Is the regulation of galactose 1-phosphate tuned against gene expression noise?

Biochemical Journal

Volumn 387, Issue 1, 2005, Pages 77-84

  De Atauri, Pedro ^a   Orrell, David ^a   Ramsey, Stephen ^a   Bolouri, Hamid ^a  

^a INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

Author keywords

Galactose uptake; Galactose 1 phosphate uridylyltransferase; Gene expression; Metabolic pathway; Noise transmission; Saccharomyces cerevisiae

Indexed keywords

CELLS; METABOLISM; RNA; YEAST;

GALACTOSE; GENE EXPRESSION; METABOLIC ENZYMES; MRNA MOLECULES;

GENES;

GALACTOSE; GALACTOSE 1 PHOSPHATE URIDYLYLTRANSFERASE; MESSENGER RNA;

ARTICLE; CALCULATION; CARBOHYDRATE METABOLISM; ENZYME ACTIVITY; GENE EXPRESSION; GENETIC TRANSCRIPTION; HEXOSE TRANSPORT; KINETICS; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; NONHUMAN; PRIORITY JOURNAL; REACTION ANALYSIS; RNA TRANSLATION; SACCHAROMYCES CEREVISIAE; YEAST;

GALACTOSE; GALACTOSEPHOSPHATES; GENE EXPRESSION REGULATION, FUNGAL; KINETICS; PROTEIN BIOSYNTHESIS; RNA, FUNGAL; RNA, MESSENGER; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION, GENETIC; UTP-HEXOSE-1-PHOSPHATE URIDYLYLTRANSFERASE;

EID: 17144392521     PISSN: 02646021     EISSN: None     Source Type: Journal    
DOI: 10.1042/BJ20041001     Document Type: Article

References (50)

1. Ghaemmaghami, S., Huh, W. K., Bower, K., Howson, R. W., Belle, A., Dephoure, N., O'Shea, E. K. and Weissman, J. S. (2003) Global analysis of protein expression in yeast. Nature (London) 425, 737-741
2. Holstege, F. C. P., Jennings, E. G., Wyrick, J. J., Lee, T. I., Hengartner, C. J., Green, M. R., Golub, T. R., Lander, E. S. and Young, R. A. (1998) Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95, 717-728
3. Fraser, H. B., Hirsh, A. E., Giaever, G., Kumm, J. and Eisen, M. B. (2004) Noise minimization in eukaryotic gene expression. PLoS Biol. 2, E137
4. Frey, P. A. (1996) The Leloir pathway: a mechanistic imperative for three enzymes to change the stereochemical configuration of a single carbon in galactose. FASEB J. 10, 461-470
5. Holden, H. M., Rayment, I. and Thoden, J. B. (2003) Structure and function of enzymes of the Leloir pathway for galactose metabolism. J. Biol. Chem. 278, 43885-43888
6. Lohr, D., Venkov, P. and Zlatanova, J. (1995) Transcriptional regulation in the yeast GAL gene family: a complex genetic network. FASEB J. 9, 777-787
7. Melcher, K. (1997) Galactose metabolism in Saccharomyces cerevisiae: a paradigm for eukaryotic gene regulation. In Yeast Sugar Metabolism (Zimmermann, F. K. and Entian, K.-D., eds.), pp. 235-269, Technomic Publishing Inc., Lancaster, PA
8. Bhat, P. J. and Murthy, T. V. (2001) Transcriptional control of the GAL/MEL regulon of yeast Saccharomyces cerevisiae: mechanism of galactose-mediated signal transduction. Mol. Microbiol. 40, 1059-1066
9. Alon, U., Surette, M. G., Barkai, N. and Leibler, S. (1999) Robustness in bacterial chemotaxis. Nature (London) 397, 168-171
10. Zhou, T. and Carlson, J. M. (2000) Dynamics and changing environments in highly optimized tolerance. Phys. Rev. E. Stat. Phys. Plasmas Fluids Relat. Interdiscip. Top. 62, 3197-3204
11. von Dassow, G., Meir, E., Munro, E. M. and Odell, G. M. (2000) The segment polarity network is a robust developmental module. Nature (London) 406, 188-192
12. de Atauri, P., Orrell, D., Ramsey, S. and Bolouri, H. (2004) Evolution of 'design' principles in biochemical networks. IEE Syst. Biol. 1, 28-40
13. Horak, J. and Wolf, D. H. (1997) Catabolite inactivation of the galactose transporter in the yeast Saccharomyces cerevisiae: ubiquitination, endocytosis, and degradation in the vacuole. J. Bacteriol. 179, 1541-1549
14. Bhat, P. J. (2003) Galactose 1-phosphate is a regulator of inositol monophosphatase: a fact or a fiction? Med. Hypotheses 60, 123-128
15. Leslie, N. D. (2003) Insights into the pathogenesis of galactosemia. Annu. Rev. Nutr. 23, 59-80
16. Mehta, D. V., Kabir, A. and Bhat, P. J. (1999) Expression of human inositol monophosphatase suppresses galactose toxicity in Saccharomyces cerevisiae: possible implications in galactosemia. Biochim. Biophys. Acta 1454, 217-226
17. Lai, K. and Elsas, L. J. (2000) Overexpression of human UDP-glucose pyrophosphorylase rescues galactose 1-phosphate uridyltransferase-deficient yeast. Biochem. Biophys. Res. Commun. 271, 392-400
18. Ostergaard, S., Olsson, L. and Nielsen, J. (2001) In vivo dynamics of galactose metabolism in Saccharomyces cerevisiae: metabolic fluxes and metabolite levels. Biotechnol. Bioeng. 73, 412-425
19. Lai, K., Langley, S. D., Khwaja, F. W., Schmitt, E. W. and Elsas, L. J. (2003) GALT deficiency causes UDP-hexose deficit in human galactosemic cells. Glycobiology 13, 285-294
20. Iyer, V. and Struhl, K. (1996) Absolute mRNA levels and transcriptional initiation rates in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A. 93, 5208-5212
21. Biggar, S. R. and Crabtree, G. R. (2001) Cell signaling can direct either binary or graded transcriptional responses. EMBO J. 20, 3167-3176
22. Raser, J. M. and O'Shea, E. K. (2004) Control of stochasticity in eukaryotic gene expression. Science 304, 1811-1814
23. Gillespie, D. T. (1976) A general method for numerically stimulating the stochastic time evolution of coupled chemical reactions. J. Comput. Phys. 22, 403-434
24. Li, J., Wang, S., VanDusen, W. J., Schultz, L. D., George, H. A., Herber, W. K., Chae, H. J., Bentley, W. E. and Rao, G. (2000) Green fluorescent protein in Saccharomyces cerevisiae: real-time studies of the GAL1 promoter. Biotechnol. Bioeng. 70, 187-196
25. Lashkari, D. A., DeRisi, J. L., McCusker, J. H., Namath, A. F., Gentile, C., Hwang, S. Y., Brown, P. O. and Davis, R. W. (1997) Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc. Natl. Acad. Sci. U.S.A. 94, 13057-13062
26. Fell, D. A. (1997) Understanding the Control of Metabolism, Portland Press, London
27. Cornish-Bowden, A. (2004) Fundamentals of Enzyme Kinetics, 3rd edn., Portland Press, London
28. Daran, J. M., Dallies, N., Thines-Sempoux, D., Paquet, V. and Francois, J. (1995) Genetic and biochemical characterization of the UGP1 gene encoding the UDP-glucose pyrophosphorylase from Saccharomyces cerevisiae. Eur. J. Biochem. 233, 520-530
29. Reifenberger, E., Boles, E. and Ciriacy, M. (1997) Kinetic characterization of individual hexose transporters of Saccharomyces cerevisiae and their relation to the triggering mechanisms of glucose repression. Eur. J. Biochem. 245, 324-333
30. Fukasawa, T., Obonai, K., Segawa, T. and Nogi, Y. (1980) The enzymes of the galactose cluster in Saccharomyces cerevisiae. II. Purification and characterization of uridine diphosphoglucose 4-epimerase. J. Biol. Chem. 255, 2705-2707
31. Schell, M. A. and Wilson, D. B. (1977) Purification and properties of galactokinase from Saccharomyces cerevisiae. J. Biol. Chem. 252, 1162-1166
32. Timson, D. J. and Reece, R. J. (2002) Kinetic analysis of yeast galactokinase: implications for transcriptional activation of the GAL genes. Biochimie 84, 265-272
33. Ramos, J., Szkutnicka, K. and Cirillo, V. P. (1989) Characteristics of galactose transport in Saccharomyces cerevisiae cells and reconstituted lipid vesicles. J. Bacteriol. 171, 3539-3544
34. Segawa, T. and Fukasawa, T. (1979) The enzymes of the galactose cluster in Saccharomyces cerevisiae: purification and characterization of galactose 1-phosphate uridylyltransferase. J. Biol. Chem. 254, 10707-10709
35. Majumdar, S., Ghatak, J., Mukherji, S., Bhattacharjee, H. and Bhaduri, A. (2004) UDPgalactose 4-epimerase from Saccharomyces cerevisiae: a bifunctional enzyme with aldose 1-epimerase activity. Eur. J. Biochem. 271, 753-759
36. Braun, E. and Brenner, N. (2004) Transient responses and adaptation to steady state in a eukaryotic gene regulation system. Phys. Biol. 1, 67-76
37. Jazwinsky, S. M. (1990) Aging and senescence of the budding yeast Saccharomyces cerevisiae. Mol. Microbiol. 4, 337-343
38. Christacos, N. C., Marson, M. J., Wells, L., Riehman, K. and Fridovich-Keil, J. L. (2000) Subcellular localization of galactose-1-phosphate uridylyltransferase in the yeast Saccharomyces cerevisiae. Mol. Genet. Metab. 70, 272-280
39. Pratt, J. M., Petty, J., Riba-Garcia, I., Robertson, D. H., Gaskell, S. J., Oliver, S. G. and Beynon, R. J. (2002) Dynamics of protein turnover, a missing dimension in proteomics. Mol. Cell. Proteomics 1, 579-591
40. Griffin, T. J., Gygi, S. P., Ideker, T., Rist, B., Eng, J., Hood, L. and Aebersold, R. (2002) Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol. Cell. Proteomics 1, 323-333
41. Hofmeyr, J. S. and Cornish-Bowden, A. (2000) Regulating the cellular economy of supply and demand. FEBS Lett. 476, 47-51
42. Fell, D. A. and Thomas, S. (1995) Physiological control of metabolic flux: the requirement for multisite modulation. Biochem. J. 311, 35-39
43. Kacser, H. and Acerenza, L. (1993) A universal method for achieving increases in metabolite production. Eur. J. Biochem. 216, 361-367
44. Hofmeyr, J. H. and Cornish-Bowden, A. (1991) Quantitative assessment of regulation in metabolic systems. Eur. J. Biochem. 200, 223-236
45. Melcher, K. and Xu, H. E. (2001) Gal80-Gal80 interaction on adjacent Gal4p binding sites is required for complete GAL gene repression. EMBO J. 20, 841-851
46. Teusink, B., Diderich, J. A., Westerhoff, H. V., van Dam, K. and Walsh, M. C. (1998) Intracellular glucose concentration in derepressed yeast cells consuming glucose is high enough to reduce the glucose transport rate by 50%. J. Bacteriol. 180, 556-562
47. Kotyk, A. (1967) Mobility of the free and of the loaded monosaccharide carrier in Saccharomyces cerevisiae. Biochim. Biophys. Acta 135, 112-119
48. Dey, P. M. (1984) UDP-galactose 4′-epimerase from Vicia faba seeds. Phytochemistry 23, 729-732
49. Wang, Y., Liu, C. L., Storey, J. D., Tibshirani, R. J., Herschlag, D. and Brown, P. O. (2002) Precision and functional specificity in mRNA decay. Proc. Natl. Acad. Sci. U.S.A. 99, 5860-5865
50. Sherman, F. (1991) Getting started with yeast. In Guide to Yeast Genetics and Molecular Biology (Guthrie, C. and Fink, G. R., eds.), p. 17, Academic Press, San Diego