Exploiting biological complexity for strain improvement through systems biology

Nature Biotechnology

Volumn 22, Issue 10, 2004, Pages 1261-1267

  Stephanopoulos, Gregory ^a   Alper, Hal ^a   Moxley, Joel ^a  

^a Massachusetts Institute of Technology Cambridge   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOTECHNOLOGY; CELLS; MOLECULAR BIOLOGY; STRAIN;

BIOLOGICAL COMPLEXITY; BIOLOGICAL RESEARCH; CELLULAR MACHINERY; STRAIN IMPROVEMENT;

GENETIC ENGINEERING;

BIOLOGY; BIOTECHNOLOGY; CELL FUNCTION; DNA MODIFICATION; GENOMICS; HIGH THROUGHPUT SCREENING; MEASUREMENT; METABOLITE; PHENOTYPE; PRIORITY JOURNAL; REVIEW; SYSTEMS BIOLOGY;

ANIMALS; CELL PHYSIOLOGY; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE TARGETING; GENETIC ENGINEERING; HUMANS; MODELS, BIOLOGICAL; MOLECULAR BIOLOGY; SIGNAL TRANSDUCTION; SPECIES SPECIFICITY; SYSTEMS BIOLOGY;

EID: 5044237367     PISSN: 10870156     EISSN: None     Source Type: Journal    
DOI: 10.1038/nbt1016     Document Type: Review

References (37)

1. Hemmi, H. et al. Identification of genes affecting lycopene formation in Escherichia coli transformed with carotenoid biosynthetic genes: candidates for early genes in isoprenoid biosynthesis. J. Biochem. 123, 1088-1096 (1998).
2. Badarinarayana, V. et al. Selection analyses of insertional mutants using subgenic-resolution arrays. Nat. Biotechnol. 19, 1060-1065 (2001).
3. Ideker, T. & Lauffenburger, D. Building with a scaffold: emerging strategies for high to low-level cellular modeling. Trends Biotechnol. 21, 255-262 (2003).
4. Edwards, J.S. & Palsson, B. The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities. Proc. Natl. Acad. Sci. USA 97, 5528-5533 (2000).
5. 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).
6. Stepnanopoulos, G., Aristidou, A. & Nielsen, J. Metabolic Engineering: Principles and Methodologies (Academic Press, San Diego, 1998).
7. Stephanopoulos, G. & Vallino, J.J. Network rigidity and metabolic engineering in metabolite overproduction. Science 252, 1675-1681 (1991).
8. Kacser, H. & Burns, J.A. The control of flux. Symp. Soc. Exp. Biol. 27, 65-104 (1973).
9. Koffas, M.A., Jung, G.Y. & Stephanopoulos, G. Engineering metabolism and product formation in Corynebacterium glutamicum by coordinated gene overexpression. Metab. Eng. 5, 32-41 (2003).
10. Stephanopoulos, G. Metabolic Fluxes and Metabolic Engineering. Metab. Eng. 1, 1-10 (1999).
11. Colon, G.E., Nguyen, T.T., Jetten, M.S., Sinskey, A.J. & Stephanopoulos, G. Production of isoleucine by overexpression of ilvA in a Corynebacterium lactofermenfumthreonine producer. Appl. Microbiol. Biotechnol. 43, 482-488 (1995).
12. Cremer, J. et al. Control of the lysine biosynthesis sequence in Corynebacterium glutamicum as analyzed by overexpression of the individual corresponding genes. Appl. Environ. Microbiol. 57, 1746-1752 (1991).
13. Koffas, M.A., Jung, G.Y., Aon, J.C. & Stephanopoulos, G. Effect of pyruvate carboxylase overexpression on the physiology of Corynebacterium glutamicum. Appl. Environ. Microbiol. 68, 5422-5428 (2002).
14. Berrios-Rivera, S.J., Bennett, G.N. & San, K.-Y. The effect of increasing NADH availability on the redistribution of metabolic fluxes in Escherichia coli chemostat cultures. Metab. Eng. 4, 230-237 (2002).
15. Cameron, D.C. et al. Metabolic engineering of propanediol pathways. Biotechnol. Prog. 14, 116-125(1998).
16. Causey, T.B., Shanmugam, K.T., Yomano, L.P. & Ingram, L.O. Engineering Escherichia coli for efficient conversion of glucose to pyruvate. Proc. Natl. Acad. Sci. USA 101, 2235-2240 (2003).
17. Farmer, W.R. & Liao, J.C. Improving lycopene production in Escherichia coli by engineering metabolic control. Nat. Biotechnol. 18, 533-537 (2000).
18. Fussenegger, M. & Betenbaugh, M.J. Metabolic engineering II. Eukaryotic systems. Biotechnol. Bioeng. 79, 509-531 (2002).
19. Kaup, B. et al. Metabolic engineering of Escherichia coli: construction of an efficient biocatalyst for o-mannitol formation in a whole-cell biotransformation. Appl. Microbiol. Biotechnol. 64, 333-339 (2004).
20. Khosla, C. & Bailey, J.E. Heterologous expression of a bacterial hemoglobin improves the growth properties of recombinant Escherichia coli. Nature 331, 633-635 (1988).
21. Lee, S.Y. & Lee, Y. Metabolic engineering of Escherichia coliior production of enantiomerically pure (R)-(-)-hydroxycarboxylic acids. Appl. Environ. Microbiol. 69, 3421-3426 (2003).
22. Martin, V.J.J. et al. Engineering the mevalonate pathway in Escherichia coli for production of terpenoids. Nat. Biotechnol. 21, 796-802 (2003).
23. Nakamura, C. & Whited, G. Metabolic engineering for the microbial production of 1,3-propanediol. Curr. Opin. Biotechnol. 14, 454-459 (2003).
24. Ostergaard, S. et al. Increasing galactose consumption by Saccharomyces cerevisiae through metabolic engineering of the GAL gene regulatory network. Nat. Biotechnol. 18, 1283-1286 (2000).
25. Snell, K. & Peoples, O. Polyhydroxyalkanoate polymers and their production in transgenic plants. Metab. Eng. 4, 29-40 (2002).
26. Stafford, D.E. et al. Optimizing bioconversion pathways through systems analysis and metabolic engineering. Proc. Natl. Acad. Sci. USA 99, 1801-1806 (2002).
27. Stephanopoulos, G. & Kelleher, J. Biochemistry: how to make a superior cell. Science 292, 2024-2025 (2001).
28. Viswanathan, K. et al. Engineering sialic acid synthetic ability into insect cells: identifying metabolic bottlenecks and devising strategies to overcome them. Biochemistry 42, 15215-15225 (2003).
29. Xue, Y. & Sherman, D.H. Alternative modular polyketide synthase expression controls macrolactone structure. Nature 403, 571-575 (2000).
30. Askenazi, M. et al. Integrating transcriptional and metabolite profiles to direct the engineering of lovastatin-producing fungal strains. Nat. Biotechnol. 21, 150-156 (2003).
31. von Mering, C. et al. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417, 399-403 (2002).
32. Lee, T.I. et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799-804 (2002).
33. Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498-2504 (2003).
34. Ideker, T. et al. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292, 929-934 (2001).
35. Ideker, T., Ozier, O., Schwikowski, B. & Siegel, A.F. Discovering regulatory and signaling circuits in molecular interaction networks. Bioinformatics 18 (suppl. 1) 233-240 (2002).
36. Stephanopoulos, G., Hwang, D., Schmitt, W.A., Misra, J. & Stephanopoulos, G. Mapping physiological states from microarray expression measurements. Bioinformatics 18, 1054-1063 (2002).
37. Allen, J. et al. High-throughput classification of yeast mutants for functional genomics using metabolic footprinting. Nat. Biotechnol. 21, 692-696 (2003).