Environmental systems biology of cold-tolerant phenotype in Saccharomyces species adapted to grow at different temperatures

Molecular Ecology

Volumn 23, Issue 21, 2014, Pages 5241-5257

  Paget, Caroline Mary ^a   Schwartz, Jean Marc ^a   Delneri, Daniela ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

adaptation; Saccharomyces kudriavzevii; systems biology; temperature; thermodynamics

Indexed keywords

SACCHAROMYCES; SACCHAROMYCES KUDRIAVZEVII;

ADH3 PROTEIN, S CEREVISIAE; ALCOHOL DEHYDROGENASE; GLYCEROL 3 PHOSPHATE DEHYDROGENASE; GLYCEROL-3-PHOSPHATE DEHYDROGENASE (NAD(P)+); SACCHAROMYCES CEREVISIAE PROTEIN;

ADAPTATION; COLD; FUNGAL GENE; GENETICS; REPRODUCTIVE FITNESS; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE; SYSTEMS BIOLOGY; THERMODYNAMICS;

ADAPTATION, PHYSIOLOGICAL; ALCOHOL DEHYDROGENASE; COLD TEMPERATURE; GENES, FUNGAL; GENETIC FITNESS; GLYCEROLPHOSPHATE DEHYDROGENASE; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SYSTEMS BIOLOGY; THERMODYNAMICS;

EID: 84911369928     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.12930     Document Type: Article

References (52)

1. Albe KR, Butler MH, Wright BE, (1990) Cellular concentrations of enzymes and their substrates. Journal of Theoretical Biology, 143, 163-195.
2. Alberty RA, (2003) Thermodynamics of Biochemical Reactions. John Wiley & Sons Inc, Hoboken, New Jersey.
3. Arroyo-Lopez FN, Orlic S, Querol A, Barrio E, (2009) Effects of temperature, pH and sugar concentration on the growth parameters of Saccharomyces cerevisiae, S. kudriavzevii and their interspecific hybrid. International Journal of Food Microbiology, 131, 120-127.
4. Arroyo-Lõpez FN, Pérez-Torrado R, Querol A, Barrio E, (2010) Modulation of the glycerol and ethanol syntheses in the yeast Saccharomyces kudriavzevii differs from that exhibited by Saccharomyces cerevisiae and their hybrid. Food Microbiology, 27, 628-637.
5. Beard DA, Liang SD, Qian H, (2002) Energy balance for analysis of complex metabolic networks. Biophysical Journal, 83, 79-86.
6. Berovic M, Herga M, (2007) Heat shock on Saccharomyces cerevisiae inoculum increases glycerol production in wine fermentation. Biotechnology Letters, 29, 891-894.
7. Ciriacy M, (1975) Genetics of alcohol dehydrogenase in Saccharomyces cerevisiae. II. Two loci controlling synthesis of the glucose-repressible ADH II. Molecular and General Genetics, 138, 157-164.
8. Cruz LAB, Hebly M, Duong G-H, et al,. (2012) Similar temperature dependencies of glycolytic enzymes: an evolutionary adaptation to temperature dynamics? BMC Systems Biology, 6, 151.
9. Daniel Gietz R, Woods RA, (2002) Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method. In: Methods in Enzymology (eds, Christine G, Gerald RF,), pp. 87-96. Academic Press, San Francisco.
10. Delneri D, (2011) Competition experiments coupled with high-throughput analyses for functional genomics studies in yeast. In: Yeast Systems Biology (eds, Castrillo JI, Oliver SG,), pp. 271-282. Humana Press, New York.
11. Delneri D, Hoyle DC, Gkargkas K, et al,. (2008) Identification and characterization of high-flux-control genes of yeast through competition analyses in continuous cultures. Nature Genetics, 40, 113-117.
12. Duarte NC, Herrgard MJ, Palsson BO, (2004) Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Research, 14, 1298-1309.
13. Enquist BJ, Economo EP, Huxman TE, et al,. (2003) Scaling metabolism from organisms to ecosystems. Nature, 423, 639-642.
14. Feist AM, Zielinski DC, Orth JD, et al,. (2010) Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli. Metabolic Engineering, 12, 173-186.
15. Fleming RMT, Thiele I, Provan G, Nasheuer HP, (2010) Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism. Journal of Theoretical Biology, 264, 683-692.
16. Gasch AP, Spellman PT, Kao CM, et al,. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Molecular Biology of the Cell, 11, 4241-4257.
17. Ghisla S, Massey V, (1989) Mechanisms of flavoprotein-catalyzed reactions. European Journal of Biochemistry, 181, 1-17.
18. Hayashi M, Maeda T, (2006) Activation of the HOG pathway upon cold stress in Saccharomyces cerevisiae. Journal of Biochemistry, 139, 797-803.
19. Henry CS, Jankowski MD, Broadbelt LJ, Hatzimanikatis V, (2006) Genome-scale thermodynamic analysis of Escherichia coli metabolism. Biophysical Journal, 90, 1453-1461.
20. Henry CS, Broadbelt LJ, Hatzimanikatis V, (2007) Thermodynamics-based metabolic flux analysis. Biophysical Journal, 92, 1792-1805.
21. Herrgard MJ, Swainston N, Dobson P, et al,. (2008) A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature Biotechnology, 26, 1155-1160.
22. da Huang W, Sherman BT, Lempicki RA, (2009a) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Research, 37, 1-13.
23. da Huang W, Sherman BT, Lempicki RA, (2009b) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols, 4, 44-57.
24. Jankowski MD, Henry CS, Broadbelt LJ, Hatzimanikatis V, (2008) Group contribution method for thermodynamic analysis of complex metabolic networks. Biophysical Journal, 95, 1487-1499.
25. Jayatilaka P, Narendra A, Reid SF, Cooper P, Zeil J, (2011) Different effects of temperature on foraging activity schedules in sympatric Myrmecia ants. The Journal of Experimental Biology, 214, 2730-2738.
26. Jol SJ, Kümmel A, Terzer M, Stelling J, Heinemann M, (2012) System-level insights into yeast metabolism by thermodynamic analysis of elementary flux modes. PLoS Computational Biology, 8, e1002415.
27. Kanehisa M, (2000) Post-Genome Informatics. Oxford University Press (OUP), Oxford.
28. Keen WH, Travis J, Juilianna J, (1984) Larval growth in three sympatric Ambystoma salamander species: species differences and the effects of temperature. Canadian Journal of Zoology, 62, 1043-1047.
29. King RD, Whelan KE, Jones FM, et al,. (2004) Functional genomic hypothesis generation and experimentation by a robot scientist. Nature, 427, 247-252.
30. Lai CH, Morley SA, Tan KS, Peck LS, (2011) Thermal niche separation in two sympatric tropical intertidal Laternula (Bivalvia: Anomalodesmata). Journal of Experimental Marine Biology and Ecology, 405, 68-72.
31. Los DA, Murata N, (2004) Membrane fluidity and its roles in the perception of environmental signals. Biochimica et Biophysica Acta (BBA)-Biomembranes, 1666, 142-157.
32. Milo R, Jorgensen P, Moran U, Weber G, Springer M, (2010) BioNumbers-the database of key numbers in molecular and cell biology. Nucleic Acids Research, 38, D750-D753.
33. Mo ML, Palsson BO, Herrgard MJ, (2009) Connecting extracellular metabolomic measurements to intracellular flux states in yeast. BMC Systems Biology, 3, 37.
34. Norris M, Lovell S, Delneri D, (2013) Characterization and prediction of haploinsufficiency using systems-level gene properties in yeast. G3: Genes|Genomes|Genetics, 3, 1965-1977.
35. Oliveira BM, Barrio E, Querol A, Pérez-Torrado R, (2014) Enhanced enzymatic activity of glycerol-3-phosphate dehydrogenase from the cryophilic Saccharomyces kudriavzevii. PLoS ONE, 9, e87290.
36. Omori T, Ogawa K, Umemoto Y, et al,. (1996) Enhancement of glycerol production by brewing yeast (Saccharomyces cerevisiae) with heat shock treatment. Journal of Fermentation and Bioengineering, 82, 187-190.
37. Panadero J, Pallotti C, Rodríguez-Vargas S, Randez-Gil F, Prieto JA, (2006) A downshift in temperature activates the high osmolarity glycerol (HOG) pathway, which determines freeze tolerance in Saccharomyces cerevisiae. Journal of Biological Chemistry, 281, 4638-4645.
38. Piper PW, (1995) The heat shock and ethanol stress responses of yeast exhibit extensive similarity and functional overlap. FEMS Microbiology Letters, 134, 121-127.
39. Postmus J, Canelas AB, Bouwman J, et al,. (2008) Quantitative analysis of the high temperature-induced glycolytic flux increase in Saccharomyces cerevisiae reveals dominant metabolic regulation. Journal of Biological Chemistry, 283, 23524-23532.
40. Salvadõ Z, Arroyo-Lõpez FN, Guillamõn JM, et al,. (2011) Temperature adaptation markedly determines evolution within the genus Saccharomyces. Applied and Environmental Microbiology, 77, 2292-2302.
41. Sampaio JP, Goncalves P, (2008) Natural populations of Saccharomyces kudriavzevii in Portugal are associated with oak bark and are sympatric with S. cerevisiae and S. paradoxus. Applied and Environment Microbiology, 74, 2144-2152.
42. Schade B, Jansen G, Whiteway M, Entian KD, Thomas DY, (2004) Cold adaptation in budding yeast. Molecular Biology of the Cell, 15, 5492-5502.
43. Schwartz J-M, Gaugain C, Nacher J, de Daruvar A, Kanehisa M, (2007) Observing metabolic functions at the genome scale. Genome Biology, 8, R123.
44. Smallbone K, Simeonidis E, Swainston N, Mendes P, (2010) Towards a genome-scale kinetic model of cellular metabolism. BMC Systems Biology, 4, 6.
45. Smith AM, Heisler LE, Mellor J, et al,. (2009) Quantitative phenotyping via deep barcode sequencing. Genome Research, 19, 1836-1842.
46. Smith AM, Heisler LE, St.Onge RP, et al,. (2010) Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples. Nucleic Acids Research, 38, e142.
47. Vigh L, Maresca B, Harwood JL, (1998) Does the membrane's physical state control the expression of heat shock and other genes? Trends in Biochemical Sciences, 23, 369-374.
48. Vriesekoop F, Barber A, Pamment N, (2007) Acetaldehyde mediates growth stimulation of ethanol-stressed Saccharomyces cerevisiae: evidence of a redox-driven mechanism. Biotechnology Letters, 29, 1099-1103.
49. Vriesekoop F, Haass C, Pamment NB, (2009) The role of acetaldehyde and glycerol in the adaptation to ethanol stress of Saccharomyces cerevisiae and other yeasts. FEMS Yeast Research, 9, 365-371.
50. Wach A, Brachat A, Pöhlmann R, Philippsen P, (1994) New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae. Yeast, 10, 1793-1808.
51. Woolf PJ, Alvarez A, Keshamouni VG, (2010) Systems approach for understanding metastasis lung cancer metastasis. In: Lung Cancer Metastasis (eds, Keshamouni V, Arenberg D, Kalemkerian G,), pp. 383-394. Springer, New York, NY.
52. Young ET, Pilgrim D, (1985) Isolation and DNA sequence of ADH3, a nuclear gene encoding the mitochondrial isozyme of alcohol dehydrogenase in Saccharomyces cerevisiae. Molecular and Cellular Biology, 5, 3024-3034.