Progress in the applications of flux analysis of metabolic networks

Chinese Science Bulletin

Volumn 55, Issue 22, 2010, Pages 2315-2322

  Chen, Qi ^a   Wang, Zhuo ^a   Wei, Dong Qing ^a  

^a SHANGHAI JIAO TONG UNIVERSITY   (China)

Author keywords

flux balance analysis; gene regulation; metabolic network; minimization of metabolic adjustment; topological property

Indexed keywords

EID: 77955546535     PISSN: 10016538     EISSN: 18619541     Source Type: Journal    
DOI: 10.1007/s11434-010-3022-x     Document Type: Review

References (41)

1. Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res, 2000, 28: 27-30.
2. Schilling C H, Edwards J S, Palsson B O. Toward metabolic phenomics: Analysis of genomic data using flux balances. Biotechnol Prog, 1999, 15: 288-295.
3. Schilling C H, Schuster S, Palsson B O, et al. Metabolic pathway analysis: Basic concepts and scientific applications in the post-genomic era. Biotechnol Prog, 1999, 15: 296-303.
4. Schuster S, Dandekar T, Fell D A. Detection of elementary flux modes in biochemical networks: A promising tool for pathway analysis and metabolic engineering. Trends Biotechnol, 1999, 17: 53-60.
5. Schuster S, Fell D A, Dandekar T. A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat Biotechnol, 2000, 18: 326-332.
6. Schuster S, Hilgetag C, Woods J H, et al. Exploring the pathway structure of metabolism: Decomposition into subnetworks and application to Mycoplasma pneumoniae. Bioinformatics, 2002, 18: 351-361.
7. Schilling C H, Edwards J S, Letscher D, et al. Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems. Biotechnol Bioeng, 2000, 71: 286-306.
8. 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.
9. Jeong H, Tombor B, Albert R, et al. The large-scale organization of metabolic networks. Nature, 2000, 407: 651-654.
10. Wagner A, Fell D A. The small world inside large metabolic networks. Proc Biol Sci, 2001, 268: 1803-1810.
11. Varner J, Ramdrishna D. Metabolic engineering from a cybernetic perspective. 1. Theoretical preliminaries. Biotechnol Prog, 1999, 15: 407-425.
12. Fell D. Understanding the Control of Metabolism. London: Porland Press, 1996.
13. Kauffman K J, Prakash P, Edwards J S. Advances in flux balance analysis. Curr Opin Biotechnol, 2003, 14: 491-496.
14. Segre D, Vitkup D, Church G M. Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci USA, 2002, 99: 15112-15117.
15. Papp B, Pál C, Hurst L D. Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast. Nature, 2004, 429: 661-664.
16. Alper H, Jin Y S, Moxley J F, et al. Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli. Metab Eng, 2005, 7: 155-164.
17. Lee J M, Gianchandani E P, Papin J A. Flux balance analysis in the era of metabolomics. Brief Bioinform, 2006, 7: 140-150.
18. Shlomi T, Berkman O, Ruppin E. Regulatory on/off minimization of metabolic flux changes after genetic perturbations. Proc Natl Acad Sci USA, 2005, 102: 7695-700.
19. Mahadevan R, Edwards J S, Doyle F J. Dynamic flux balance analysis of diauxic growth in Escherichia coli. Biophys J, 2002, 83: 1331-1340.
20. Uygun K, Matthew H W T, Huang Y L. DFBA-LQR: An optimal control approach to flux balance analysis. Ind Eng Chem Res, 2006, 45: 8554-8564.
21. Klamt S, Stelling J, Ginkel M, et al. FluxAnalyzer: Exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps. Bioinformatics, 2003, 19: 261-269.
22. Segre D, Zucker J, Katz J, et al. From annotated genomes to metabolic flux models and kinetic parameter fitting. OMICS, 2003, 7: 301-316.
23. Price N D, Reed J L, Palsson B Ø. Genome-scale models of microbial cells: Evaluating the consequences of constraints. Nat Rev Microbiol, 2004, 2: 886-897.
24. Becker S A, Feist A M, Mo M L, et al. Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox. Nat Protoc, 2007, 2: 727-738.
25. Luo R Y, Liao S, Zeng S Q. FluxExplorer: A general platform for modeling and analyses of metabolic networks based on stoichiometry. Chinese Sci Bull, 2006, 51: 689-696.
26. Lee S Y, Lee D-Y, Hong S H, et al. MetaFluxNet, a program package for metabolic pathway construction and analysis, and its use in large-scale metabolic flux analysis of Escherichia coli. Genome Inform, 2003, 14: 23-33.
27. Raman K, Chandra N. Pathway Analyser: A systems biology tool for flux analysis of metabolic pathways. Nat Prec, 2008, doi: 10. 1038/npre. 2008. 1868. 1.
28. Covert M W, Schilling C H, Palsson B O. Regulation of gene expression in flux balance models of metabolism. J Theor Biol, 2001, 213: 73-88.
29. Åkesson M, Förster J, Nielsena J. Integration of gene expression data into genome-scale metabolic models. Metab Eng, 2004, 6: 285-293.
30. Pascale D-L, Mickel L A J, Jean-Marc D, et al. Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae. J Biol Chem, 2004, 279: 9125-9138.
31. Vitkup D, Kharchenko P, Wagner A. Influence of metabolic networks structure and function on enzyme evolution. Genome Biol, 2006, 7: R39.
32. Raman K, Rajagopalan P, Chandra N. Flux balance analysis of mycolic acid pathway: Targets for anti-tubercular drugs. PLoS Comput Biol, 2005, 1: 0349-0358.
33. Duarte N C, Becker S A, Jamshidi N, et al. Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci USA, 2007, 104: 1777-1782.
34. Shlomi T, Cabili M N, Herrgärd M J, et al. Network-based prediction of human tissue-specific metabolism. Nat Biotechnol, 2008, 26: 1003-1010.
35. Zhou Q H, Shiu S C K, Pal S K. New results on energy balance analysis of metabolic networks. PReMI, 2007, LNCS4815: 433-438.
36. Xu Z X, Sun X. Constrain-based analysis of gene deletion on the metabolic flux redistribution of Saccharomyces cerevisiae. J Biomed Sci Eng, 2008, 1: 121-126.
37. Zhou Q H, Wang D, Xiong M M. Dynamic flux balance analysis of metabolic networks using the penalty function methods. SMC IEEE, 2007: 3594-3599.
38. Luo R Y, Liao S, Tao G Y, et al. Dynamic analysis of optimality in myocardial energy metabolism under normal and ischemic conditions. Mol Syst Biol, 2006, doi: 2006. 0031.
39. Luo R Y, Wei H B, Ye L. Photosynthetic metabolism of C3 plants shows highly cooperative regulation under changing environments: A systems biological analysis. Proc Natl Acad Sci USA, 2009, 106: 847-852.
40. Wunderlichi Z, Mirnyy L A. Using the topology of metabolic networks to predict viability of mutant strains. Biophys J, 2006, 91: 2304-2311.
41. Ao P, Lee L W, Lidstrom M E, et al. Towards kinetic modeling of global metabolic networks: Methylobacterium extorquens AM1 growth as validation. Chin J Biotech, 2008, 24: 980-994.