit E, Neves AR, Santos H (2006) The intricate side of systems biology. Proc Natl Acad Sci U S A 103:9452–9457
Article
CAS
Google Scholar
Hoefnagel MHN, Starrenburg MJC, Martens DE, Hugenholtz J, Kleerebezem M, Van Swam II, Bongers R, Westerhoff HV, Snoep JL (2002) Metabolic engineering of lactic acid bacteria, the combined approach: kinetic modeling, metabolic control and experimental analysis. Microbiol 148:1003–1013
Article
CAS
Google Scholar
Kremling A, Jahreis K, Lengeler JW, Gilles ED (2000) The organization of metabolic reaction networks: a signal-oriented approach to cellular models. Metab Eng 2:190–200
Article
CAS
Google Scholar
Kremling A, Gilles ED (2001) The organization of metabolic reaction networks. II. Signal processing in hierarchical structured functional units. Metab Eng 3:138–150
Article
CAS
Google Scholar
Kremlng A, Fischer S, Sauter T, Bettenbrock K, Gilles ED (2004) Time hierarchies in the Escherichia coli carbohydrate uptake and metabolism. BioSystems 73:57–71
Article
CAS
Google Scholar
Sauter T, Gilles ED (2004) Modeling and experimental validation of the signal transduction via the Escherichia coli sucrose phospho transferase system. J Biotech 110:181–199
Article
CAS
Google Scholar
Bettenbrock K, Fischer S, Kremling A, Jahreis K, Sauter T, Gilles ED (2006) A quantitative approach to catabolite repression in Escherichia coli. J Biol Chem 281:2578–2584
Article
CAS
Google Scholar
Nishio Y, Usuda Y, Matsui K, Kurata H (2008) Computer-aided rational design of the phosphotransferase system for enhanced glucose uptake in Escherichia coli. Mol Syst Biol 4:160
Article
CAS
Google Scholar
Majewski RA, Domach MM (1990) Simple constrained-optimization view of acetate overflow in Escherichia coli. Biotech Bioeng 35:732–738
Article
CAS
Google Scholar
Rabinowitz J, Silhavy TJ (2012) Metabolite turns master regulator. Nature 500:283–284
Article
CAS
Google Scholar
Doucette CD, Schwab DJ, Wingreen NS, Rabinowitz JD (2011) Alpha-ketoglutarate coordinates carbon and nitrogen utilization via enzyme I inhibition. Nat Chem Biol 7:894–901
Article
CAS
Google Scholar
Scott M, Gunderson CW, Mateescu EM, Zhang Z, Hwa T (2010) Interdependence of cell growth and gene expression: origins and consequences. Science 330:1099–1102
Article
CAS
Google Scholar
You C, Okano H, Hui S, Zhang Z, Kim M, Gunderson CW, Wang Y-P, Lenz P, Yan D, Hwa T (2013) Coordination of bacterial proteome with metabolism by cyclic AMP signaling. Nature 500:301–306
Article
CAS
Google Scholar
Vinuselvi P, Kim MK, Lee SK, Ghim C-M (2012) Rewiring carbon catabolite repression for microbial cell factory. BMB Rep 45(2):59–70
Article
CAS
Google Scholar
Gorke B, Stulke J (2008) Carbon catabolite repression in bacteria: many ways to make the most out of nutrients. Nature Rev Microbiol 6:613–24
Article
CAS
Google Scholar
Vasudevan P, Briggs M (2008) Biodiesel production-current state of the art and challenges. J Ind Microbiol Biotechnol 35:421–430
Article
CAS
Google Scholar
Dharmadi Y, Murarka A, Gonzalez R (2006) Anaerobic fermentation of glycerol by Escherichia coli: a new platform for metabolic engineering. Biotechnol Bioeng 94:821–829
Article
CAS
Google Scholar
Clomburg JM, Gonzalez R (2013) Anaerobic fermentation of glycerol: a platform for renewable fuels and chemicals. Trends Biotechnol 31:20–28
Article
CAS
Google Scholar
Almeida JRM, Fávaro LCL, Betania F, Quirino BF (2012) Biodiesel biorefinery: opportunities and challenges for microbial production of fuels and chemicals from glycerol waste. Biotechnol for Biofuels 5:48
Article
CAS
Google Scholar
Martínez-Gómez K, Flores N, Castañeda HM, Martínez-Batallar G, Hernández-Chávez G, Ramírez OT, Gosset G, Encarnación S, Bolivar F (2012) New insights into Escherichia coli metabolism: carbon scavenging, acetate metabolism and carbon recycling responses during growth on glycerol. Micob Cell Fact 11:46
Article
CAS
Google Scholar
Oh MK, Liao JC (2000) Gene expression profiling by DNA microarrays and metabolic fluxes in Escherichia coli. Biotechnol Prog 16:278–286
Article
CAS
Google Scholar
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
Article
CAS
Google Scholar
Cintolesi A, Clomburg JM, Rigou V, Zygourakis K, Gonzalez R (2012) Quantitative analysis of the fermentative metabolism of glycerol in Escherichia coli. Biotechnol Bioeng 109:187–198
Article
CAS
Google Scholar
Saier MH, Ramseier TM (1996) The catabolite repressor/activator (Cra) protein of enteric bacteria. Journal of Bacteriology 178:3411–3417
CAS
Google Scholar
Kornberg HL (2001) Routes for fructose utilization by Escherichia coli. J Mol Microbiol Biotechnol 3:355–359
CAS
Google Scholar
Yao R, Shimizu K (2013) Recent progress in metabolic engineering for the production of biofuels and biochemicals from renewable sources with particular emphasis on catabolite regulation and its modulation. Process Biochem 48:1409–1417
Article
CAS
Google Scholar
Crasnier-Mednansky M, Park MC, Studley WK, Saier MH Jr (1997) Cra-mediated regulations of Escherichia coli adenylate cyclase. Microbiology 143:785–792
Article
CAS
Google Scholar
Griffith JK, Baker ME, Rouch DA, Page MG, Skurray RA, Paulsen IT, Chater KF, Baldwin SA, Henderson PJ (1992) Membrane transport proteins: implications of sequence comparisons. Curr Opin Cell Biol 4:684–695
Article
CAS
Google Scholar
Sumiya M, Davis EO, Packman LC, McDonald TP, Henderson PJ (1995) Molecular genetics of a receptor protein for d-xylose, encoded by the gene xylF, in Escherichia coli. Receptors Channels 3:117–128
CAS
Google Scholar
Song S, Park C (1997) Organization and regulation of the d-xylose operons in Escherichia coli K-12: XylR acts as a transcriptional activator. J Bacteriol 179:7025–7032
CAS
Google Scholar
Altintas MM, Eddy CK, Zhang M, McMillan JD, Kompala DS (2006) Kinetic modeling to optimize pentose fermentation in Zymomonas mobilis. Biotechnol Bioeng 94:273–295
Article
CAS
Google Scholar
Yang C, Hua Q, Shimizu K (1999) Development of a kinetic model for L-lysine biosynthesis in Corynebacterium glutamicum and its application to metabolic control analysis. J Biosci Bioeng 88:393–403
Article
CAS
Google Scholar
Hua Q, Yang C, Shimizu K (2000) Metabolic control analysis for lysine synthesis using Corynebacterium glutamicum and experimental verification. J Biosci Bioeng 90:184–192
Article
CAS
Google Scholar
Nishio Y, Ogishima S, Ichikawa M, Yamada Y, Usuda Y, Masuda T, Tanaka H (2013) Analysis of L-glutamic acid fermentation by using a dynamic metabolic simulation model of Escherichia coli. BMC Sys Biol 7:92
Article
CAS
Google Scholar
Li R-D, Li Y-Y, Lu L-Y, Ren C, Li Y-X, Liu L (2011) An improved kinetic model for the acetone-butanol-etahnol pathway of Clostridium acetobutyricum and model-based perturbation analysis. BMC Sys Biol 5:S12
Article
CAS
Google Scholar
Shinto H, Tashiro Y, Kobayashi G, Sekiguchi T, Hanai T, Kuriya Y, Okamoto M, Sonomoto K (2007) Kinetic modeling and sensitivity analysis of acetone-butanol-ethanol production. J Biotechnol 131:45–56
Article
CAS
Google Scholar
Shinto H, Tashiro Y, Kobayashi G, Sekiguchi T, Hanai T, Kuriya Y, Okamoto M, Sonomoto K (2008) Kinetic study of substrate dependency for higher butanol production in acetone-butanol-ethanol fermentation. Proc Biochem 43:1452–1461
Article
CAS
Google Scholar
Alexeeva S, Hellingwerf KJ, de Mattos JT (2003) Requirement of ArcA for redox regulation in Escherichia coli under microaerobic but not anaerobic or aerobic conditions. J Bacteriol 185:204–209
Article
CAS
Google Scholar
Shalel-Levanon S, San K-Y, Bennett GN (2005) Effect of oxygen, and ArcA and FNR regulators on the expression of genes related to the electron transfer chain and the TCA cycle in Escherichia coli. Metab Eng 7:364–374
Article
CAS
Google Scholar
Cox SJ, Levanon SS, Bennett GN, San K-Y (2005) Genetically constrained metabolic flux analysis. Metab Eng 7:445–456
Article
CAS
Google Scholar
van Heeswijk WC, Westerhoff HV, Boogerd FC (2013) Nitrogen assimilation in Escherichia coli: putting molecular data into a systems perspective. Microbiol Mol Biol Rev 77:628–695
Article
CAS
Google Scholar
Rhee SG, Chock PB, Stadtman ER (1985) Glutamine synthetase from Escherichia coli. Methods Enzymol 113:213–241
Article
CAS
Google Scholar
Sakamoto N, Kotre AM, Savageau MA (1975) Glutamate dehydrogenase from Escherichia coli: purification and properties. J Bacteriol 124:775–783
CAS
Google Scholar
Bruggeman FJ, Boogerd FC, Westerhoff HV (2005) The multifarious short-term regulation of ammonium assimilation of Ecsherichia coli: dissection using an in silico replica. FEBS J 272:1965–1985
Article
CAS
Google Scholar
Atkinson MR, Blauwkamp TA, Bondarenko V, Studitsky V, Ninfa AJ (2002) Activation of the glnA, glnK, and nac promoters as Escherichia coli undergoes the transition from nitrogen excess growth to nitrogen starvation. J Bacteriol 184:5358–5363
Article
CAS
Google Scholar
Reitzer L (2003) Nitrogen assimilation and global regulation in Escherichia coli. Annu Rev Microbiol 57:155–176
Article
CAS
Google Scholar
Ma H, Boogerd FC, Goryanin I (2009) Modelling nitrogen assimilation of Escherichia coli at low ammonium concentration. J Biotechnol 144:175–183
Article
CAS
Google Scholar
Yuan J, Doucette CD, Fowler WU, Feng XJ, Piazza M, Rabitz HA, Wingreen NS, Rabinowitz JD (2009) Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli. Mol Syst Biol 5:302
Article
CAS
Google Scholar
Lodeiro A, Melgarejo A (2008) Robustness in Escherichia coli glutamate and glutamine synthesis studied by a kinetic mode. J Biol Phys 34:91–106
Article
CAS
Google Scholar