OptKnock: A Bilevel Programming Framework for Identifying Gene Knockout Strategies for Microbial Strain Optimization

Biotechnology and Bioengineering

Volumn 84, Issue 6, 2003, Pages 647-657

  Burgard, Anthony P ^a   Pharkya, Priti ^a   Maranas, Costas D ^a  

^a The Pennsylvania State University   (United States)

Author keywords

Bilevel programming; Genome scale stoichiometric models; Strain optimization

Indexed keywords

BIOMASS; CARBON; GENES; MICROORGANISMS; STOICHIOMETRY;

GENOME-SCALE MODELS;

BIOTECHNOLOGY;

ADAPTATION; ARTICLE; BACTERIAL GROWTH; BACTERIAL STRAIN; BIOMASS; ENERGY YIELD; ESCHERICHIA COLI; GENE DELETION; GENE IDENTIFICATION; GENETIC MANIPULATION; GENOME; KNOCKOUT GENE; MATHEMATICAL ANALYSIS; MUTANT; NONHUMAN; OPTKNOCK COMPUTATIONAL PROCEDURE; OXIDATION; REACTION ANALYSIS; REDUCTION; STOICHIOMETRY;

ALGORITHMS; COMBINATORIAL CHEMISTRY TECHNIQUES; COMPUTER SIMULATION; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; GENE SILENCING; GENETIC ENHANCEMENT; LACTIC ACID; MODELS, BIOLOGICAL; MULTIENZYME COMPLEXES; PROPYLENE GLYCOLS; RECOMBINANT PROTEINS; SOFTWARE; SUCCINIC ACID;

EID: 0242487787     PISSN: 00063592     EISSN: None     Source Type: Journal    
DOI: 10.1002/bit.10803     Document Type: Article

References (43)

1. Badarinarayana V, Estep PW 3rd, Shendure J, Edwards J, Tavazoie S, Lam F, Church GM. 2001. Selection analyses of insertional mutants using subgenic-resolution arrays. Nat Biotechnol 19:1060-1065.
2. Bard JF. 1998. Practical bilevel optimization: algorithms and applications. Dordrecht: Kluwer Academic.
3. Biebl H, Menzel K, Zeng AP, Deckwer WD. 1999. Microbial production of 1,3-propanediol. Appl Environ Microbiol 52:289-297.
4. Burgard AP, Maranas CD. 2001. Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions. Biotechnol Bioeng 74:364-375.
5. Burgard AP, Maranas CD. 2003. Optimization-based framework for inferring and testing hypothesized metabolic objective functions. Biotechnol Bioeng 82:670-677.
6. Burgard AP, Vaidyaraman S, Maranas CD. 2001. Minimal reaction sets for Escherichia coli metabolism under different growth requirements and uptake environments. Biotechnol Prog 17:791-797.
7. Cameron DC, Altaras NE, Hoffman ML, Shaw AJ. 1998. Metabolic engineering of propanediol pathways. Biotechnol Prog 14:116-125.
8. Compagno C, Boschi F, Ranzi BM. 1996. Glycerol production in a triose phosphate isomerase deficient mutant of Saccharomyces cerevisiae. Biotechnol Prog 12:591-595.
9. Covert MW, Palsson BO. 2002. Transcriptional regulation in constraints-based metabolic models of Escherichia coli. J Biol Chem 277:28058-28064.
10. Covert MW, Schilling CH, Palsson BO. 2001. Regulation of gene expression in flux balance models of metabolism. J Theor Biol 213:73-88.
11. Datta R, Tsai S, Bonsignore P, Moon S, Frank JR. 1995. Technological and economic potential of poly(lactic acid) and lactic acid derivatives. FEMS Microbiol Rev 16:221-231.
12. Edwards JS, Palsson BO. 2000. The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc Natl Acad Sci USA 97:5528-5533.
13. Edwards JS, Ibarra RU, Palsson BO. 2001. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotechnol 19:125-130.
14. Forster J, Famili I, Fu PC, Palsson B, Nielsen J. 2003. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res 13:244-253.
15. Gupta S, Clark DP. 1989. Escherichia coli derivatives lacking both alcohol dehydrogenase and phosphotransacetylase grow anaerobically by lactate fermentation. J Bacteriol 171:3650-3655.
16. Hartlep M, Hussmann W, Prayitno N, Meynial-Salles I, Zeng AP. 2002. Study of two-stage processes for the microbial production of 1,3-propanediol from glucose. Appl Microbiol Biotechnol 60:60-66.
17. Hatzimanikatis V, Emmerling M, Sauer U, Bailey JE. 1998. Application of mathematical tools for metabolic design of microbial ethanol production. Biotechnol Bioeng 58:154-161.
18. Heinrich R, Rapoport TA. 1974. A linear steady-state treatment of enzymatic chains. Eur J Biochem 41:89-95.
19. Hugler M, Menendez C, Schagger H, Fuchs G. 2002. Malonyl-coenzyme A reductase from Chloroflexus aurantiacus, a key enzyme of the 3-hydroxypropionate cycle for autotrophic CO(2) fixation. J Bacteriol 184:2404-2410.
20. Ibarra RU, Edwards JS, Palsson BO. 2002. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 420:186-189.
21. Ignizio JP, Cavalier TM. 1994. Linear programming. Englewood Cliffs, NJ: Prentice Hall.
22. Kacser H, Burns JA. 1973. The control of flux. Symp Soc Exp Biol 27:65-104.
23. Kompala DS, Ramkrishna D, Tsao GT. 1984. Cybernetic modeling of microbial growth on multiple substrates. Biotechnol Bioeng 26:1272-1281.
24. Majewski RA, Domach MM. 1990. Simple constrained optimization view of acetate overflow in Escherichia coli. Biotechnol Bioeng 35:732-738.
25. Menendez C, Bauer Z, Huber H, Gad'on N, Stetter KO, Fuchs G. 1999. Presence of acetyl coenzyme A (CoA) carboxylase and propionyl-CoA carboxylase in autotrophic Crenarchaeota and indication for operation of a 3-hydroxypropionate cycle in autotrophic carbon fixation. J Bacteriol 181:1088-1098.
26. Nakamura CE. 2002. Production of 1,3-propanediol by E. coli. Metab Eng IV Conf: Tuscany, Italy.
27. Neidhardt FC, Curtiss R. 1996. Escherichia coli and Salmonella: cellular and molecular biology. Washington, DC: ASM Press.
28. Papin JA, Price ND, Wiback SJ, Fell DA, Palsson B. 2003. Metabolic pathways in the post-genome era. Trends Biochem Sci 28:250-258.
29. Price ND, Papin JA, Schilling CH, Palsson B. 2003. Genome-scale microbial in silico models: the constraints-based approach. Trends Biotechnol 21:162-169
30. Ramakrishna R, Ramakrishna D, Konopka AE. 1996. Cybernetic modeling of growth in mixed, substitutable substrate environments: preferential and simultaneous utilization. Biotechnol Bioeng 52:141-151.
31. Ramakrishna R, Edwards JS, McCulloch A, Palsson BO. 2001. Flux-balance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraints. Am J Physiol Regul Integr Comp Physiol 280:R695-704.
32. Schilling CH, Palsson BO. 2000. Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis. J Theor Biol 203:249-283.
33. Schilling CH, Covert MW, Famili I, Church GM, Edwards JS, Palsson BO. 2002. Genome-scale metabolic model of Helicobacter pylori 26695. J Bacteriol 184:4582-4593.
34. Segre D, Vitkup D, Church GM. 2002. Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci USA 99:15112-15117.
35. Stephanopoulos G, Aristidou AA, Nielsen J. 1998. Metabolic engineering: principles and methodologies. San Diego: Academic Press.
36. Stols L, Donnelly MI. 1997. Production of succinic acid through overexpression of NAD(+)-dependent malic enzyme in an Escherichia coli mutant. Appl Environ Microbiol 63:2695-2701.
37. Varma A, Palsson BO. 1993. Metabolic capabilities of Escherichia coli. II. Optimal growth patterns. J Theor Biol 165:503-522.
38. Varma A, Palsson BO. 1994. Metabolic flux balancing: basic concepts, scientific and practical use. Bio/Technology 12:994-998.
39. Varma A, Boesch BW, Palsson BO. 1993. Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates. Appl Environ Microbiol 59:2465-2473.
40. Varner J, Ramakrishna D. 1999. Metabolic engineering from a cybernetic perspective. 1. Theoretical preliminaries. Biotechnol Prog 15:407-425.
41. Zeikus JG, Jain MK, Elankovan P. 1999. Biotechnology of succinate acid production and markets for derived industrial products. Appl Microbiol Biotechnol 51:545-552.
42. Zeng AP, Biebl H. 2002. Bulk chemicals from biotechnology: the case of 1,3-propanediol production and the new trends. Adv Biochem Eng Biotechnol 74:239-259.
43. Zhu MM, Lawman PD, Cameron DC. 2002. Improving 1,3-propanediol production from glycerol in a metabolically engineered Escherichia coli by reducing accumulation of sn-glycerol-3-phosphate. Biotechnol Prog 18:694-699.