Transcriptional regulation of respiration in yeast metabolizing differently repressive carbon substrates

BMC Systems Biology

Volumn 4, Issue , 2010, Pages

  Fendt, Sarah Maria ^a,b,c   Sauer, Uwe ^a,c  

^a ETH ZURICH   (Switzerland)

^b Life Science Zurich   (Switzerland)

^c Competence Center for Systems Physiology and Metabolic Diseases ^*  (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); SACCHAROMYCES CEREVISIAE;

CARBON; SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; BIOLOGICAL MODEL; CARBOHYDRATE METABOLISM; CELL RESPIRATION; COMPUTER SIMULATION; GENE EXPRESSION REGULATION; METABOLISM; PHYSIOLOGY; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION INITIATION;

CARBOHYDRATE METABOLISM; CARBON; CELL RESPIRATION; COMPUTER SIMULATION; GENE EXPRESSION REGULATION; MODELS, BIOLOGICAL; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTIONAL ACTIVATION;

EID: 77949447610     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-4-12     Document Type: Article

References (41)

1. Gancedo JM. Yeast carbon catabolite repression. Microbiol Mol Biol Rev 1998, 62(2):334-361. 98918, 9618445.
2. Johnston M. Feasting, fasting and fermenting. Glucose sensing in yeast and other cells. Trends Genet 1999, 15:29-33. 10.1016/S0168-9525(98)01637-0, 10087931.
3. Rolland F, Winderickx J, Thevelein JM. Glucose-sensing and -signalling mechanisms in yeast. FEMS Yeast Res 2002, 2:183-201.
4. Schüller HJ. Transcriptional control of nonfermentative metabolism in the yeast Saccharomyces cerevisiae. Curr Genet 2003, 43(3):139-160.
5. Liu Z, Butow RA. Mitochondrial retrograde signaling. Annu Rev Genet 2006, 40:159-185. 10.1146/annurev.genet.40.110405.090613, 16771627.
6. Zaman S, Lippman SI, Zhao X, Broach JR. How Saccharomyces responds to nutrients. Annu Rev Genet 2008, 42:27-81. 10.1146/annurev.genet.41.110306.130206, 18303986.
7. Klein CJ, Olsson L, Nielsen J. Glucose control in Saccaromyces cerevisiae: The role of MIG1 in metabolic functions. Microbiology 1998, 144:13-24. 10.1099/00221287-144-1-13, 9467897.
8. Ronne H. Glucose repression in fungi. Trends Genet 1995, 11:12-17. 10.1016/S0168-9525(00)88980-5, 7900189.
9. Santangelo GM. Glucose signaling in Saccharomyces cerevisiae. Microbiol Mol Biol Rev 2006, 70:253-282. 10.1128/MMBR.70.1.253-282.2006, 1393250, 16524925.
10. Turcotte B, Liang XB, Robert F, Soontorngun N. Transcriptional regulation of nonfermentable carbon utilization in budding yeast. FEMS Yeast Res 2009, 1-12.
11. Bro C, Knudsen S, Regensberg B, Olsson L, Nielsen J. Improvement of galactose uptake in Saccaromyces cerevisiae through overexpression of phosphoglucomutase: Example of transcript analysis as a tool in inverse metabolic engineering. Appl Environ Microbiol 2005, 71:6465-6472. 10.1128/AEM.71.11.6465-6472.2005, 1287681, 16269670.
12. Herrero P, Fernández R, Moreno R. Differential sensitivities to glucose and galactose repression of gluconeogenic and respiratory enzymes from Saccharomyces cerevisiae. Arch Microbiol 1985, 143:216-219. 10.1007/BF00411238, 3006623.
13. Küpfer L, Sauer U, Blank LM. Metabolic functions of duplicate genes in Saccharomyces cerevisiae. Genome Res 2005, 15:1421-1430. 10.1101/gr.3992505, 1240085, 16204195.
14. Dynesen J, Smits HP, Olssen L, Nielsen J. Carbon catabolite repression of invertase during batch cultivations of Saccharomyces cerevisiae: the role of glucose, fructose, and mannose. Appl Microbiol Biotechnol 1998, 50:579-582. 10.1007/s002530051338, 9866176.
15. Sauer U. Metabolic networks in motion: 13C-based flux analysis. Mol Sys Biol 2006, 2:62.
16. Nielsen J. It is all about metabolic fluxes. J Bacteriol 2003, 185(24):7031-7035. 10.1128/JB.185.24.7031-7035.2003, 296266, 14645261.
17. Wiechert W. 13C metabolic flux analysis. Metab Eng 2001, 3:195-206. 10.1006/mben.2001.0187, 11461141.
18. Huh WK, Flavo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O'Shea EK. Global analysis of protein localization in budding yeast. Nature 2003, 425:686-691. 10.1038/nature02026, 14562095.
19. Newman JRS, Ghaemmaghami S, Ihmels J, Breslow DK, Noble M, DeRisi JL, Weissman JS. Single - cell proteomic analysis of S. cerevisiae reveal the architecture of biological noise. Nature 2006, 44:840-846.
20. Fischer E, Sauer U. Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism using GC-MS. Eur J Biochem 2003, 270:880-891. 10.1046/j.1432-1033.2003.03448.x, 12603321.
21. Blank LM, Sauer U. TCA cycle activity in Saccharomyces cerevisiae is a function of the environmentally determined specific growth and glucose uptake rates. Microbiol 2004, 150:1085-1093.
22. Zamboni N, Fendt SM, Rühl M, Sauer U. 13C-based metabolic flux analysis. Nat Protoc 2009, 4(6):878-892. 10.1038/nprot.2009.58, 19478804.
23. Blank LM, Küpfer L, Sauer U. Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast. Genome Biol 2005, 6:R49. 10.1186/gb-2005-6-6-r49, 1175969, 15960801.
24. Polakis ES, Bartley W. Changes in the enzyme activity of Saccharomyces cerevisiae during aerobic growth on different carbon sources. Biochem J 1965, 97:284-297. 1264573, 16749116.
25. Berg MA, de Jong-Gubbels P, Steensma HY. Transient mRNA responses in chemostat cultures as a method of defining putative regulatory elements: Application to genes involved in Saccharomyces cerevisiae acetylcoenzyme A metabolism. Yeast 1998, 14(12):1089-1104. 10.1002/(SICI)1097-0061(19980915)14:12<1089::AID-YEA312>3.0.CO;2-K, 9778795.
26. Przybyla-Zawislak B, Gadde DM, Durcharme K, McCammon MT. Genetic and biochemical interactions involving tricarboxylic acid cycle (TCA) function using a collection of mutants defective in all TCA cycle genes. Genetics 1999, 152:153-166. 1460613, 10224250.
27. Teixeira MC, Monteiro P, Jain P, Tenreiro S, Fernandes AR, Mira NP, Alenquer M, Oliveira AL, Sá-Correira I. The YEASTRACT database: A tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Res 2006, (34 Database):446-451.
28. Boyle EI, Weng S, Gollub J, Jin H, Botstein D, Cherry JM, Sherlock G. GO: TermFinder - open source software for accessing gene ontology information and finding significantly enriched gene ontology terms associated with a list of genes. Bioinformatics 2004, 20(18):3710-3715. 10.1093/bioinformatics/bth456, 15297299.
29. Kümmel A, Ewald JC, Fendt SM, Jol S, Picotti P, Aebersold R, Sauer U, Zamboni N, Heinemann M. Differential glucose repression in common yeast strains in response to HXK2 deletions. FEMS Yeast Res 2010,
30. Sasaki H, Uemura H. Influence of low glycolytic activities in GCR1 and GCR2 mutants on the expression of other metabolic pathway genes in Saccharomyces cerevisiae. Yeast 2005, 22:111-127. 10.1002/yea.1198, 15645478.
31. Hedges D, Proft M, Entian K. CAT8, a new zinc cluster-encoding gene necessary for derepression of gluconeogenic enzymes in the yeast Saccharomyces cerevisiae. Mol Cell Biol 1995, 15:1915-1922. 230417, 7891685.
32. Dimmer KS, Fritz S, Fuchs F, Messerschmitt NM, Weinbach, Neupert W, Westermann B. Genetic basis of mitochondrial function and morphology in Saccharomyces cerevisiae. Mol Biol Cell 2002, 13(3):847-853. 10.1091/mbc.01-12-0588, 99603, 11907266.
33. Liu Z, Butow RA. A transcriptional switch in the expression of yeast tricaroxylic acid cycle genes in response to a reduction or loss of respiratory function. Mol Cell Biol 1999, 19(10):6720-6728. 84662, 10490611.
34. Pastor MM, Proft M, Pascual-Ahuir A. Mitochondrial function is an inducible determinant of osmotic stress adaptation in yeast. J Biol Chem 2009, 284(44):30307-30317. 10.1074/jbc.M109.050682, 19720830.
35. Duetz WA, Ruedi L, Hermann R, O'Conner K, Büchs J, Witholt B. Methods for intense aeration, growth, storage and replication of bacterial strains in microtiter plates. Appl Environ Microbiol 2000, 66:2641-2646. 10.1128/AEM.66.6.2641-2646.2000, 110593, 10831450.
36. Nissen TL, Schulz U, Nielsen J, Villadsen J. Flux distribution in anaerobic, glucose-limited continuous cultures of Saccharomyces cerevisiae. Microbiology 1997, 143:203-218. 10.1099/00221287-143-1-203, 9025295.
37. Heer D, Sauer U. Identification of furfural as the key toxin in lignocellulosic hydrolysates and evolution of a tolerant yeast strain. Microbial Biotechnol 2008, 1:497-506.
38. Zamboni N, Fischer E, Sauer U. FiatFlux-A software for metabolic flux analysis from 13C -glucose experiments. BMC Bioinformatics 2005, 25(6):209.
39. Fischer E, Zamboni N, Sauer U. High-throughput metabolic flux analysis based on gas chromatographymass spectrometry derived 13C constraints. Anal Biochem 2004, 325:308-316. 10.1016/j.ab.2003.10.036, 14751266.
40. Kensy F, Büchs J. Online-Monitoring von Microfermentationen. Laborwelt 2006, 7.
41. Winston F, Dollard C, Ricupero-Hovasse SL. Construction of a set of convenient Saccharomyces cerevisiae strains that are isogenic to S288C. Yeast 1995, 11:53-55. 10.1002/yea.320110107, 7762301.