The effect of scale on gene expression: Commercial versus laboratory wine fermentations

Applied Microbiology and Biotechnology

Volumn 93, Issue 3, 2012, Pages 1207-1219

  Rossouw, Debra ^a   Jolly, Neil ^b   Jacobson, Dan ^a   Bauer, Florian F ^a  

^a STELLENBOSCH UNIVERSITY   (South Africa)

^b ARC INFRUITEC NIETVOORBIJ   (South Africa)

Author keywords

Commercial wine fermentation; Scale; Transcriptomics

Indexed keywords

CELLULAR PROCESS; DATA REPRODUCIBILITY; DATA SETS; ENVIRONMENTAL CONDITIONS; ENVIRONMENTAL PARAMETER; FERMENTATION PRODUCTS; GRAPE JUICE; INDUSTRIAL CONDITIONS; INDUSTRIAL ENVIRONMENTS; INDUSTRIAL FERMENTATION; INDUSTRIAL PROCESSS; MOLECULAR PROCESS; PHYSIOLOGICAL STATE; PRODUCT YIELDS; SCALE; SYNTHETIC MEDIA; SYNTHETIC MEDIUM; TRANSCRIPTOME ANALYSIS; TRANSCRIPTOMICS; WINE FERMENTATION; WINE YEAST;

APPROXIMATION THEORY; EXTRAPOLATION; FRUIT JUICES; GENE EXPRESSION; INDUSTRY; LABORATORIES; PHYSIOLOGICAL MODELS; RESEARCH; WINE; YEAST;

FERMENTATION;

OXYGEN; PEPTIDOGLYCAN;

ALCOHOL; BIOTECHNOLOGY; BREWING INDUSTRY; CELL ORGANELLE; ENVIRONMENTAL CONDITIONS; FERMENTATION; GENE EXPRESSION; LABORATORY METHOD; MOLECULAR ANALYSIS; OXYGEN; PHENOTYPE; RESEARCH WORK; YEAST;

AEROBIC FERMENTATION; ALCOHOL PRODUCTION; ARTICLE; CELL PROLIFERATION; COMPARATIVE STUDY; GENE EXPRESSION; GLUCOSE UTILIZATION; GRAPE JUICE; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; LARGE SCALE PRODUCTION; NONHUMAN; OPTICAL DENSITY; RNA PROCESSING; SACCHAROMYCES CEREVISIAE; SCALE UP; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION; TRANSCRIPTOMICS; WINE; WINE INDUSTRY; YEAST; YEAST CELL;

BIOREACTORS; BIOTECHNOLOGY; CULTURE MEDIA; FERMENTATION; FOOD INDUSTRY; GENE EXPRESSION; GENE EXPRESSION PROFILING; SACCHAROMYCES CEREVISIAE; TRANSCRIPTOME; WINE;

VITACEAE;

EID: 84856405310     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-011-3564-0     Document Type: Article

References (42)

1. Abbott DA, Knijnenburg TA, de Poorter LM, Reinders MJ, Pronk JT, van Maris AJ (2007) Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae. FEMS Yeast Res 7:819-833 (Pubitemid 47256357)
2. Abramova N, Sertil O, Mehta S, Lowry CV (2001) Reciprocal regulation of anaerobic and aerobic cell wall mannoprotein gene expression in Saccharomyces cereivisiae. J Bacteriol 183:2881-2887 (Pubitemid 32319292)
3. Andréasson C, Neve EP, Ljungdahl PO (2004) Four permeases import proline and the toxic proline analogue azetidine-2-carboxylate into yeast. Yeast 21:193-199 (Pubitemid 38256419)
4. Attfield PV (1997) Stress tolerance: the key to effective strains of baker's yeast. Nat Biotechnol 15:1351-1357 (Pubitemid 28022728)
5. Ben-Dor A, Shamir R, Yakhini Z (1999) Clustering gene expression patterns. J Comp Biol 6:281-297
6. Boer VM, de Winde JH, Pronk JT, Piper MD (2003) The genome-wide transcriptional responses of Saccharomyces cerevisiae grown on glucose in aerobic chemostat cultures limited for carbon, nitrogen, phosphorus or sulfur. J Biol Chem 278:3265-3274 (Pubitemid 36801239)
7. Boulton RB, Singleton VL, Bisson LF, Kunkee RE (1996) Principles and practices of winemaking. Chapman & Hall, New York, pp 200-203
8. Cramer G, Ergül A, Grimplet J, Tillett R, Tattersall E, Bohlman M, Vincent D, Sonderegger J, Evans J, Osborne C, Quilici D, Schlauch K, Schooley D, Cushman J (2007) Water and salinity stress in grape-vines: early and late changes in transcript and metabolite profiles. Funct Integr Genomics 7:111-134 (Pubitemid 46336167)
9. Cullin C, Baudin-Baillieu A, Guillemet E, Ozier-Kalogeropoulos O (1996) Functional analysis of YCL09C: evidence for a role as the regulatory subunit of acetolactate synthase. Yeast 12:1511-1518 (Pubitemid 26420086)
10. Da Silva FG, Iandolino A, Al-Kayal F, Bohlmann MC, Cushman Ma, Lim H, Ergul A, Figueroa R, Kabuloglu EK, Osborne C, Rowe J, Tattersall E, Leslie A, Xu J, Baek J, Cramer GR, Cushman JC, Cook DR (2005) Characterizing the grape transcriptome. Analysis of expressed sequence tags from multiple Vitis species and development of a compendium of gene expression during berry development. Plant Physiol 139:574-597 (Pubitemid 43907089)
11. Denis CL, Young ET (1983) Isolation and characterization of the positive regulatory gene ADR1 from Saccharomyces cerevisiae. Mol Cell Biol 3:360-370 (Pubitemid 13165201)
12. Dickinson JR, Salgado LE, Hewlins MJ (2003) The catabolism of amino acids to long chain and complex alcohols in Saccharomyces cerevisiae. J Biol Chem 278:8028-8034 (Pubitemid 36800541)
13. Driesel A, Lommele A, Drescher B, Töpfer R, Bell M, Cartharius I, Cheutin N, Huck J-F, Kubiak J, Regnard P (2003) Towards the transcriptome of grapevine (Vitis vinifera L.). Acta Hort 603:239-250
14. Duetz WA (2007) Microtiter plates as mini-bioreactors: miniaturization of fermentation methods. Trends Microbiol 15:469-475 (Pubitemid 350026353)
15. Frezier V, Dubourdieu D (1992) Ecology of yeast strain Saccharomyces cerevisiae during spontaneous fermentation in a Bordeaux winery. Am J Enol Vitic 43:375-380
16. Gasch AP, Werner-Washburne M (2002) The genomics of yeast responses to environmental stress and starvation. Funct Integr Genomics 2:181-192 (Pubitemid 41449152)
17. Gasch A, Spellman P, Kao C, Carmel-Harel O, Eisen M, Storz G, Botstein D, Brown P (2000) Genomic expression changes in the response of yeast cells to environmental changes. Mol Biol Cell 11:4241-4257
18. Huang HL, Brandriss MC (2000) The regulator of the yeast proline utilization pathway is differentially phosphorylated in response to the quality of the nitrogen source. Mol Cell Biol 20:892-899 (Pubitemid 30044226)
19. Ideker T, Thorsson V, Ranish JA, Christmas R, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlett DR, Aebersold R, Hood L (2001) Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292:929-934 (Pubitemid 32422490)
20. Iraqui I, Vissers S, Cartiaux M, Urrestarazu A (1998) Characterisation of Saccharomyces cerevisiae ARO8 and ARO9 genes encoding aromatic aminotransferases I and II reveals a new aminotransferase subfamily. Mol Gen Genet 257:238-248 (Pubitemid 28076079)
21. Köffel R, Tiwari R, Falquet L, Schneiter R (2005) The Saccharomyces cerevisiae YLL012/YEH1, YLR020/YEH2, and TGL1 genes encode a novel family of membrane-anchored lipases that are required for steryl ester hydrolysis. Mol Cell Biol 25:1655-1668 (Pubitemid 40280135)
22. Lamb DC, Kelly DE, Manning NJ, Kaderbhai MA, Kelly SL (1999) Biodiversity of the P450 catalytic cycle: yeast cytochrome b5/NADH cytochrome b5 reductase complex efficiently drives the entire sterol 14-demethylation (CYP51) reaction. FEBS Lett 462:283-288
23. Lambrechts MG, Pretorius IS (2000) Yeast and its importance to wine aroma. S Afr J Eno Vitic 21:97-129
24. Lander ES (1999) Array of hope. Nat Genet 21:3-4 (Pubitemid 29031483)
25. Landolfo S, Zara G, Zara S, Budroni M, Ciani M, Mannazzu I (2010) Oleic acid and ergosterol supplementation mitigates oxidative stress in wine strains of Saccharomyces cerevisiae. Int J Food Microbiol 141:229-235
26. Liccioli T, Tran TMT, Cozzolino D, Jiranek V, Chambers PJ, Schmidt SA (2011) Microvinification-how small can we go? Appl Microbiol Biotechnol 89:1621-1628
27. Mardia KV, Kent JT, Bibby JH (1979) Multivariate analysis. Academic, UK
28. Marks VD, Ho Sui SJ, Erasmus D, van den Merwe GK, Brumm J, Wasserman WW, Bryan J, van Vuuren HJJ (2008) Dynamics of the yeast transcriptome during wine fermentation reveals a novel fermentation stress response. FEMS Yeast Res 8:35-52
29. Petersen JG, Kielland-Brandt MC, Nilsson-Tillgren T, Bornaes C, Holmberg S (1988) Molecular genetics of serine and threonine catabolism in Saccharomyces cerevisiae. Genetics 119:527-534
30. Rossignol T, Dulau L, Julien A, Blondin B (2003) Genome-wide monitoring of wine yeast gene expression during alcoholic fermentation. Yeast 20:1369-1385 (Pubitemid 38016631)
31. Rossouw D, Bauer FF (2009) Comparing the transcriptomes of wine yeast strains: toward understanding the interaction between environment and transcriptome during fermentation. Appl Microbiol Biotechnol 84:937-954
32. Rossouw D, Naes T, Bauer FF (2008) Linking gene regulation and the exo-metabolome: a comparative transcriptomics approach to identify genes that impact on the production of volatile aroma compounds in yeast. BMC Genomics 9:530
33. Rossouw D, Olivares-Hernandes R, Nielsen J, Bauer FF (2009) Comparative transcriptomic approach to investigate differences in wine yeast physiology and metabolism during fermentation. Appl Environ Microbiol 75:6600-6612
34. Rossouw D, van den Dool AH, Jacobson D, Bauer FF (2010) Comparative transcriptomic and proteomic profiling of industrial wine yeast strains. Appl Environ Microbiol 76:3911-3923
35. Shobayashi M, Mitsueda SI, Ago M, Fuji T, Iwashita K, Iefuji H (2005) Effects of culture conditions on ergosterol biosynthesis by Saccharomyces cerevisiae. Biosci Biotechnol Biochem 69:2381-2388 (Pubitemid 43004381)
36. Smyth GK (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Molec Biol 3:3
37. Tusher CG, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 98:5116-5121 (Pubitemid 32397092)
38. Valachovic M, Hronská L, Hapala I (2001) Anaerobiosis induces complex changes in sterol esterification pattern in the yeast Saccharomyces cereivisiae. FEMS Microbiol Lett 197:41-45 (Pubitemid 32245750)
39. Varela C, Cardenas J, Melo F, Agosin E (2005) Quantitative analysis of wine yeast gene expression profiles under winemaking conditions. Yeast 22:369-383 (Pubitemid 40561553)
40. Vestrepen KJ, Van Laere SD, Vanderhaegen BM, Derdelinckx G, Dufour JP, Pretorius IS, Winderickx J, Thevelein JM, Delvaux FR (2003) Expression levels of the yeast alcohol acetyltransferase genes ATF1, Lg-ATF1, and ATF2 control the formation of a broad range of volatile esters. Appl Environ Microbiol 69:5228-5237 (Pubitemid 37150744)
41. Young ET, Dombek KM, Tachibana C, Ideker T (2003) Multiple pathways are co-regulated by the protein kinase Snf1 and the transcription factors Adr1 and Cat8. J Biol Chem 28:26146-26158 (Pubitemid 36835384)
42. Zara G, Angelozzi D, Belviso S, Bardi L, Goffrini P, Lodi T, Budroni M, Mannazzu I (2009) Oxygen is required to restore flor strain viability and lipid biosynthesis under fermentative conditions. FEMS Yeast Res 9:217-225