Computing complex metabolic intervention strategies using constrained minimal cut sets

Metabolic Engineering

Volumn 13, Issue 2, 2011, Pages 204-213

  Hädicke, Oliver ^a,b   Klamt, Steffen ^a,b  

^a MAX PLANCK INSTITUTE FOR DYNAMICS OF COMPLEX TECHNICAL SYSTEMS   (Germany)

^b Magdeburg Centre for Systems Biology MaCS   (Germany)

Author keywords

Elementary modes; Ethanol production; Metabolic engineering; Minimal cut sets; Strain optimization; Targeted modification

Indexed keywords

ELEMENTARY MODE; ETHANOL PRODUCTION; METABOLIC ENGINEERING; MINIMAL CUT SETS; STRAIN OPTIMIZATION; TARGETED MODIFICATION;

ESCHERICHIA COLI; ETHANOL; GENES; OPTIMIZATION;

METABOLISM;

ALCOHOL PRODUCTION; ANALYTIC METHOD; ARTICLE; BIOMASS; ESCHERICHIA COLI; GENE DELETION; METABOLIC ENGINEERING; MINIMAL CUT SET; PRIORITY JOURNAL;

ALGORITHMS; COMPUTER SIMULATION; ESCHERICHIA COLI; ETHANOL; GENE DELETION; GENE KNOCKOUT TECHNIQUES; GENETIC ENGINEERING; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL;

ESCHERICHIA COLI;

EID: 79952103372     PISSN: 10967176     EISSN: 10967184     Source Type: Journal    
DOI: 10.1016/j.ymben.2010.12.004     Document Type: Article

References (33)

1. Behre J., Wilhelm T., von Kamp A., Ruppin E., Schuster S. Structural robustness of metabolic networks with respect to multiple knockouts. J. Theor. Biol. 2008, 252:433-441.
2. Berge C. Hypergraphs: Combinatorics of Finite Sets 1989, North-Holland Mathematical Library, Amsterdam.
3. Bordel S., Nielsen J. Identification of flux control in metabolic networks using non-equilibrium thermodynamics. Metab. Eng. 2010, 12:369-377.
4. Burgard A.P., Pharkya P., Maranas C.D. Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol. Bioeng. 2003, 84:647-657.
5. Carlson R., Fell D., Srienc F. Metabolic pathway analysis of a recombinant yeast for rational strain development. Biotechnol. Bioeng. 2002, 79:121-134.
6. Edwards J.S., Palsson B.O. Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions. BMC Bioinformatics. 2000, 1:1.
7. Fong S.S., Burgard A.P., Herring C.D., Knight E.M., Blattner F.R., Maranas C.D., Palsson B.O. In silico design and adaptive evolution of Escherichia coli for production of lactic acid. Biotechnol. Bioeng. 2005, 91:643-648.
8. Hädicke O., Klamt S. CASOP: A computational approach for strain optimization aiming at high productivity. J. Biotechnol. 2010, 147:88-101.
9. Haus U.-U., Klamt S., Stephen T. Computing knock-out strategies in metabolic networks. J. Comput. Biol. 2008, 15:259-268.
10. Ibarra R.U., Edwards J.S., Palsson B.O. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 2002, 420:186-189.
11. Imielinski M., Belta C. Exploiting the pathway structure of metabolism to reveal high-order epistasis. BMC Syst. Biol. 2008, 2:40.
12. Jantama K., Haupt M.J., Svoronos S.A., Zhang X., Moore J.C., Shanmugam K.T., Ingram L.O. Combining metabolic engineering and metabolic evolution to develop nonrecombinant strains of Escherichia coli C that produce succinate and malate. Biotechnol. Bioeng. 2008, 99:1140-1153.
13. Kaleta, C., de Figueiredo, L. F., Behre, J., Schuster, S., 2009. EFMEvolver: Computing elementary flux modes in genome-scale metabolic networks. In: Grosse, I., Neumann, S., Posch, S., Schreiber, F., Stadler, P. (Eds.), Lecture Notes in Informatics-Proceedings, Vol. P-157, Gesellschaft für Informatik, Bonn, pp. 179-189.
14. Kim J., Reed J.L. OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains. BMC Syst. Biol. 2010, 4:53.
15. Klamt S. Generalized concept of minimal cut sets in biochemical networks. BioSystems. 2006, 83:233-247.
16. Klamt S., Gilles E.D. Minimal cut sets in biochemical reaction networks. Bioinformatics. 2004, 20:226-234.
17. Klamt S., Saez-Rodriguez J., Gilles E.D. Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Syst. Biol. 2007, 1:2.
18. Oberhardt M.A., Palsson B.O., Papin J.A. Applications of genome-scale metabolic reconstructions. Mol. Syst. Biol. 2009, 5:320.
19. Patil K.R., Rocha I., Förster J., Nielsen J. Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinformatics. 2005, 6:308.
20. Pharkya P., Burgard A.P., Maranas C.D. OptStrain: A computational framework for redesign of microbial production systems. Genome Res. 2004, 14:2367-2376.
21. Pharkya P., Maranas C.D. An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems. Metab. Eng. 2006, 8:1-13.
22. 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.
23. Schuster S., Hilgetag S. On elementary flux modes in biochemical reaction systems at steady state. J. Biol. Syst. 1994, 165-168.
24. Schuster S, Pfeiffer T, Fell DA. Is maximization of molar yield in metabolic networks favoured by evolution?. J. Theor. Biol. 2008, 252:497-504.
25. Suthers P.F., Zomorrodi A., Maranas C.D. Genome-scale gene/reaction essentiality and synthetic lethality analysis. Mol. Syst. Biol. 2009, 5:301.
26. Tepper N., Shlomi T. Predicting metabolic engineering knockout strategies for chemical production: Accounting for competing pathways. Bioinformatics. 2010, 26:536-543.
27. Terzer M., Stelling J. Large-scale computation of elementary flux modes with bit pattern trees. Bioinformatics. 2008, 24:2229-2235.
28. Trinh C.T., Carlson R., Wlaschin A., Srienc F. Design, construction and performance of the most efficient biomass producing E. coli. bacterium. Metab Eng. 2006, 8:628-638.
29. Trinh C.T., Srienc F. Metabolic engineering of Escherichia coli for efficient conversion of glycerol to ethanol. Appl. Environ. Microbiol. 2009, 75:6696-6705.
30. Trinh C.T., Unrean P., Srienc F. Minimal Escherichia coli cell for the most efficient production of ethanol from hexoses and pentoses. Appl. Environ. Microbiol. 2008, 74:3634-3643.
31. Trinh C.T., Wlaschin A., Srienc F. Elementary mode analysis: A useful metabolic pathway analysis tool for characterizing cellular metabolism. Appl. Microbiol. Biotechnol. 2009, 81:813-826.
32. Unrean P., Trinh C.T., Srienc F. Rational design and construction of an efficient E. coli. for production of diapolycopendioic acid. Metab. Eng. 2010, 12:112-122.
33. Yazdani S.S., Gonzalez R. Engineering Escherichia coli for the efficient conversion of glycerol to ethanol and co-products. Metab. Eng. 2008, 10:340-351.