In silico strategy to rationally engineer metabolite production: A case study for threonine in Escherichia coli

Biotechnology and Bioengineering

Volumn 103, Issue 3, 2009, Pages 609-620

  Rodríguez Prados, Juan Carlos ^a,b   De Atauri, Pedro ^a   Maury, Jerôme ^b   Ortega, Fernando ^c   Portais, Jean Charles ^b   Chassagnole, Christophe ^b   Acerenza, Luis ^d   Lindley, Nic D ^b   Cascante, Marta ^a  

^a UNIVERSITY OF BARCELONA   (Spain)

^b UMR792 INGÉNIERIE DES SYSTÈMES BIOLOGIQUES ET DES PROCÉDÉS   (France)

^c UNIVERSITY OF BIRMINGHAM   (United Kingdom)

^d UNIVERSIDAD DE LA REPÚBLICA   (Uruguay)

Author keywords

Metabolic control analysis; Metabolic engineering; Threonine synthesis; Universal method

Indexed keywords

CELLULAR PROCESS; ECONOMIC INTERESTS; ENZYME CONCENTRATIONS; IN-SILICO; METABOLIC CONTROL ANALYSIS; METABOLIC ENGINEERING; METABOLIC PATHWAYS; METABOLITE CONCENTRATIONS; METABOLITE PRODUCTION; PYRUVATE KINASE; THREONINE SYNTHESIS; UNIVERSAL METHOD;

BIOMOLECULES; ESCHERICHIA COLI; GENETIC ENGINEERING; LEAD; METABOLITES; SENSITIVITY ANALYSIS;

METABOLISM;

PYRUVATE KINASE; THREONINE; ESCHERICHIA COLI PROTEIN;

AMINO ACID SYNTHESIS; ARTICLE; BACTERIAL METABOLISM; ESCHERICHIA COLI; GENETIC ENGINEERING; METABOLITE; NONHUMAN; SENSITIVITY ANALYSIS; BIOLOGICAL MODEL; BIOLOGY; BIOSYNTHESIS; GENE DELETION; GENETICS; METABOLISM; PROTEIN ENGINEERING; SYSTEMS BIOLOGY;

ESCHERICHIA COLI;

COMPUTATIONAL BIOLOGY; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE DELETION; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; PROTEIN ENGINEERING; PYRUVATE KINASE; SYSTEMS BIOLOGY; THREONINE;

EID: 65549146264     PISSN: 00063592     EISSN: 10970290     Source Type: Journal    
DOI: 10.1002/bit.22271     Document Type: Article

References (59)

1. Acerenza L. 2000a. On the Universality of the Universal Method. In: Cornish-Bowden AJ, Cárdenas ML, editors. Technological and medical implications of metabolic control analysis. The Netherlands: Kluwer Academic Publishers. pp. 33-37.
2. Acerenza L. 2000b. Design of large metabolic responses. Constraints and sensitivity analysis. J Theor Biol 207:265-282.
3. Acerenza L, Ortega F. 2007. Modular metabolic control analysis of large responses. The general case for two modules and one linking intermediate. FEBS J 274:188-201.
4. 13C-labeling experiments together with measurements of enzyme activities and intracellular metabolite concentrations. Appl Microbiol Biotechnol 63:407-417.
5. Albe KR, Butler MH, Wright BE. 1990. Cellular concentrations of enzymes and their substrates. J Theor Biol 143:163-195. (Pubitemid 20141560)
6. Belfaiza J, Fazel A, Muller K, Cohen GN. 1984. E. coli aspartokinase II-homoserine dehydrogenase II polypeptide chain has a triglobular structure. Biochem Biophys Res Commun 123:16-20.
7. Boiteux A, Markus M, Plesser T, Hess B, Malcovati M. 1983. Analysis of progress curves. Interaction of pyruvate kinase from Escherichia coli with fructose 1,6-bisphosphate and calcium ions. Biochem J 211:631-640.
8. Chassagnole C, Rais B, Quentin E, Fell DA, Mazat JP. 2001a. An integrated study of threonine-pathway enzyme kinetics in Escherichia coli. Biochem J 356:415-423. (Pubitemid 32532352)
9. Chassagnole C, Fell DA, Rais B, Kudla B, Mazat JP. 2001b. Control of the threonine-synthesis pathway in Escherichia coli: A theoretical and experimental approach. Biochem J 356:433-444. (Pubitemid 32532354)
10. Chassagnole C, Noisommit-Rizzi N, Schmid JW, Mauch K, Reuss M. 2002. Dynamic modeling of the central carbon metabolism of Escherichia coli. Biotechnol Bioeng 79:53-73. (Pubitemid 34746765)
11. Colón GE, Jetten MS, Nguyen TT, Gubler ME, Follettie MT, Sinskey AJ, Stephanopoulos G. 1995. Effect of inducible thrB expression on amino acid production in Corynebacterium lactofermentum ATCC 21799. Appl Microbiol Biotechnol 61:74-78.
12. Debabov VG, Kozlov YI, Khurges EM, Livshits VA, Zhdanova NI, Gusyatiner MM, Sokolov AK, Bachina TA, Chustoserdov AY, Yankovsky NK, Mashko SV, Lapidus AL, Gavrilova OF, Rodionov OA. 1994. European Patent EP 0 593 792 A1.
13. Edwards JS, Palsson BO. 1998. How will bioinformatics influence metabolic engineering? Biotech Bioeng 58:162-169.
14. Fell DA. 1996. Understanding the control of metabolism. London: Portland Press.
15. Fell DA. 1998. Increasing the flux in metabolic pathways: A metabolic control analysis perspective. Biotechnol Bioeng 58:121-124. (Pubitemid 28136367)
16. Fell DA, Thomas S. 1995. Physiological control of flux: The requirement for multisite modulation. Biochem J 311:35-39.
17. Flores N, Xiao J, Berry A, Bolivar F, Valle F. 1996. Pathway engineering for the production of aromatic compounds in Escherichia coli. Nature Biotechnol 14:620-623. (Pubitemid 26135127)
18. Gosset G. 2005. Improvement of Escherichia coli production strains by modification of the phosphoenolpyruvate:sugar phosphotransferase system. Microb Cell Fact 4:14-24. (Pubitemid 41460822)
19. Gottschalk G. 1986. Bacterial metabolism, 2nd edition. New York: Springer- Verlag.
20. Gourdon P, Lindley ND. 1999. Metabolic analysis of glutamate production by Corynebacterium glutamicum. Metab Eng 1:224-231. (Pubitemid 129499379)
21. Hermann T. 2003. Industrial production of amino acids by coryneform bacteria. J Biotechnol 104:155-172. (Pubitemid 37011355)
22. Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, Singhal M, Xu L, Mendes P, Kummer U. 2006. COPASI - A COmplex PAthway SImulator. Bioinformatics 22:3067-3074. (Pubitemid 44884083)
23. Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novère N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J. SBML Forum. 2003. The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models. Bioinformatics 19:524-531. (Pubitemid 36336519)
24. Ikeda M. 2003. Amino acid production processes. In: Faurie R, Thommel J, editors. Microbial production of L-amino acids. Advances in Biochemical Engineering/Biotechnology volume79. Berlin Heidelberg: Springer-Verlag. pp. 1-35.
25. Kacser H, Acerenza L. 1993. A universal method for achieving increases in metabolite production. Eur J Biochem 216:361-367. (Pubitemid 23276282)
26. Kacser H, Burns JA. 1973. The control of flux. Symp Soc Exp Biol 27: 65-104.
27. Reprinted in Biochem Soc Trans 23: 341-366, 1995.
28. Kauffman KJ, Prakash P, Edwards JS. 2003. Advances in flux balance analysis. Curr Opin Biotechnol 14:491-496. (Pubitemid 37298033)
29. Kholodenko BN, Cascante M, Hoek JB, Westerhoff HV, Schwaber J. 1998. Metabolic design: How to engineer a living cell to desired metabolite concentrations and fluxes. Biotechnol Bioeng 59:239-247. (Pubitemid 28277750)
30. Kotlarz D, Garreau H, Buc H. 1975. Regulation of the amount and of the activity of phosphofructokinases and pyruvate kinases in Escherichia coli. Biochim Biophys Acta 381:257-268.
31. Lee S, Phalakornkule C, Domach MM, Grossmann IE. 2000. Recursive MILP model for finding all the alternate optima in LP models for metabolic networks. Comput Chem Eng 24:711-716. (Pubitemid 30608305)
32. Lee KH, Park JH, Kim TY, Kim HU, Lee SY. 2007. Systems metabolic engineering of Escherichia coli for L-threonine production. Mol Syst Biol 3:149. (Pubitemid 350223361)
33. Leuchtenberger W. 1996. Amino acids-technical production and use. In: Roehr M, editor. Biotechnology volume6. Weinheim: Wiley-VCH. pp. 465-502.
34. Maury J. 2004. Metabolic Engineering of E.coli B-5318 overproducing threonine. Combination of physiological and transcriptomic analyses for the rational improvement of the strains. Toulouse: PhD thesis, INSA Toulouse.
35. Mendes P, Kell D. 1998. Non-linear optimization of biochemical pathways: Applications to metabolic engineering and parameter estimation. Bioinformatics 14:869-883. (Pubitemid 29041543)
36. Meynial-Salles I, Cervin MA, Soucaille P. 2005. A new tool for metabolic pathway engineering in Escherichia coli: A step method to modulate the expression of chromosomal genes. Appl Environ Microbiol 71:2140-2144. (Pubitemid 40546140)
37. Neidhardt FC, Ingraham JL, Schaechter M. 1990. Physiology of the bacterial cell: A molecular approach. Sunderland, Mass: Sinauer Associates, Inc.
38. Nicolas C, Kiefer P, Letisse F, Krömer J, Massou S, Soucaille P, Wittmann C, Lindley ND, Portais JC. 2007. Response of central metabolism of Escherichia coli to modified expression of the gene encoding the glucose-6-phosphate dehydrogenase. FEBS Lett 581:3771-3776. (Pubitemid 47411510)
39. Palsson BO. 2006. Systems biology. Properties of reconstructed networks. Cambridge: Cambridge University Press.
40. 13C-labelling experiments together with enzyme activity assays and intracellular metabolite measurements. FEMS Microbiol Lett 235:17-23.
41. Pharkya P, Burgard AP, Maranas CD. 2003. Exploring the overproduction of amino acids using the bilevel optimization framework OptKnock. Biotechnol Bioeng 84:887-899. (Pubitemid 38089702)
42. Ponce E, Flores N, Martinez A, Valle F, Bolivar F. 1995. Cloning of the two pyruvate kinase isoenzyme structural genes from Escherichia coli: The relative roles of these enzymes in pyruvate biosynthesis. J Bacteriol 177:5719-5722. (Pubitemid 26028888)
43. Ponce E, Martinez A, Bolivar F, Valle F. 1998. Stimulation of glucose catabolism through the pentose pathway by the absence of the two pyruvate kinase isoenzymes in Escherichia coli. Biotechnol Bioeng 58:292-295. (Pubitemid 28136390)
44. Price ND, Reed JL, Palsson BO. 2004. Genome scale models of microbial cells: Evaluating the consequences of constraints. Nat Rev Microbiol 2:886-897. (Pubitemid 39567269)
45. Rodriguez N, Donizelli M, Le Novere N. 2007. SBMLeditor: Effective creation of models in the Systems Biology Markup Language (SBML). BMC Bioinformatics 8:79. (Pubitemid 46487084)
46. Rohwer JM, Meadow ND, Roseman S, Westerhoff HV, Postma PW. 2000. Understanding glucose transport by the bacterial phosphoenolpyruvate: glycose phosphotransferase system on the basis of kinetic measurements in vitro. J Biol Chem 275:34909-34921.
47. 13C-based flux analysis. Mol Syst Biol 2:62.
48. Sauro HM, Hucka M, Finney A, Wellock C, Bolouri H, Doyle J, Kitano H. 2003. Next generation simulation tools: The Systems Biology Workbench and BioSPICE integration. OMICS 7:355-372. (Pubitemid 38018642)
49. Schuster S, Pfeiffer T, Fell DA. 2008. Is maximization of molar yield in metabolic networks favoured by evolution? J Theor Biol 252:497-504.
50. Valentini G, Chiarelli L, Fortin R, Speranza ML, Galizzi A, Mattevi A. 2000. The allosteric regulation of pyruvate kinase. J Biol Chem 275:18145-18152.
51. Vallino JJ, Stephanopoulos G. 1993. Metabolic flux distributions in Corynebacterium glutamicum during growth and lysine overproduction. Biotech Bioeng 41:633-646. (Pubitemid 23067907)
52. Varma A, Palsson BO. 1993. Metabolic capabilities of Escherichia coli II. Optimal growth patterns. J Theor Biol 165:503-522. (Pubitemid 24044951)
53. Varma A, Boesch BW, Palsson BO. 1993. Biochemical production capabilities of Escherichia coli. Biotech Bioeng 42:59-73. (Pubitemid 23166025)
54. Visser D, Heijnen JJ. 2003. Dynamic simulation and metabolic re-design of a branched pathway using linlog kinetics. Metab Eng 5:164-176. (Pubitemid 37124115)
55. Waygood EB, Sanwal BD. 1974. The control of pyruvate kinases of Escherichia coli. I. Physicochemical and regulatory properties of the enzyme activated by fructose 1,6-diphosphate. J Biol Chem 249:265-274.
56. Waygood EB, Mort JS, Sanwal BD. 1976. The control of pyruvate kinase of Escherichia coli. Binding of substrate and allosteric effectors to the enzyme activated by fructose 1,6-bisphosphate. Biochemistry 15:277-282.
57. Wolfram S. 2003. The mathematica book, 5th edition. Champaign, IL: Wolfram Media, Inc.
58. Yagi T, Kagamiyama H, Nozaki M, Soda K. 1985. Glutamate-aspartate transaminase from microorganisms. Methods Enzymol 113:83-89. (Pubitemid 16195777)
59. Zhu T, Phalakornkule C, Koepsel RR, Domach MM, Ataai MM. 2001. Cell growth and by product formation in pyruvate kinase mutant of E. coli. Biotechnol Prog 17:624-628. (Pubitemid 32748050)