Using the topology of metabolic networks to predict viability of mutant strains

Biophysical Journal

Volumn 91, Issue 6, 2006, Pages 2304-2311

  Wunderlich, Zeba ^a   Mirny, Leonid A ^b,c  

^a HARVARD UNIVERSITY   (United States)

^b HARVARD MIT DIVISION OF HEALTH SCIENCES AND TECHNOLOGY   (United States)

^c MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL METABOLISM; BACTERIAL STRAIN; BACTERIUM MUTANT; CELL VIABILITY; CONTROLLED STUDY; ESCHERICHIA COLI; METABOLIC REGULATION; METABOLISM; NONHUMAN; SACCHAROMYCES CEREVISIAE; STOCHASTIC MODEL; YEAST;

ESCHERICHIA COLI; SACCHAROMYCES CEREVISIAE;

EID: 33748448689     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.105.080572     Document Type: Article

References (28)

1. Varma, A., and B. O. Palsson. 1994. Metabolic flux balancing - basic concepts, scientific and practical use. Biotechnology. 12:994-998.
2. Edwards, J. S., and B. O. Palsson. 1999. Systems properties of the Haemophilus influenzae Rd metabolic genotype. J. Biol. Chem. 274:17410-17416.
3. Edwards, J. S., and B. O. Palsson. 2000. Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions. BMC Bioinformatics. 1:1.
4. Edwards, J. S., and B. O. Palsson. 2000. The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc. Natl. Acad. Sci. USA. 97:5528-5533.
5. Forster, J., I. Famili, P. Fu, B. O. Palsson, and J. Nielsen. 2003. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res. 13:244-253.
6. Reed, J. L., T. D. Vo, C. H. Schilling, and B. O. Palsson. 2003. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol. 4:R54.
7. Burgard, A. P., and C. D. Maranas. 2001. Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions. Biotechnol. Bioeng. 74:364-375.
8. Duarte, N. C., M. J. Herrgard, and B. O. Palsson. 2004. Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res. 14:1298-1309.
9. Badarinarayana, V., P. W. Estep 3rd, J. Shendure, J. Edwards, S. Tavazoie, F. Lam, and G. M. Church. 2001. Selection analyses of insertional mutants using subgenic-resolution arrays. Nat. Biotechnol. 19:1060-1065.
10. Segre, D., D. Vitkup, and G. M. Church. 2002. Analysis of optimality in natural and perturbed metabolic networks. Proc. Natl. Acad. Sci. USA. 99:15112-15117.
11. Stelling, J., S. Klamt, K. Bettenbrock, S. Schuster, and E. D. Gilles. 2002. Metabolic network structure determines key aspects of functionality and regulation. Nature. 420:190-193.
12. Klamt, S., and J. Stelling. 2002. Combinatorial complexity of pathway analysis in metabolic networks. Mol. Biol. Rep. 29:233-236.
13. Giaever, G., A. M. Chu, L. Ni, C. Connelly, L. Riles, S. Veronneau, S. Dow, A. Lucau-Danila, K. Anderson, B. Andre, A. P. Arkin, A. Astromoff, et al. 2002. Functional profiling of the Saccharomyces cerevisiae genome. Nature. 418:387-391.
14. Steinmetz, L. M., C. Scharfe, A. M. Deutschbauer, D. Mokranjac, Z. S. Herman, T. Jones, A. M. Chu, G. Giaever, H. Prokisch, P. J. Oefner, and R. W. Davis. 2002. Systematic screen for human disease genes in yeast. Nat. Genet. 31:400-404.
15. Albert, R., H. Jeong, and A. L. Barabasi. 2000. Error and attack tolerance of complex networks. Nature. 406:378-382.
16. Jeong, H., S. P. Mason, A. L. Barabasi, and Z. N. Oltvai. 2001. Lethality and centrality in protein networks. Nature. 411:41-42.
17. Myatt, G. J. 1994. Computer aided estimation of synthetic accessibility. PhD Thesis. University of Leeds, Leeds, UK.
18. Handorf, T., O. Ebenhoh, and R. Heinrich. 2005. Expanding metabolic networks: scopes of compounds, robustness, and evolution. J. Mol. Evol. 61:498-512.
19. Neidhardt, F. C., and H. E. Umbarger. 1996. Chemical composition of Escherichia coli. In Escherichia coli and Salmonella: Cellular and Molecular Biology. F. C. Neidhardt and R. Curtis, editors. ASM Press, Washington, DC. 13-16.
20. Romero, P. R., and P. Karp. 2001. Nutrient-related analysis of pathway/genome databases. Pac. Symp. Biocomput. 471-482.
21. Gerdes, S. Y., M. D. Scholle, J. W. Campbell, G. Balazsi, E. Ravasz, M. D. Daugherty, A. L. Somera, N. C. Kyrpides, I. Anderson, M. S. Gelfand, A. Bhattacharya, V. Kapatral, et al. 2003. Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J. Bacteriol. 185:5673-5684.
22. Newman, M. E. 2001. Scientific collaboration networks. I. Network construction and fundamental results. Phys. Rev. E. 64:016131.
23. Newman, M. E. 2001. Scientific collaboration networks. II. Shortest paths, weighted networks, and centrality. Phys. Rev. E. 64:016132.
24. Papp, B., C. Pal, and L. D. Hurst. 2004. Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast. Nature. 429:661-664.
25. Jeong, H., B. Tombor, R. Albert, Z. N. Oltvai, and A. L. Barabasi. 2000. The large-scale organization of metabolic networks. Nature. 407:651-654.
26. Ma, H., and A. P. Zeng. 2003. Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics. 19:270-277.
27. 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast. Genome Biol. 6:R49.
28. Mahadevan, R., and B. O. Palsson. 2005. Properties of metabolic networks: structure versus function. Biophys. J. 88:L07-L09.