{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T03:04:54Z","timestamp":1775012694578,"version":"3.50.1"},"reference-count":103,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2014,2,20]],"date-time":"2014-02-20T00:00:00Z","timestamp":1392854400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1003483","type":"journal-article","created":{"date-parts":[[2014,2,20]],"date-time":"2014-02-20T22:03:21Z","timestamp":1392933801000},"page":"e1003483","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":324,"title":["Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism"],"prefix":"10.1371","volume":"10","author":[{"given":"Elad","family":"Noor","sequence":"first","affiliation":[]},{"given":"Arren","family":"Bar-Even","sequence":"additional","affiliation":[]},{"given":"Avi","family":"Flamholz","sequence":"additional","affiliation":[]},{"given":"Ed","family":"Reznik","sequence":"additional","affiliation":[]},{"given":"Wolfram","family":"Liebermeister","sequence":"additional","affiliation":[]},{"given":"Ron","family":"Milo","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2014,2,20]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1111\/j.1432-1033.1997.0191a.x","article-title":"Theoretical approaches to the evolutionary optimization of glycolysis: thermodynamic and kinetic constraints","volume":"243","author":"R Heinrich","year":"1997","journal-title":"Eur J Biochem"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1111\/j.1432-1033.1997.t01-1-00527.x","article-title":"Theoretical approaches to the evolutionary optimization of glycolysis\u2013chemical analysis","volume":"244","author":"E Melendez-Hevia","year":"1997","journal-title":"Eur J Biochem"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1006\/jtbi.1999.0942","article-title":"Optimal stoichiometric designs of ATP-producing systems as determined by an evolutionary algorithm","volume":"199","author":"A Stephani","year":"1999","journal-title":"J Theor Biol"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1006\/bulm.2000.0197","article-title":"Evolutionary optimization of metabolic pathways. Theoretical reconstruction of the stoichiometry of ATP and NADH producing systems","volume":"63","author":"O Ebenhoh","year":"2001","journal-title":"Bull Math Biol"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"15112","DOI":"10.1073\/pnas.232349399","article-title":"Analysis of optimality in natural and perturbed metabolic networks","volume":"99","author":"D Segre","year":"2002","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1016\/j.jtbi.2007.12.008","article-title":"Is maximization of molar yield in metabolic networks favoured by evolution?","volume":"252","author":"S Schuster","year":"2008","journal-title":"J Theor Biol"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1038\/msb.2009.82","article-title":"Shifts in growth strategies reflect tradeoffs in cellular economics","volume":"5","author":"D Molenaar","year":"2009","journal-title":"Mol Syst Biol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"809","DOI":"10.1016\/j.molcel.2010.08.031","article-title":"Central carbon metabolism as a minimal biochemical walk between precursors for biomass and energy","volume":"39","author":"E Noor","year":"2010","journal-title":"Mol Cell"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"1646","DOI":"10.1016\/j.bbabio.2012.05.002","article-title":"Thermodynamic constraints shape the structure of carbon fixation pathways","volume":"1817","author":"A Bar-Even","year":"2012","journal-title":"Biochim Biophys Acta"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1038\/nchembio.971","article-title":"Rethinking glycolysis: on the biochemical logic of metabolic pathways","volume":"8","author":"A Bar-Even","year":"2012","journal-title":"Nat Chem Biol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"2325","DOI":"10.1093\/jxb\/err417","article-title":"A survey of carbon fixation pathways through a quantitative lens","volume":"63","author":"A Bar-Even","year":"2012","journal-title":"J Exp Bot"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1126\/science.1216882","article-title":"Multidimensional optimality of microbial metabolism","volume":"336","author":"R Schuetz","year":"2012","journal-title":"Science"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"10039","DOI":"10.1073\/pnas.1215283110","article-title":"Glycolytic strategy as a tradeoff between energy yield and protein cost","volume":"110","author":"A Flamholz","year":"2013","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"8889","DOI":"10.1073\/pnas.0907176107","article-title":"Design and analysis of synthetic carbon fixation pathways","volume":"107","author":"A Bar-Even","year":"2010","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"780","DOI":"10.1002\/bit.22309","article-title":"Influence of uncertainties in pH, pMg, activity coefficients, metabolite concentrations, and other factors on the analysis of the thermodynamic feasibility of metabolic pathways","volume":"103","author":"V Vojinovic","year":"2009","journal-title":"Biotechnol Bioeng"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1016\/j.jbiotec.2005.08.012","article-title":"Thermodynamics of microbial growth and metabolism: an analysis of the current situation","volume":"121","author":"U von Stockar","year":"2006","journal-title":"J Biotechnol"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"1603","DOI":"10.1093\/bioinformatics\/bti213","article-title":"Exploring the diversity of complex metabolic networks","volume":"21","author":"V Hatzimanikatis","year":"2005","journal-title":"Bioinformatics"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"532","DOI":"10.1002\/bit.22285","article-title":"Thermodynamic analysis of biodegradation pathways","volume":"103","author":"SD Finley","year":"2009","journal-title":"Biotechnol Bioeng"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1016\/j.tibtech.2010.05.003","article-title":"Production of biofuels and biochemicals: in need of an ORACLE","volume":"28","author":"L Miskovic","year":"2010","journal-title":"Trends Biotechnol"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"1039","DOI":"10.1016\/j.bbabio.2012.10.013","article-title":"Design and analysis of metabolic pathways supporting formatotrophic growth for electricity-dependent cultivation of microbes","volume":"1827","author":"A Bar-Even","year":"2013","journal-title":"Biochim Biophys Acta"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"E633","DOI":"10.1152\/ajpendo.00239.2004","article-title":"Thermodynamic-based computational profiling of cellular regulatory control in hepatocyte metabolism","volume":"288","author":"DA Beard","year":"2005","journal-title":"Am J Physiol Endocrinol Metab"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"2037","DOI":"10.1093\/bioinformatics\/bts317","article-title":"An integrated open framework for thermodynamics of reactions that combines accuracy and coverage","volume":"28","author":"E Noor","year":"2012","journal-title":"Bioinformatics"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"e144","DOI":"10.1371\/journal.pone.0000144","article-title":"Relationship between thermodynamic driving force and one-way fluxes in reversible processes","volume":"2","author":"DA Beard","year":"2007","journal-title":"PLoS One"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1016\/S0006-3495(73)86004-7","article-title":"The thermodynamic description of enzyme-catalyzed reactions. The linear relation between the reaction rate and the affinity","volume":"13","author":"H Rottenberg","year":"1973","journal-title":"Biophys J"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"488","DOI":"10.1016\/0005-2728(80)90179-6","article-title":"Linear relation between rate and thermodynamic force in enzyme-catalyzed reactions","volume":"591","author":"R Van Der Meer","year":"1980","journal-title":"Biochim Biophys Acta"},{"key":"ref26","first-page":"65","article-title":"The control of flux","volume":"27","author":"H Kacser","year":"1973","journal-title":"Symp Soc Exp Biol"},{"key":"ref27","doi-asserted-by":"crossref","unstructured":"Westerhoff HV (1987) Thermodynamics and Control of Biological Free-Energy Transduction: Elsevier Science Ltd.","DOI":"10.1007\/978-1-4899-2551-0_11"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1006\/jtbi.1993.1177","article-title":"Metabolic control design","volume":"165","author":"L Acerenza","year":"1993","journal-title":"J Theor Biol"},{"key":"ref29","doi-asserted-by":"crossref","unstructured":"Crabtree B, Newsholme EA, Reppas NB (1997) Principles of regulation and control in biochemistry: a pragmatic, flux-oriented approach. In: Hoffman JF, Jamieson JD, editors. Handbook of Physiology. New York, USA: Oxford University Press.pp. 117\u2013180.","DOI":"10.1002\/cphy.cp140105"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1042\/bj3210133","article-title":"Metabolic control analysis of biochemical pathways based on a thermokinetic description of reaction rates","volume":"321 (Pt 1)","author":"J Nielsen","year":"1997","journal-title":"Biochem J"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"4402","DOI":"10.1021\/bi2002289","article-title":"The moderately efficient enzyme: evolutionary and physicochemical trends shaping enzyme parameters","volume":"50","author":"A Bar-Even","year":"2011","journal-title":"Biochemistry"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"e1003098","DOI":"10.1371\/journal.pcbi.1003098","article-title":"Consistent estimation of GIbbs energy using component contributions","volume":"9","author":"E Noor","year":"2013","journal-title":"Plos Comp Biol"},{"key":"ref33","doi-asserted-by":"crossref","unstructured":"Alberty RA (2003) Thermodynamics of Biochemical Reactions: Wiley-Interscience.","DOI":"10.1002\/0471332607"},{"key":"ref34","first-page":"1","article-title":"Biochemical thermodynamics: applications of Mathematica","volume":"48","author":"RA Alberty","year":"2006","journal-title":"Methods Biochem Anal"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"2874","DOI":"10.1093\/bioinformatics\/bth314","article-title":"Thermodynamics of enzyme-catalyzed reactions\u2013a database for quantitative biochemistry","volume":"20","author":"RN Goldberg","year":"2004","journal-title":"Bioinformatics"},{"key":"ref36","first-page":"1347","article-title":"Thermodynamics of enzyme-catalyzed reactions: Part 7\u20142007 update J Phys Chem Ref Data","volume":"36","author":"RN Goldberg","year":"2007"},{"key":"ref37","volume":"55","unstructured":"Slonczewski JL, Fujisawa M, Dopson M, Krulwich TA (2009) Cytoplasmic pH measurement and homeostasis in bacteria and archaea. Adv Microb Physiol <volume>55<\/volume>: : 1\u201379, 317."},{"key":"ref38","unstructured":"McNaught AD, Wilkinson A (1997) Compendium of Chemical Terminology, 2nd ed. (the IUPAC \u201cGold Book\u201d). Oxford: Blackwell Scientific Publications."},{"key":"ref39","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1016\/S0006-3495(96)79252-4","article-title":"Calculation of biochemical net reactions and pathways by using matrix operations","volume":"71","author":"RA Alberty","year":"1996","journal-title":"Biophys J"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"e1002758","DOI":"10.1371\/journal.pcbi.1002758","article-title":"Impact of stoichiometry representation on simulation of genotype-phenotype relationships in metabolic networks","volume":"8","author":"AR Brochado","year":"2012","journal-title":"PLoS Comput Biol"},{"key":"ref41","first-page":"275","article-title":"Identification of localized and distributed bottlenecks in metabolic pathways","volume":"1","author":"ML Mavrovouniotis","year":"1993","journal-title":"Proc Int Conf Intell Syst Mol Biol"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1057\/palgrave.jors.2600523","article-title":"Rate control for communication networks: shadow prices, proportional fairness and stability","volume":"49","author":"FP Kelly","year":"1998","journal-title":"J Oper Res Soc"},{"key":"ref43","unstructured":"Bertsimas D, Tsitsiklis JN, Tsitsiklis J (1997) Introduction to Linear Optimization."},{"key":"ref44","doi-asserted-by":"crossref","first-page":"e1002166","DOI":"10.1371\/journal.pcbi.1002166","article-title":"Hydrophobicity and charge shape cellular metabolite concentrations","volume":"7","author":"A Bar-Even","year":"2011","journal-title":"PLoS Comput Biol"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1038\/nchembio.186","article-title":"Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli","volume":"5","author":"BD Bennett","year":"2009","journal-title":"Nat Chem Biol"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1038\/msb.2013.11","article-title":"Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast","volume":"9","author":"GG Zampar","year":"2013","journal-title":"Mol Syst Biol"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"1068","DOI":"10.1021\/bi00534a038","article-title":"Phosphorus-31 nuclear magnetic resonance studies of bioenergetics in wild-type and adenosinetriphosphatase(1-) Escherichia coli cells","volume":"21","author":"K Ugurbil","year":"1982","journal-title":"Biochemistry"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"3909","DOI":"10.1128\/JB.184.14.3909-3916.2002","article-title":"The glycolytic flux in Escherichia coli is controlled by the demand for ATP","volume":"184","author":"BJ Koebmann","year":"2002","journal-title":"J Bacteriol"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1126\/science.1132067","article-title":"Multiple high-throughput analyses monitor the response of E. coli to perturbations","volume":"316","author":"N Ishii","year":"2007","journal-title":"Science"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"2351","DOI":"10.1128\/JB.181.8.2351-2357.1999","article-title":"The steady-state internal redox state (NADH\/NAD) reflects the external redox state and is correlated with catabolic adaptation in Escherichia coli","volume":"181","author":"MR de Graef","year":"1999","journal-title":"J Bacteriol"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1016\/0014-5793(79)80642-0","article-title":"Evidence suggesting that the NADPH\/NADP ratio modulates the splitting of the isocitrate flux between the glyoxylic and tricarboxylic acid cycles, in Escherichia coli","volume":"105","author":"J Bautista","year":"1979","journal-title":"FEBS Lett"},{"key":"ref52","unstructured":"Stiefel EI, George GN (1994) Ferredoxins, Hydrogenases, and Nitrogenases: Metal-Sulfide Proteins. Bioinorganic Chemistry. pp. 365\u2013453."},{"key":"ref53","doi-asserted-by":"crossref","first-page":"2244","DOI":"10.1073\/pnas.75.5.2244","article-title":"31P nuclear magnetic resonance studies of bioenergetics and glycolysis in anaerobic Escherichia coli cells","volume":"75","author":"K Ugurbil","year":"1978","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"699","DOI":"10.1128\/jb.177.3.699-704.1995","article-title":"Kinetic analysis by in vivo 31P nuclear magnetic resonance of internal Pi during the uptake of sn-glycerol-3-phosphate by the pho regulon-dependent Ugp system and the glp regulon-dependent GlpT system","volume":"177","author":"KB Xavier","year":"1995","journal-title":"J Bacteriol"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"1048","DOI":"10.1046\/j.1365-2958.2001.02303.x","article-title":"Non-growing Escherichia coli cells starved for glucose or phosphate use different mechanisms to survive oxidative stress","volume":"39","author":"PL Moreau","year":"2001","journal-title":"Mol Microbiol"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"5686","DOI":"10.1128\/jb.172.10.5686-5689.1990","article-title":"Pyrophosphatase is essential for growth of Escherichia coli","volume":"172","author":"J Chen","year":"1990","journal-title":"J Bacteriol"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"18538","DOI":"10.1074\/jbc.M110.214510","article-title":"Enhancement of the rate of pyrophosphate hydrolysis by nonenzymatic catalysts and by inorganic pyrophosphatase","volume":"286","author":"RB Stockbridge","year":"2011","journal-title":"J Biol Chem"},{"key":"ref58","unstructured":"Fell D (1996) Understanding the Control of Metabolism: Portland Pr."},{"key":"ref59","unstructured":"Klipp E, Liebermeister W, Wierling C, Kowald A, Lehrach H, <etal>et al<\/etal>.. (2009) Systems Biology: Wiley-Blackwell."},{"key":"ref60","unstructured":"Haldane JBS (1930) Enzymes. London: Longmans &amp; Green."},{"key":"ref61","doi-asserted-by":"crossref","first-page":"2772","DOI":"10.1016\/j.febslet.2013.07.028","article-title":"A note on the kinetics of enzyme action: A decomposition that highlights thermodynamic effects","volume":"587","author":"E Noor","year":"2013","journal-title":"FEBS Lett"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/1758-2946-3-33","article-title":"Open Babel: An open chemical toolbox","volume":"3","author":"NM O'Boyle","year":"2011","journal-title":"J Cheminform"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"D480","DOI":"10.1093\/nar\/gkm882","article-title":"KEGG for linking genomes to life and the environment","volume":"36","author":"M Kanehisa","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"46446","DOI":"10.1074\/jbc.M307968200","article-title":"A novel metabolic cycle catalyzes glucose oxidation and anaplerosis in hungry Escherichia coli","volume":"278","author":"E Fischer","year":"2003","journal-title":"J Biol Chem"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1016\/j.ymben.2010.11.004","article-title":"Synergy between (13)C-metabolic flux analysis and flux balance analysis for understanding metabolic adaptation to anaerobiosis in E. coli","volume":"13","author":"X Chen","year":"2011","journal-title":"Metab Eng"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"3101","DOI":"10.1016\/S0021-9258(19)50700-1","article-title":"Systems analysis of the tricarboxylic acid cycle in Dictyostelium discoideum. I. The basis for model construction","volume":"267","author":"BE Wright","year":"1992","journal-title":"J Biol Chem"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"1428","DOI":"10.1126\/science.1159747","article-title":"Biochemistry. How enzymes work","volume":"320","author":"D Ringe","year":"2008","journal-title":"Science"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1023\/B:ORIG.0000043128.30559.fe","article-title":"Kinetics of organic transformations under mild aqueous conditions: implications for the origin of life and its metabolism","volume":"34","author":"AL Weber","year":"2004","journal-title":"Orig Life Evol Biosph"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1016\/S1096-7176(03)00008-9","article-title":"Review of the BRENDA Database","volume":"5","author":"P Pharkya","year":"2003","journal-title":"Metab Eng"},{"key":"ref70","doi-asserted-by":"crossref","first-page":"15008","DOI":"10.1016\/S0021-9258(18)95694-2","article-title":"Substrate channeling of oxalacetate in solid-state complexes of malate dehydrogenase and citrate synthase","volume":"260","author":"A Datta","year":"1985","journal-title":"J Biol Chem"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"6089","DOI":"10.1016\/S0021-9258(18)45541-X","article-title":"Quantitation of the interaction between citrate synthase and malate dehydrogenase","volume":"262","author":"P Tompa","year":"1987","journal-title":"J Biol Chem"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1146\/annurev.bi.56.070187.000513","article-title":"Complexes of sequential metabolic enzymes","volume":"56","author":"PA Srere","year":"1987","journal-title":"Annu Rev Biochem"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"29540","DOI":"10.1074\/jbc.273.45.29540","article-title":"Interaction between citrate synthase and malate dehydrogenase. Substrate channeling of oxaloacetate","volume":"273","author":"I Morgunov","year":"1998","journal-title":"J Biol Chem"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1016\/j.bbabio.2012.10.007","article-title":"Does acetogenesis really require especially low reduction potential?","volume":"1827","author":"A Bar-Even","year":"2013","journal-title":"Biochim Biophys Acta"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"6892","DOI":"10.1128\/JB.182.24.6892-6899.2000","article-title":"Functions of the membrane-associated and cytoplasmic malate dehydrogenases in the citric acid cycle of Escherichia coli","volume":"182","author":"ME van der Rest","year":"2000","journal-title":"J Bacteriol"},{"key":"ref76","doi-asserted-by":"crossref","first-page":"3204","DOI":"10.1128\/JB.182.11.3204-3209.2000","article-title":"Another unusual type of citric acid cycle enzyme in Helicobacter pylori: the malate:quinone oxidoreductase","volume":"182","author":"B Kather","year":"2000","journal-title":"J Bacteriol"},{"key":"ref77","doi-asserted-by":"crossref","first-page":"6884","DOI":"10.1128\/JB.182.24.6884-6891.2000","article-title":"Functions of the membrane-associated and cytoplasmic malate dehydrogenases in the citric acid cycle of Corynebacterium glutamicum","volume":"182","author":"D Molenaar","year":"2000","journal-title":"J Bacteriol"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"10020","DOI":"10.1073\/pnas.1733211100","article-title":"Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome","volume":"100","author":"A Dufresne","year":"2003","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1016\/j.femsle.2005.03.034","article-title":"Malate:quinone oxidoreductase (MqoB) is required for growth on acetate and linear terpenes in Pseudomonas citronellolis","volume":"246","author":"K Forster-Fromme","year":"2005","journal-title":"FEMS Microbiol Lett"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1016\/j.tplants.2010.05.006","article-title":"Not just a circle: flux modes in the plant TCA cycle","volume":"15","author":"LJ Sweetlove","year":"2010","journal-title":"Trends Plant Sci"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"e7344","DOI":"10.1371\/journal.pone.0007344","article-title":"An ATP and oxalate generating variant tricarboxylic acid cycle counters aluminum toxicity in Pseudomonas fluorescens","volume":"4","author":"R Singh","year":"2009","journal-title":"PLoS One"},{"key":"ref82","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1093\/jb\/mvh147","article-title":"The energetic conversion competence of Escherichia coli during aerobic respiration studied by 31P NMR using a circulating fermentation system","volume":"136","author":"Y Noguchi","year":"2004","journal-title":"J Biochem"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"650","DOI":"10.1111\/j.1399-3054.1988.tb09177.x","article-title":"A reassessment of glycolysis and gluconeogenesis in higher plants","volume":"72","author":"SJS Sung","year":"1988","journal-title":"Physiol Plant"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1042\/bj20021472","article-title":"The unique features of glycolytic pathways in Archaea","volume":"375","author":"CH Verhees","year":"2003","journal-title":"Biochem J"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1016\/S0378-4274(99)00160-5","article-title":"Methylglyoxal in living organisms: chemistry, biochemistry, toxicology and biological implications","volume":"110","author":"MP Kalapos","year":"1999","journal-title":"Toxicol Lett"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"14871","DOI":"10.1021\/ja027063x","article-title":"Functional specificities of methylglyoxal synthase and triosephosphate isomerase: a combined QM\/MM analysis","volume":"124","author":"X Zhang","year":"2002","journal-title":"J Am Chem Soc"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1016\/0014-5793(71)80538-0","article-title":"The regulation of Escherichia coli methylglyoxal synthase; a new control site in glycolysis?","volume":"13","author":"DJ Hopper","year":"1971","journal-title":"FEBS Lett"},{"key":"ref88","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1016\/j.mib.2005.10.014","article-title":"Unusual pathways and enzymes of central carbohydrate metabolism in Archaea","volume":"8","author":"B Siebers","year":"2005","journal-title":"Curr Opin Microbiol"},{"key":"ref89","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1042\/BJ20041711","article-title":"The semi-phosphorylative Entner-Doudoroff pathway in hyperthermophilic archaea: a re-evaluation","volume":"390","author":"H Ahmed","year":"2005","journal-title":"Biochem J"},{"key":"ref90","doi-asserted-by":"crossref","first-page":"2892","DOI":"10.1128\/AEM.70.5.2892-2897.2004","article-title":"Metabolic engineering of a phosphoketolase pathway for pentose catabolism in Saccharomyces cerevisiae","volume":"70","author":"M Sonderegger","year":"2004","journal-title":"Appl Environ Microbiol"},{"key":"ref91","doi-asserted-by":"crossref","unstructured":"Bogorad IW, Lin TS, Liao JC (2013) Synthetic non-oxidative glycolysis enables complete carbon conservation. Nature.","DOI":"10.1038\/nature12575"},{"key":"ref92","doi-asserted-by":"crossref","first-page":"1114","DOI":"10.1126\/science.1223193","article-title":"Evolution. Efficiency in evolutionary trade-offs","volume":"336","author":"E Noor","year":"2012","journal-title":"Science"},{"key":"ref93","doi-asserted-by":"crossref","first-page":"4934","DOI":"10.1128\/JB.182.17.4934-4940.2000","article-title":"Effects of limited aeration and of the ArcAB system on intermediary pyruvate catabolism in Escherichia coli","volume":"182","author":"S Alexeeva","year":"2000","journal-title":"J Bacteriol"},{"key":"ref94","doi-asserted-by":"crossref","first-page":"556","DOI":"10.1002\/bit.20381","article-title":"Effect of oxygen on the Escherichia coli ArcA and FNR regulation systems and metabolic responses","volume":"89","author":"SS Levanon","year":"2005","journal-title":"Biotechnol Bioeng"},{"key":"ref95","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1002\/bit.21219","article-title":"The YfiD protein contributes to the pyruvate formate-lyase flux in an Escherichia coli arcA mutant strain","volume":"97","author":"J Zhu","year":"2007","journal-title":"Biotechnol Bioeng"},{"key":"ref96","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nbt.2489","article-title":"Systematic identification of allosteric protein-metabolite interactions that control enzyme activity in vivo","volume":"31","author":"H Link","year":"2013","journal-title":"Nat Biotechnol"},{"key":"ref97","doi-asserted-by":"crossref","first-page":"28581","DOI":"10.1074\/jbc.M113.497867","article-title":"A bacterial glucanotransferase can replace the complex maltose metabolism required for starch to sucrose conversion in leaves at night","volume":"288","author":"C Ruzanski","year":"2013","journal-title":"J Biol Chem"},{"key":"ref98","doi-asserted-by":"crossref","first-page":"542","DOI":"10.1038\/msb.2011.76","article-title":"Carbohydrate-active enzymes exemplify entropic principles in metabolism","volume":"7","author":"O Kartal","year":"2011","journal-title":"Mol Syst Biol"},{"key":"ref99","unstructured":"Fersht A (1998) Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding. New York: W. H. Freeman."},{"key":"ref100","doi-asserted-by":"crossref","first-page":"378","DOI":"10.1016\/j.ymben.2004.07.001","article-title":"Optimal re-design of primary metabolism in Escherichia coli using linlog kinetics","volume":"6","author":"D Visser","year":"2004","journal-title":"Metab Eng"},{"key":"ref101","doi-asserted-by":"crossref","first-page":"3750","DOI":"10.1529\/biophysj.104.048090","article-title":"Metabolic control analysis under uncertainty: framework development and case studies","volume":"87","author":"L Wang","year":"2004","journal-title":"Biophys J"},{"key":"ref102","volume":"2","unstructured":"Kummel A, Panke S, Heinemann M (2006) Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data. Mol Syst Biol <volume>2<\/volume> : 2006 0034."},{"key":"ref103","doi-asserted-by":"crossref","first-page":"1283","DOI":"10.1016\/S0021-9258(18)49327-1","article-title":"Phosphorolytic cleavage of fructose-6-phosphate by fructose-6-phosphate phosphoketolase from Acetobacter xylinum","volume":"233","author":"M Schramm","year":"1958","journal-title":"J Biol Chem"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003483","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,5,1]],"date-time":"2025-05-01T22:10:20Z","timestamp":1746137420000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003483"}},"subtitle":[],"editor":[{"given":"Daniel A.","family":"Beard","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2014,2,20]]},"references-count":103,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2014,2,20]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1003483","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,2,20]]}}}