Development of thermodynamic optimum searching (TOS) to improve the prediction accuracy of flux balance analysis

Biotechnology and Bioengineering

Volumn 110, Issue 3, 2013, Pages 914-923

  Zhu, Yan ^a,b   Song, Jiangning ^c,d   Xu, Zixiang ^c   Sun, Jibin ^c   Zhang, Yanping ^a   Li, Yin ^a   Ma, Yanhe ^a  

^a INSTITUTE OF MICROBIOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c Chinese Academy of Sciences   (China)

^d MONASH UNIVERSITY   (Australia)

Author keywords

Constraint based metabolic model; Energy loop law; Flux balance analysis; Maximum entropy production principle

Indexed keywords

ENERGY BALANCE ANALYSIS; ENERGY LOOP LAW; FLUX BALANCE ANALYSIS; FLUX DISTRIBUTIONS; GIBBS FREE ENERGY CHANGES; MAXIMUM ENTROPY; METABOLIC MODELS; OPTIMAL SOLUTIONS; OPTIMIZATION METHOD; PHYSIOLOGICAL CONDITION; PREDICTION ACCURACY; PREDICTION TOOLS; SECOND LAW OF THERMODYNAMICS;

ESCHERICHIA COLI; FORECASTING; METABOLIC ENGINEERING; THERMODYNAMICS;

MAXIMUM ENTROPY METHODS;

CARBON 13;

ACCURACY; ANALYSIS; ARTICLE; CALCULATION; ENTROPY; ESCHERICHIA COLI; FLUX BALANCE ANALYSIS; GROWTH RATE; METABOLIC ENGINEERING; NONHUMAN; PREDICTION; THERMODYNAMIC OPTIMUM SEARCHING; THERMODYNAMICS;

COMPUTATIONAL BIOLOGY; ENERGY METABOLISM; ESCHERICHIA COLI; METABOLIC ENGINEERING; METABOLIC NETWORKS AND PATHWAYS; THERMODYNAMICS;

ESCHERICHIA COLI; TOSCANA VIRUS;

EID: 84872659403     PISSN: 00063592     EISSN: 10970290     Source Type: Journal    
DOI: 10.1002/bit.24739     Document Type: Article

References (43)

1. Beard DA, Qian H. 2007. Relationship between thermodynamic driving force and one-way fluxes in reversible processes. PLoS ONE 2(1): e144.
2. Beard DA, Liang SD, Qian H. 2002. Energy balance for analysis of complex metabolic networks. Biophys J 83(1): 79-86.
3. Bennett BD, Kimball EH, Gao M, Osterhout R, Van Dien SJ, Rabinowitz JD. 2009. Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli Nat Chem Biol 5(8): 593-599.
4. Bordel S, Nielsen J. 2010. Identification of flux control in metabolic networks using non-equilibrium thermodynamics. Metab Eng 12(4): 369-377.
5. 13C-metabolic flux analysis and flux balance analysis for understanding metabolic adaption to anaerobiosis in E. coli Metab Eng 13(1): 38-48.
6. Conrad TM, Joyce AR, Applebee MK, Barrett CL, Xie B, Gao Y, Palsson BO. 2009. Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations. Genome Biol 10(10): R118.
7. Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO. 2004. Integrating high-throughput and computational data elucidates bacterial networks. Nature 429(6987): 92-96.
8. Duarte NC, Palsson BO, Fu P. 2004. Integrated analysis of metabolic phenotypes in Saccharomyces cerevisiae BMC Genomics 5(1): 63.
9. Edwards JS, Ramakrishna R, Palsson BO. 2002. Characterizing the metabolic phenotype: A phenotype phase plane analysis. Biotechnol Bioeng 77(1): 27-36.
10. Feist AM, Palsson BO. 2008. The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli Nat Biotechnol 26(6): 659-667.
11. Feist AM, Palsson BO. 2010. The biomass objective function. Curr Opin Microbiol 13(3): 344-349.
12. Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO. 2007. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol 3: 121.
13. Feist A, Zielinski D, Orth J, Schellenberger J, Herrgard M, Palsson B. 2010. Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli Metab Eng 12: 173-186.
14. Fendt SM, Buescher JM, Rudroff F, Picotti P, Zamboni N, Sauer U. 2010. Tradeoff between enzyme and metabolite efficiency maintains metabolic homeostasis upon perturbations in enzyme capacity. Mol Syst Biol 6: 356.
15. Fleming RM, Thiele I, Nasheuer HP. 2009. Quantitative assignment of reaction directionality in constraint-based models of metabolism: Application to Escherichia coli Biophys Chem 145(2-3): 47-56.
16. Fleming RM, Thiele I, Provan G, Nasheuer HP. 2010. Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism. J Theor Biol 264(3): 683-692.
17. Henry CS, Broadbelt LJ, Hatzimanikatis V. 2007. Thermodynamics-based metabolic flux analysis. Biophys J 92(5): 1792-1805.
18. 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(5824): 593-597.
19. Jankowski MD, Henry CS, Broadbelt LJ, Hatzimanikatis V. 2008. Group contribution method for thermodynamic analysis of complex metabolic networks. Biophys J 95(3): 1487-1499.
20. Juretic D, Zupanovic P. 2003. Photosynthetic models with maximum entropy production in irreversible charge transfer steps. Comput Biol Chem 27(6): 541-553.
21. Kummel A, Panke S, Heinemann M. 2006. Systematic assignment of thermodynamic constraints in metabolic network models. BMC Bioinformatics 7: 512.
22. Lee S, Phalakornkule C, Domach MM, Grossmann IE. 2000. Recursive MILP model for finding all the alternate optima in LP models for metabolic networks. Comput Chem Eng 24(2-7): 711-716.
23. Liu M, Durfee T, Cabrera JE, Zhao K, Jin DJ, Blattner FR. 2005. Global transcriptional programs reveal a carbon source foraging strategy by Escherichia coli J Biol Chem 280(16): 15921-15927.
24. Liu L, Agren R, Bordel S, Nielsen J. 2010. Use of genome-scale metabolic models for understanding microbial physiology. FEBS Lett 584(12): 2556-2564.
25. Mahadevan R, Schilling CH. 2003. The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab Eng 5(4): 264-276.
26. Martyushev LM, Seleznev VD. 2006. Maximum entropy production principle in physics, chemistry and biology. Phys Rep 426(1): 1-45.
27. Meysman FJ, Bruers S. 2010. Ecosystem functioning and maximum entropy production: A quantitative test of hypotheses. Philos Trans R Soc Lond B Biol Sci 365(1545): 1405-1416.
28. Murarka A, Clomburg JM, Moran S, Shanks JV, Gonzalez R. 2010. Metabolic analysis of wild-type Escherichia coli and a pyruvate dehydrogenase complex (PDHC)-deficient derivative reveals the role of PDHC in the fermentative metabolism of glucose. J Biol Chem 285(41): 31548-31558.
29. Nnyepi MR, Peng Y, Broderick JB. 2007. Inactivation of E. coli pyruvate formate-lyase: Role of AdhE and small molecules. Arch Biochem Biophys 459(1): 1-9.
30. Orth JD, Thiele I, Palsson BO. 2010. What is flux balance analysis? Nat Biotech 28(3): 245-248.
31. Orth JD, Conrad TM, Na J, Lerman JA, Nam H, Feist AM, Palsson BO. 2011. A comprehensive genome-scale reconstruction of Escherichia coli metabolism-2011. Mol Syst Biol 7: 535.
32. Palsson B. 2006. Systems Biology: Properties of reconstructed networks. New York: Cambridge University Press. 322 p.
33. Papp B, Notebaart RA, Pal C. 2011. Systems-biology approaches for predicting genomic evolution. Nat Rev Genet 12(9): 591-602.
34. Price ND, Reed JL, Palsson BO. 2004. Genome-scale models of microbial cells: Evaluating the consequences of constraints. Nat Rev Microbiol 2(11): 886-897.
35. Qian H, Beard DA. 2005. Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium. Biophys Chem 114(2-3): 213-220.
36. Raman K, Chandra N. 2009. Flux balance analysis of biological systems: Applications and challenges. Brief Bioinform 10(4): 435-449.
37. Reed JL, Palsson BO. 2004. Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: Assessment of correlated reaction subsets that comprise network states. Genome Res 14(9): 1797-1805.
38. Samal A. 2008. Conservation of high-flux backbone in alternate optimal and near-optimal flux distributions of metabolic networks. Syst Synth Biol 2(3-4): 83-93.
39. Sawers G, Bock A. 1988. Anaerobic regulation of pyruvate formate-lyase from Escherichia coli K-12. J Bacteriol 170(11): 5330-5336.
40. Schellenberger J, Lewis NE, Palsson BO. 2010. Elimination of thermodynamically infeasible loops in steady-state metabolic models. Biophys J 100(3): 544-553.
41. Schuetz R, Kuepfer L, Sauer U. 2007. Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli Mol Syst Biol 3: 119.
42. van der Werf MJ, Overkamp KM, Muilwijk B, Coulier L, Hankemeier T. 2007. Microbial metabolomics: Toward a platform with full metabolome coverage. Anal Biochem 370(1): 17-125.
43. Zhang W, Wong KK, Magliozzo RS, Kozarich JW. 2001. Inactivation of pyruvate formate-lyase by dioxygen: Defining the mechanistic interplay of glycine 734 and cysteine 419 by rapid freeze-quench EPR. Biochemistry 40(13): 4123-4130.