Continuous modeling of metabolic networks with gene regulation in yeast and in vivo determination of rate parameters

Biotechnology and Bioengineering

Volumn 109, Issue 9, 2012, Pages 2325-2339

  Moisset, P ^a   Vaisman, D ^a   Cintolesi, A ^a   Urrutia, J ^a   Rapaport, I ^a   Andrews, B A ^a   Asenjo, J A ^a  

^a UNIVERSITY OF CHILE   (Chile)

Author keywords

Continuous modeling of metabolic networks; Enzyme synthesis; Gene regulation; Yeast

Indexed keywords

BATCH CULTIVATION; CARBON SOURCE; COMPLEX KINETICS; CONTINUOUS MODELING; CONTINUOUS MODELS; DETERMINATION OF PARAMETERS; ENZYME INDUCTION; ENZYME SYNTHESIS; EXPERIMENTAL DATA; EXPONENTIAL GROWTH; EXPONENTIAL GROWTH PHASE; GENE REGULATION NETWORK; GENETIC NETWORKS; GLOBAL BEHAVIORS; GLUCONEOGENESIS; IN-VIVO; METABOLIC FLUX; METABOLIC FLUX ANALYSIS; METABOLIC NETWORK; OBJECTIVE FUNCTIONS; PROTEIN SYNTHESIS; RATE PARAMETERS; S.CEREVISIAE; TRICARBOXYLIC ACID CYCLE; TWO-POINT; YEAST FERMENTATION; YEAST SACCHAROMYCES CEREVISIAE;

BIOMASS; BIOSYNTHESIS; ECOLOGY; ENZYME KINETICS; ETHANOL; FERMENTATION; GENE EXPRESSION; GENES; GLUCOSE; GLYCEROL; KINETICS; METABOLISM; ORDINARY DIFFERENTIAL EQUATIONS; YEAST;

COMPUTER SIMULATION;

ALCOHOL; GLUCOSE; GLYCEROL;

ALCOHOL CONSUMPTION; ARTICLE; BIOMASS FERMENTATION; CARBON SOURCE; ENZYME INDUCTION; ENZYME KINETICS; ENZYME REPRESSION; ENZYME SYNTHESIS; GENE CONTROL; GENE EXPRESSION; GLUCONEOGENESIS; GLYCOLYSIS; GROWTH CURVE; MATHEMATICAL MODEL; MATHEMATICAL PARAMETERS; METABOLIC FLUX ANALYSIS; METABOLISM; NONHUMAN; SACCHAROMYCES CEREVISIAE; SPECIES CULTIVATION; VALIDATION STUDY; YEAST;

COMPUTER SIMULATION; GENE EXPRESSION REGULATION, FUNGAL; GLUCOSE; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; REPRODUCIBILITY OF RESULTS; SACCHAROMYCES CEREVISIAE; SYSTEMS BIOLOGY;

SACCHAROMYCES CEREVISIAE;

EID: 84864318798     PISSN: 00063592     EISSN: 10970290     Source Type: Journal    
DOI: 10.1002/bit.24503     Document Type: Article

References (36)

1. Albe KR, Butler MH, Wright BE. 1990. Cellular concentration of enzymes and their substrates. J Theor Biol 143: 163-195.
2. Alon U. 2007. An introduction to systems biology: Designs principles of biological circuits. USA: Chapman & Hall. p 301.
3. Asenjo JA, Ramírez P, Rapaport I, Aracena J, Goles E, Andrews BA. 2007. A discrete mathematical model applied to genetic regulation and metabolic networks. J Microbiol Biotechnol 17: 496-510.
4. Bailey JE, Ollis DF. 1986. Biochemical engineering fundamentals. 2nd edn. USA: Mc Graw-Hill. p 984.
5. Benanti JA, Cheung SK, Brady MC, Toczyski DP. 2007. A proteomic screen reveals SCFGrr1 targets that regulate the glycolytic gluconeogenic switch. Nat Cell Biol 9: 1184-1191.
6. Boube M, Joulia L, Cribbs DL, Bourbon HM. 2002. Evidence for a mediator of RNA polymerase II transcriptional regulation conserved from yeast to man. Cell 110: 143-151.
7. Brusch L, Cuniberti G, Bertau M. 2004. Model evaluation for glycolytic oscillations in yeast biotransformations of xenobiotics. Biophys Chem 109: 413-426.
8. Cox SJ, Levanon SS, Bennett GN, San K. 2005. Genetically constrained metabolic flux analysis. Metab Eng 7: 445-456.
9. Daran-Lapujade P, Jansen ML, Daran JM, van Gulik W, de Winde JH, Pronk JP. 2004. Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae. A Chemostat culture study. J Biol Chem 279: 9125-9138.
10. Díaz H, Andrews BA, Hayes A, Castrillo JI, Oliver SG, Asenjo JA. 2009. Global gene expression in recombinant and non-recombinant yeast Saccharomyces cerevisiae in three different metabolic states. Biotechnol Adv 27: 1092-1117.
11. Engl HW, Hanke M, Neubauer A. 2000. Regularization of inverse problems (mathematics and its applications). Dordrecht, The Netherlands: Kluwer Academic Publishers.
12. Famili I, Förster J, Nielsen J, Palsson BO. 2003. Saccharomyces cerevisiae phenotypes can be prediBTed by using constraint-based analysis of a genome-scale reconstruBTed metabolic network. Proc Natl Acad Sci USA 100: 13134-13139.
13. Gagneur J, Casari G. 2005. From molecular networks to qualitative cell behavior. Sys Biol FEBS Lett 579: 1867-1871.
14. Gancedo J. 1998. Yeast carbon catabolite repression. Microbiol Mol Biol Rev 62: 334-361.
15. Gombert AK, Moreira dos Santos M, Christensen B, Nielsen J. 2001. Network identification and flux quantification in the central metabolism of Saccharomyces cerevisiae under different conditions of glucose repression. J Bacteriol 183: 1441-1451.
16. González R, Andrews BA, Molitor J, Asenjo JA. 2003. Metabolic analysis of the synthesis of high levels of intracellular human SOD in Saccharomyces cerevisiae rhSOD 2060 411 SGA 122. Biotechnol Bioeng 82: 152-169.
17. Hatzimanikatis V. 2010. Course: Systems biology. Santiago, Chile: Institute for Cell Dynamics and Biotechnology, University of Chile.
18. Hynne F, Danø S, Sørensen PG. 2001. Full-scale model of glycolysis in Saccharomyces cerevisiae Biophys Chem 94: 121-163.
19. Jacob F, Monod J. 1961. Genetic regulatory mechanism in the synthesis of proteins. J Mol Biol 3: 318-356.
20. Kaushik K, Condo S, Venkatasubramanian K. 1979. Modeling of inducible enzyme biosynthesis in microbial cells. Ann N Y Acad Sci 326: 57-71.
21. Klein CJL, Olsson L, Nielsen J. 1998. Glucose control in Saccharomyces cerevisiae: The role of M/G7 in metabolic functions. Microbiology 144: 13-24.
22. Lagunas R, Gancedo C. 1983. Role of phosphate in the regulation of the Pasteur effect inSaccharomyces cerevisiae. Eur J Biochem 137: 479-483.
23. Müller S, Bole E, May M, Zimmermann F. 1995. Different internal metabolites trigger the inductions of glycolytic gene expression in Saccharomyces cerevisiae J Bacteriol 177: 4517-4519.
24. Özcan S, Dover J, Rosenwald AG, Wölfl S, Johnston M. 1996. Two glucose transporters in Saccharomyces cerevisiae are glucose sensors that generate a signal for induction of gene expression. Proc Natl Acad Sci USA 93: 12428-12432.
25. Özcan S, Dover J, Johnston M. 1998. Glucose sensing and signaling by two glucose receptors in the yeast Saccharomyces cerevisiae EMBO J 17: 2566-2573.
26. Rizzi M, Baltes M, Theobald U, Reuss M. 1997. In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae: II. Mathematical model. Biotechnol Bioeng 55: 592-608.
27. Rolland F, Winderickx J, Thevelein JM. 2002. Glucose-sensing and -signalling mechanism in yeast. FEMS Yeast Res 2: 183-201.
28. Santangelo GM. 2006. Glucose signaling in Saccharomyces cerevisiae Microbiol Mol Biol Rev 70: 253-282.
29. Schüller HJ. 2003. Transcriptional control of nonfermentative metabolism in the yeast Saccharomyces cerevisiae Curr Genet 43: 139-160.
30. Soontorngun N, Larochelle M, Drouin S, Robert F, Turcotte B. 2007. Regulation of gluconeogenesis in Saccharomyces cerevisiae is mediated by activator and repressor functions of Rds2. Mol Cell Biol 27: 7895-7905.
31. Teusink B, Passarge J, Reijenga CA, Esgalhado E, van der Weijden CC, Schepper M, Walsh MC, Bakker BM, van Dam K, Westerhoff HV, Snoep JL. 2000. Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry. Eur J Biochem 267: 5313-5329.
32. Theobald U, Mailinger W, Baltes M, Rizzi M, Reuss M. 1997. In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae: I. Experimental observations. Biotechnol Bioeng 55: 305-316.
33. Wang L, Hatzimanikatis V. 2006. Metabolic engineering under uncertainty-II: Analysis of yeast metabolism. Metab Eng 8: 142-159.
34. Wiechert W. 2002. Modeling and simulation: Tools for metabolic engineering. J Biotechnol 94: 37-63.
35. Yagil G, Yagil E. 1971. On the relation between effect or concentration and the rate of induced enzyme synthesis. Biophys J 11: 11-27.
36. Zhang N, Wu J, Oliver SG. 2009. Gis1 is required for transcriptional reprogramming of carbon metabolism and the stress response during transition into stationary phase in yeast. Microbiology 155: 1690-1698.