Large-scale in vivo flux analysis shows rigidity and suboptimal performance of Bacillus subtilis metabolism

Nature Genetics

Volumn 37, Issue 6, 2005, Pages 636-640

  Fischer, Eliane ^a   Sauer, Uwe ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACILLUS SUBTILIS; BACTERIAL GROWTH; BACTERIAL METABOLISM; BACTERIUM MUTANT; IN VIVO STUDY; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; QUALITATIVE ANALYSIS; STOICHIOMETRY; THEORY;

ACETYL COENZYME A; ADAPTATION, PHYSIOLOGICAL; BACILLUS SUBTILIS; BIOMASS; FEEDBACK; GLUCOSE; MUTATION; REGULATORY SEQUENCES, NUCLEIC ACID;

BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS); BACTERIUM SUBTILIS;

EID: 20044375201     PISSN: 10614036     EISSN: None     Source Type: Journal    
DOI: 10.1038/ng1555     Document Type: Article

References (30)

1. Arita, M. The metabolic world of Escherichia coli is not small. Proc. Natl. Acad. Sci. USA 101, 1543-1547 (2004).
2. Barabasi, A.L. & Oltvai, Z.N. Network biology: understanding the cell's functional organization. Nat. Rev. Genet. 5, 101-113 (2004).
3. Stelling, J., Klamt, S., Bettenbrock, K., Schuster, S. & Gilles, E.D. Metabolic network structure determines key aspects of functionality and regulation. Nature 420, 190-193 (2002).
4. Almaas, E., Kovacs, B., Vicsek, T., Oltvai, Z.N. & Barabasi, A.L. Global organization of metabolic fluxes in the bacterium Escherichia coli. Nature 427, 839-843 (2004).
5. Burgard, A.P., Nikolaev, E.V., Schilling, C.H. & Maranas, C.D. Flux coupling analysis of genome-scale metabolic network reconstructions. Genome Res. 14, 301-312 (2004).
6. Papin, J.A. et al. Comparison of network-based pathway analysis methods. Trends Biotechnol. 22, 400-405 (2004).
7. Segre, D., Vitkup, D. & Church, G.M. Analysis of optimality in natural and perturbed metabolic networks. Proc. Natl. Acad. Sci. USA 99, 15112-15117 (2002).
8. Edwards, J.S., Ibarra, R.U. & Palsson, B.O. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat. Biotechnol. 19, 125-130 (2001).
9. Hellerstein, M.K. In vivo measurement of fluxes through metabolic pathways: the missing link in functional genomics and pharmaceutical research. Annu. Rev. Nutr. 23, 379-402 (2003).
10. Sauer, U. High-throughput phenomics: experimental methods for mapping fluxomes. Curr. Opin. Biotechnol. 15, 58-63 (2004).
11. Csete, M.E. & Doyle, J. Bow ties, metabolism and disease. Trends Biotechnol. 22, 446-450 (2004).
12. Fischer, E. & Sauer, U. A novel metabolic cycle catalyzes glucose oxidation and anaplerosis in hungry Escherichia coli. J. Biol. Chem. 278, 46446-46451 (2003).
13. Fischer, E. & Sauer, U. Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism using GC-MS. Eur. J. Biochem. 270, 880-891 (2003).
14. 13C-constraints. Anal. Biochem. 325, 308-316 (2004).
15. Duetz, W.A. et al. Methods for intense aeration, growth, storage, and replication of bacterial strains in microtiter plates. Appl. Environ. Microbiol. 66, 2641-2646 (2000).
16. Zamboni, N. & Sauer, U. Knockout of the high-coupling cytochrome aa3 oxidase reduces TCA cycle fluxes in Bacillus subtilis. FEMS Microbiol. Lett. 226, 121-126 (2003).
17. Zamboni, N. et al. The Bacillus subtilis yqjl gene encodes the NADP-dependent 6-P-gluconate dehydrogenase in the pentose phosphate pathway. J. Bacteriol. 186, 4528-4534 (2004).
18. Msadek, T. When going gets tough: survival strategies and environmental signaling networks in Bacillus subtilis. Trends Microbiol. 7, 201-207 (1999).
19. Servant, P., Le Coq, D. & Aymerich, S. CcpN (YqzB), a regulator for CcpA-independent catabolite repression of Bacillus subtilis gluconeogenic genes. Mol. Microbiol. 55, 1435-1451 (2005).
20. Sauer, U. et al. Metabolic fluxes in riboflavin-producing Bacillus subtilis. Nat. Biotechnol. 15, 448-452 (1997).
21. Moritz, B., Striegel, K., De Graaf, A.A. & Sahm, H. Kinetic properties of the glucose-6-phosphate and 6-phosphogluconate dehydrogenases from Corynebacterium glutamicum and their application for predicting pentose phosphate pathway flux in vivo. Eur. J. Biochem. 267, 3442-3452 (2000).
22. Zamboni, N. et al. Transient expression and flux changes during a shift from high to low riboflavin production in continuous cultures of Bacillus subtilis. Biotechnol. Bioeng. 89, 219-232 (2005).
23. Dauner, M., Storni, T. & Sauer, U. Bacillus subtilis metabolism and energetics in carbon-limited and carbon-excess chemostat culture. J. Bacteriol. 183, 7308-7317 (2001).
24. Sonenshein, A.L., Hoch, J.A. & Losick, R. Bacillus subtilis and its closest relatives. From genes to cells. (ASM Press, Washington, DC, 2002).
25. Pfeiffer, T., Schuster, S. & Bonhoeffer, S. Cooperation and competition in the evolution of ATP-producing pathways. Science 292, 504-507 (2001).
26. Giaever, G. et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature 418, 387-391 (2002).
27. Ibarra, R.U., Edwards, J.S. & Palsson, B.O. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 420, 186-189 (2002).
28. Nudler, E. & Mironov, A.S. The riboswitch control of bacterial metabolism. Trends Biochem. Sci. 29, 11-17 (2004).
29. Stelling, J., Sauer, U., Szallasi, Z., Doyle III, F.J. & Doyle, J. Robustness of cellular functions. Cell 118, 675-685 (2004).
30. Dauner, M. & Sauer, U. Stoichiometric growth model for riboflavin-producing Bacillus subtilis. Biotechnol. Bioeng. 76, 132-143 (2001).