Metabolic network analysis of perfused livers under fed and fasted states: Incorporating thermodynamic and futile-cycle-associated regulatory constraints

Journal of Theoretical Biology

Volumn 293, Issue , 2012, Pages 101-110

  Orman, Mehmet A ^a   Androulakis, Ioannis P ^a,b   Berthiaume, Francois ^b   Ierapetritou, Marianthi G ^a  

^a The State University of New Jersey   (United States)

^b RUTGERS UNIVERSITY   (United States)

Author keywords

Effect of fasting; Futile cycles; Liver metabolism; Pathway analysis; Thermodynamic constraints

Indexed keywords

CITRIC ACID; FATTY ACID; GLUCOSE; GLUTAMIC ACID; GLUTAMINE; KETONE BODY; LACTIC ACID;

ENZYME ACTIVITY; FATTY ACID; METABOLISM; METABOLITE; NETWORK ANALYSIS; OXIDATION; THERMODYNAMICS;

ANALYTIC METHOD; ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; CITRIC ACID CYCLE; CONTROLLED STUDY; ELECTRON TRANSPORT; ENZYME ANALYSIS; ENZYME METABOLISM; ENZYME REGULATION; FATTY ACID OXIDATION; FEMALE; GLUCONEOGENESIS; GLYCOGENOLYSIS; INTRACELLULAR TRANSPORT; LIVER PERFUSION; METABOLIC NETWORK ANALYSIS; NONHUMAN; PRIORITY JOURNAL; RAT; SIGNAL TRANSDUCTION; THERMODYNAMICS;

ANIMALS; FASTING; FATTY ACIDS; FEMALE; GLUCONEOGENESIS; LIVER; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; PERFUSION; RATS; RATS, INBRED LEW; THERMODYNAMICS;

ANIMALIA;

EID: 80155143484     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2011.10.019     Document Type: Article

References (41)

1. Arai K., Lee K., Berthiaume F., Tompkins R.G., Yarmush M.L. Intrahepatic amino acid and glucose metabolism in a d-galactosamine-induced rat liver failure model. Hepatology 2001, 34:360-371.
2. Banta S., Yokoyama T., Berthiaume F., Yarmush M.L. Effects of dehydroepiandrosterone administration on rat hepatic metabolism following thermal injury. J. Surg. Res. 2005, 127:93-105.
3. Banta S., Vemula M., Yokoyama T., Jayaraman A., Berthiaume F., Yarmush M.L. Contribution of gene expression to metabolic fluxes in hypermetabolic livers induced through burn injury and cecal ligation and puncture in rats. Biotechnol. Bioeng. 2007, 97:118-137.
4. Beard D.A., Qian H. Thermodynamic-based computational profiling of cellular regulatory control in hepatocyte metabolism. Am. J. Physiol.-Endocrinol. Metab. 2005, 288:E633-E644.
5. Boghigian B., Shi H., Lee K., Pfeifer B. Utilizing elementary mode analysis, pathway thermodynamics, and a genetic algorithm for metabolic flux determination and optimal metabolic network design. BMC Syst. Biol. 2010, 4:49.
6. Boyd M.E., Albright E.B., Foster D.W., Denis McGarry J. In vitro reversal of the fasting state of liver metabolism in the rat. Reevaluation of the roles of insulin and glucose. J. Clin. Invest. 1981, 68:142-152.
7. Chan C., Berthiaume F., Lee K., Yarmush M.L. Metabolic flux analysis of cultured hepatocytes exposed to plasma. Biotechnol. Bioeng. 2003, 81:33-49.
8. Covert M.W., Palsson B.O. Transcriptional regulation in constraints-based metabolic models of Escherichia coli. J. Biol. Chem. 2002, 277:28058-28064.
9. Covert M.W., Schilling C.H., Palsson B. Regulation of gene expression in flux balance models of metabolism. J. Theor. Biol. 2001, 213:73-88.
10. De Koning T.J., Snell K., Duran M., Berger R., Poll-The B.T., Surtees R. L-serine in disease and development. Biochem. J. 2003, 371:653-661.
11. Iyer V.V., Yang H., Ierapetritou M.G., Roth C.M. Effects of glucose and insulin on HepG2-C3A cell metabolism. Biotechnol. Bioeng. 2010, 107:347-356. 10.1002/bit.22799.
12. Iyer V.V., Ovacik M.A., Androulakis I.P., Roth C.M., Ierapetritou M.G. Transcriptional and metabolic flux profiling of triadimefon effects on cultured hepatocytes. Toxicol. Appl. Pharmacol. 2010, 248:165-177. 10.1016/j.taap.2010.07.015.
13. Kaleta C., de Figueiredo L.F., Werner S., Guthke R., Ristow M., Schuster S. Evidence for gluconeogenesis from fatty acids in humans. PLoS Comput. Biol. 2011, 7:e1002116.
14. Klamt S., Stelling J. Two approaches for metabolic pathway analysis?. Trends Biotechnol. 2003, 21:64-69.
15. Klamt S., Saez-Rodriguez J., Gilles E.D. Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Syst. Biol. 2007, 1.
16. Laffel L. Ketone bodies: a review of physiology, pathophysiology and application of monitoring to diabetes. Diabetes-Metab. Res. Rev. 1999, 15:412-426.
17. Lee K., Berthiaume F., Stephanopoulos G.N., Yarmush M.L. Profiling of dynamic changes in hypermetabolic livers. Biotechnol. Bioeng. 2003, 83:400-415.
18. Lee K., Berthiaume F., Stephanopoulos G.N., Yarmush D.M., Yarmush M.L. Metabolic flux analysis of postburn hepatic hypermetabolism. Metab. Eng. 2000, 2:312-327.
19. Maskow T., von Stockar U. How reliable are thermodynamic feasibility statements of biochemical pathways?. Biotechn. Bioeng. 2005, 92:223-230.
20. Nolan R.P., Fenley A.P., Lee K. Identification of distributed metabolic objectives in the hypermetabolic liver by flux and energy balance analysis. Metab. Eng. 2006, 8:30-45.
21. Nookaew I., Meechai A., Thammarongtham C., Laoteng K., Ruanglek V., Cheevadhanarak S., Nielsen J., Bhumiratana S. Identification of flux regulation coefficients from elementary flux modes: a systems biology tool for analysis of metabolic networks. Biotechnol. Bioeng. 2007, 97:1535-1549.
22. Orman M.A., Berthiaume F., Androulakis I.P., Ierapetritou M.G. Pathway analysis of liver metabolism under stressed condition. J. Theor. Biol. 2011, 272:131-140.
23. Orman M.A., Arai K., Yarmush M.L., Androulakis I.P., Berthiaume F., Ierapetritou M.G. Metabolic flux determination in perfused livers by mass balance analysis: effect of fasting. Biotechnol. Bioeng. 2010, 107:825-835. 10.1002/bit.22878.
24. Qian H., Beard D.A. Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium. Biophys. Chem. 2005, 114:213-220.
25. Qian H., Beard D.A., Liang S-d. Stoichiometric network theory for nonequilibrium biochemical systems. Eur. J. Biochem. 2003, 270:415-421. 10.1046/j.1432-1033.2003.03357.x.
26. Rutter M.T., Zufall R.A. Pathway length and evolutionary constraint in amino acid biosynthesis. J. Mol. Evol. 2004, 58:218-224.
27. Schilling C.H., Letscher D., Palsson B.O. Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from? A pathway-oriented perspective. J. Theor. Biol. 2000, 203:229-248.
28. Schwartz J.M., Kanehisa M. A quadratic programming approach for decomposing steady-state metabolic flux distributions onto elementary modes. Bioinformatics 2005, 21:204-205.
29. Schwartz J.M., Kanehisa M. Quantitative elementary mode analysis of metabolic pathways: the example of yeast glycolysis. BMC Bioinf. 2006, 7.
30. Schwarz R., Musch P., von Kamp A., Engels B., Schirmer H., Schuster S., Dandekar T. YANA-a software tool for analyzing flux modes, gene-expression and enzyme activities. BMC Bioinf. 2005, 6.
31. Stelling J., Klamt S., Bettenbrock K., Schuster S., Gilles E.D. Metabolic network structure determines key aspects of functionality and regulation. Nature 2002, 420:190-193.
32. Trinh C.T., Wlaschin A., Srienc F. Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism. Appl. Microbiol. Biotechnol. 2009, 81:813-826.
33. Wagner A., Fell D.A. The small world inside large metabolic networks. Proc. R. Soc. London Ser. B 2001, 268:1803-1810.
34. Watford M. Glutamine and glutamate metabolism across the liver sinusoid. J. Nutr. 2000, 130:983S-987S.
35. Wiback S.J., Mahadevan R., Palsson B.Ø. Reconstructing metabolic flux vectors from extreme pathways: defining the [alpha]-spectrum. J. Theor. Biol. 2003, 224:313-324.
36. Xu M., Smith R., Sadhukhan J. Optimization of productivity and thermodynamic performance of metabolic pathways. Ind. Eng. Chem. Res. 2008, 47:5669-5679. 10.1021/ie070352f.
37. Yamaguchi Y., Yu Y.M., Zupke C., Yarmush D.M., Berthiaume F., Tompkins R.G., Yarmush M.L. Effect of burn injury on glucose and nitrogen metabolism in the liver: preliminary studies in a perfused liver system. Surgery 1997, 121:295-303.
38. Yang, H., Roth, C.M., Ierapetritou, M.G., 2011. Analysis of amino acid supplementation effects on hepatocyte cultures using flux balance analysis. OMICS: J. Integr. Biol. doi:10.1089/omi.2010.0070.
39. Yokoyama T., Banta S., Berthiaume F., Nagrath D., Tompkins R.G., Yarmush M.L. Evolution of intrahepatic carbon, nitrogen, and energy metabolism in a d-galactosamine-induced rat liver failure model. Metab. Eng. 2005, 7:88-103.
40. Yoon J., Si Y., Nolan R., Lee K. Modular decomposition of metabolic reaction networks based on flux analysis and pathway projection. Bioinformatics 2007, 23:2433-2440. 10.1093/bioinformatics/btm374.
41. Zhao Q.Y., Kurata H. Maximum entropy decomposition of flux distribution at steady state to elementary modes. J. Biosci. Bioeng. 2009, 107:84-89.