An integrated model of glucose and galactose metabolism regulated by the GAL genetic switch

Computational Biology and Chemistry

Volumn 30, Issue 3, 2006, Pages 179-192

  Demir, Ozlem ^a   Aksan Kurnaz, Isil ^b  

^a BOGAZICI UNIVERSITY   (Turkey)

^b YEDITEPE UNIVERSITY   (Turkey)

Author keywords

GAL network; Galactose metabolism; GEPASI; Glycolysis; Kinetic modeling

Indexed keywords

CARBON MONOXIDE; COMPUTER SIMULATION; MACROMOLECULES; MATHEMATICAL MODELS; METABOLISM; YEAST;

GAL NETWORK; GALACTOSE METABOLISM; GEPASI; GLYCOLYSIS;

GLUCOSE;

GALACTOSE; GLUCOSE;

ARTICLE; BIOLOGICAL MODEL; CARBOHYDRATE METABOLISM; COMPUTER SIMULATION; GENE EXPRESSION REGULATION; GENETICS; METABOLISM;

CARBOHYDRATE METABOLISM; COMPUTER SIMULATION; GALACTOSE; GENE EXPRESSION REGULATION, ENZYMOLOGIC; GENE EXPRESSION REGULATION, FUNGAL; GLUCOSE; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL;

EID: 33646876640     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2006.02.004     Document Type: Article

References (38)

1. Aksan Kurnaz I. A kinetic analysis of RSK2 and Elk-1 interaction on the serum response element and implications for cellular engineering. Biotech. Bioeng. 88 7 (2004) 890-900
2. Aksan I., and Kurnaz M.L. A computer-based model for the regulation of MAPK activation. J. Rec. Signal Transduc. 23 2-3 (2003) 197-209
3. Cruzalegui F.H., Cano E., and Treisman R. ERK activation induces phosphorylation of Elk-1 at multiple S/T-P motifs to high stoichiometry. Oncogene 18 (1999) 7948-7957
4. Diderich J.A., Schepper M., van Hoek P., Lutfik M.A.H., van Dijken P., Pronk J.T., Klaassen P., Boelens H.F.M., de Mattus M.J.T., van Dam K., and Kruckeberg A.L. Glucose uptake kinetics and transcription of HXT genes in chemostat cultures of S. Cerevisiae. J. Biol. Chem. 274 22 (1999) 15350-15359
5. Emir U.E., and Aksan Kurnaz I. An integrated model for melanocyte-specific gene expression and melanogenesis. Signal Transdu.: Rec. Mediators Genes 3 5-6 (2003) 209-217
6. Ferguson H.A., Kugel J.F., and Goodrich J.A. Kinetic and mechanistic analysis of the RNA polymerase II transcription reaction at the humen interleukin II promoter. J. Mol. Biol. 314 5 (2001) 993-1006
7. Fu L., Bounelis P., Dey N., Browne B.L., Marchase R.B., and Bedwell D.M. The posttranslational modification of phosphoglucomutase is regulated by galactose induction and glucose repression in Saccharomyces cerevisiae. J. Bacteriol. 177 11 (1995) 3087-3094
8. Heinisch J.J., Boles E., and Timpel C. A yeast phosphofructokinase insensitive to fructose-2, 6-bisphosphate. J. Biol. Chem. 271 27 (1996) 15928-15933
9. Hynne F., Danø S., and Sørensen P.G. Full-scale model of glycolysis in Saccharomyces cerevisiae. Biophys. Chem. 94 (2001) 121-163
10. Johnston M., Flick J.S., and Pexton T. Multiple mechanisms provide rapid and stringent glucose repression of GAL gene expression in Saccharomyces cerevisiae. Mol. Cell. Biol. 14 6 (1994) 3834-3841
11. Jonsen M.D., Petersen J.M., Xu Q.P., and Graves B.J. Characterization of the cooperative binding of inhibitory sequences in Ets-1. Mol. Cell. Biol. 16 (1996) 2065-2073
12. Kasahara T., and Kasahara M. Three aromatic residues critical for galactose transport in Gal2. J. Biol. Chem. 275 5 (2000) 4422-4428
13. Kroschewski H., Ortner S., Steipe B., Scheiner O., Wiedermann G., and Duchene M. Differences in substrate specificity and kinetic properties of the recombinant hexokinases HXK1 and HXK2 from Entamoeba histolytica. Mol. Biochem. Parasitol. 105 (2000) 71-80
14. Majumdar S., Ghatak J., Mukherji S., Bhattacharjee H., and Bhaduri A. UDPgalactose 4-epimerase from Saccharomyces cerevisiae. A bifunctional enzyme with aldose 1-epimerase activity. Eur. J. Biochem. 271 4 (2004) 753-759
15. McCartney R.R., and Schmidt M.C. Regulation of Snf1 kinase. Activation requires phosphorylation of threonine 210 by an upstream kinase as well as a distinct step mediated by the Snf4 subunit. J. Biol. Chem. 276 39 (2001) 36460-36466
16. Mendes P. GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems. Comput. Appl. Biosci. 9 (1993) 563-571
17. Mendes P. Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3. Trends Biochem. Sci. 22 (1997) 361-363
18. Mendes P., and Kell D. Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation. Bioinformatics 14 (1998) 869-883
19. Oh D., and Hopper J.E. Transcription of a yeast phosphoglucomutase isozyme gene is galactose inducible and glucose repressible. Mol. Cell. Biol. 10 4 (1990) 1415-1422
20. Ostergaard S., Walløe K.O., Gomes C.S.G., Olsson L., and Nielsen J. The impact of GAL6, GAL80 and MIG1 on glucose control of the GAL system in Saccharomyces cerevisiae. FEMS Yeast Res. 1 (2001) 47-55
21. Ozcan S. Two different signals regulate repression and induction of gene expression by glucose. J. Biol. Chem. 277 49 (2002) 46993-46997
22. Ozcan S., and Johnston M. Function and regulation of yeast hexose transporters. Microbiol. Mol. Biol. Rev. 63 3 (1999) 554-569
23. Peng G., and Hopper J.E. Gene activation by interaction of an inhibitor with a cytoplasmic signaling protein. Proc. Natl. Acad. Sci. U.S.A. 99 13 (2002) 8548-8553
24. Platt A., and Reece R.J. The yeast galactose genetic switch is mediated by formation of a Gal4p-Gal80p-Gal3p complex. EMBO J. 17 14 (1998) 4086-4091
25. Podesta F.E., and Plaxton W.C. Fluorescence study of ligand binding to potato tuber pyrophosphate-dependent phosphofructokinase: evidence for competitive binding between fructose-1,6-bisphosphate and fructose-2, 6-bisphosphate. Arch. Biochem. Biophys. 414 (2003) 101-107
26. Pritchard L., and Kell D.B. Schemes of flux control in a model of Saccharomyces cerevisiae glycolysis. Eur. J. Biochem. 269 (2002) 3894-3904
27. Reijenga K.A., Snoep J.L., Diderich J.A., van Verseveld H.W., Westerhoff H.V., and Teusink B. Control of glycolytic dynamics by hexose transport in Saccharomyces cerevisiae. Biophys. J. 80 (2001) 626-634
28. Rolland F., de Winde J.H., Lemaire K., Boles E., Thevelein J.M., and Winderickx J. Glucose-induced cAMP signaling in yeast requires both a G-protein coupled receptor system for extracellular glucose detection and a separable hexose kinase-dependent sensing process. Molec. Microbiol. 38 2 (2000) 348-358
29. Seiboth B., Hofmann G., and Kubicek C.P. Lactose metabolism and cellulase production in Hypocrea jecorina: the gal7 gene, encoding galactose-1-phosphate uridylyltransferase, is essential for growth on galactose but not for cellulase induction. Mol. Genet. Genomics 267 1 (2002) 124-132
30. Shirra M.K., and Arndt K.M. Evidence for the involvement of the Glc7-Reg1 phosphatase and the Snf1-Snf4 kinase in the regulation of INO1 transcription in Saccharomyces cerevisiae. Genetics 152 1 (1999) 73-87
31. Sil A.K., Alam S., Xin P., Ma L., Morgan M., Lebo C.M., Woods M.P., and Hopper J.E. The Gal3p-Gal80p-Gal4p transcription switch of yeast: Gal3p destabilizes the Gal80p-Gal4p complex in response to galactose and ATP. Mol. Cell. Biol. 19 11 (1999) 7828-7840
32. Stryer L. Glycolysis, in Biochemistry. 4th ed. (1995), WH Freeman and Co., NY pp. 483-528
33. Sun L., Cui Z., Gottlieb R.L., and Zhang B. A selected ribozyme catalyzing diverse dipeptide synthesis. Chem. Biol. 9 5 (2002) 619-628
34. Teusink B., Passarge J., Reijenga C.A., Esgalhado E., van der Weijden C.C., Schepper M., Walsh M.C., Bakker B.M., van Dam K., Westerhoff H.V., and Snoep J.L. Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes. Testing biochemistry. Eur. J. Biochem. 267 (2000) 5313-5329
35. Timson D.J., and Reece R.J. Kinetic analysis of the yeast galactokinase. Biochimie 84 (2002) 265-272
36. Venkatesh K.V., Bhat P.J., Kumar R.A., and Doshi P. Quantitative model for Gal4p-mediated expression of the galactose/melibiose regulon in Saccharomyces cerevisiae. Biotechnol. Prog. 15 (1999) 51-57
37. Verma M., Bhat P.J., and Venkatesh K.V. Quantitative analysis of GAL genetic switch of Saccharomyces cerevisiae reveals that nucleocytoplasmic shuttling of Gal80p results in a highly sensitive response to galactose. J. Biol. Chem. 278 49 (2003) 48764-48769
38. Yano K., and Fukasawa T. Galactose-dependent reversible interaction of Gal3p with Gal80p in the induction pathway of Gal4p-activated genes of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A. 94 5 (1997) 1721-1726