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Applied Microbiology and Biotechnology

, Volume 103, Issue 12, pp 4917–4929 | Cite as

Identification by comparative transcriptomics of core regulatory genes for higher alcohol production in a top-fermenting yeast at different temperatures in beer fermentation

  • Zhong-Guan Sun
  • Meng-Qi Wang
  • Ya-Ping Wang
  • Shuang Xing
  • Kun-Qiang Hong
  • Ye-Fu Chen
  • Xue-Wu GuoEmail author
  • Dong-Guang XiaoEmail author
Genomics, transcriptomics, proteomics

Abstract

Undesirable flavor caused by excessive higher alcohols restrains the development of the wheat beer industry. To clarify the regulation mechanism of the metabolism of higher alcohols in wheat beer brewing by the top-fermenting yeast Saccharomyces cerevisiae S17, the effect of temperature on the fermentation performance and transcriptional levels of relevant genes was investigated. The strain S17 produced 297.85 mg/L of higher alcohols at 20 °C, and the production did not increase at 25 °C, reaching about 297.43 mg/L. Metabolite analysis and transcriptome sequencing showed that the metabolic pathways of branched-chain amino acids, pyruvate, phenylalanine, and proline were the decisive factors that affected the formation of higher alcohols. Fourteen most promising genes were selected to evaluate the effects of single-gene deletions on the synthesis of higher alcohols. The total production of higher alcohols by the mutants Δtir1 and Δgap1 was reduced by 23.5 and 19.66% compared with the parent strain S17, respectively. The results confirmed that TIR1 and GAP1 are crucial regulatory genes in the metabolism of higher alcohols in the top-fermenting yeast. This study provides valuable knowledge on the metabolic pathways of higher alcohols and new strategies for reducing the amounts of higher alcohols in wheat beer.

Keywords

Saccharomyces cerevisiae Top-fermenting Wheat beer Higher alcohol Transcriptome Temperature 

Notes

Funding information

This work was supported by the National Natural Science Foundation of China (No. 31771969), the National Key Research and Development Program of China (No. 2016YFD0400505), the China Postdoctoral Science Foundation (No. 2017M611169), the Hebei Province Postdoctoral Research Projects (No. B2018003031) and the Public Service Platform Project for Selection and Fermentation Technology of Industrial Microorganisms (No. 17PTGCCX00190).

Compliance with ethical standards

Ethical statement

This manuscript is in compliance with ethical standards. This manuscript does not contain any studies with human participants or animals performed by any of the authors.

Conflict of interest

The authors declare that they have no competing interests.

Supplementary material

253_2019_9807_MOESM1_ESM.pdf (213 kb)
ESM 1 (PDF 212 kb)

References

  1. Abramova N, Sertil O, Mehta S, Lowry CV (2001) Reciprocal regulation of anaerobic and aerobic cell wall mannoprotein gene expression in Saccharomyces cerevisiae. J Bacteriol 183:2881–2887.  https://doi.org/10.1128/JB.183.9.2881-2887.2001 CrossRefPubMedPubMedCentralGoogle Scholar
  2. Aguilera J, Rández-Gil F, Prieto AJ (2007) Cold response in Saccharomyces cerevisiae: new functions for old mechanisms. FEMS Microbiol Rev 31:327–341.  https://doi.org/10.1111/j.1574-6976.2007.00066.x
  3. Al-Fageeh MB, Smales CM (2006) Control and regulation of the cellular responses to cold shock: the responses in yeast and mammalian systems. Biochem J 397:247–259.  https://doi.org/10.1042/BJ20060166
  4. Benjamini Y, Drai D, Elmer G, Kafkafi N, Golani I (2001) Controlling the false discovery rate in behavior genetics research. Behav Brain Res 125:279–284.  https://doi.org/10.1016/s0166-4328(01)00297-2
  5. Bornaes C, Ignjatovic MW, Schjerling P, Kielland-Brandt MC, Holmberg S (1993) A regulatory element in the CHA1 promoter which confers inducibility by serine and threonine on Saccharomyces cerevisiae genes. Mol Cell Biol 13:7604–7611.  https://doi.org/10.1128/MCB.13.12.7604
  6. Brice C, Sanchez I, Bigey F, Legras JL, Blondin B (2014) A genetic approach of wine yeast fermentation capacity in nitrogen-starvation reveals the key role of nitrogen signaling. BMC Genomics 15:495.  https://doi.org/10.1186/1471-2164-15-495 CrossRefPubMedPubMedCentralGoogle Scholar
  7. Cambon B, Monteil V, Remize F, Camarasa C, Dequin S (2006) Effects of GPD1 overexpression in Saccharomyces cerevisiae commercial wine yeast strains lacking ALD6 genes. Appl Environ Microbiol 72:4688–4694.  https://doi.org/10.1128/AEM.02975-05 CrossRefPubMedPubMedCentralGoogle Scholar
  8. Celton M, Sanchez I, Goelzer A, Fromion V, Camarasa C, Dequin S (2012) A comparative transcriptomic, fluxomic and metabolomic analysis of the response of Saccharomyces cerevisiae to increases in NADPH oxidation. BMC Genomics 13:317.  https://doi.org/10.1186/1471-2164-13-317 CrossRefPubMedPubMedCentralGoogle Scholar
  9. Chiva R, Baiges I, Mas A, Guillamon JM (2009) The role of GAP1 gene in the nitrogen metabolism of Saccharomyces cerevisiae during wine fermentation. J Appl Microbiol 107:235–244.  https://doi.org/10.1111/j.1365-2672.2009.04201.x CrossRefPubMedGoogle Scholar
  10. Colón M, Hernández F, López K, Quezada H, González J, López G, Aranda C, González A (2011) Saccharomyces cerevisiae Bat1 and Bat2 aminotransferases have functionally diverged from the ancestral-like Kluyveromyces lactis orthologous enzyme. PLoS One 6:e16099.  https://doi.org/10.1371/journal.pone.0016099
  11. Díez L, Solopova A, Fernández-Pérez R, González M, Tenorio C, Kuipers OP, Ruiz-Larrea F (2017) Transcriptome analysis shows activation of the arginine deiminase pathway in Lactococcus lactis as a response to ethanol stress. Int J Food Microbiol 257:41–48.  https://doi.org/10.1016/j.ijfoodmicro.2017.05.017
  12. Daugherty JR, Rai R, el Berry HM, Cooper TG (1993) Regulatory circuit for responses of nitrogen catabolic gene expression to the GLN3 and DAL80 proteins and nitrogen catabolite repression in Saccharomyces cerevisiae. J Bacteriol 175:64–73.  https://doi.org/10.1128/jb.175.1.64-73.1993
  13. Dickinson JR, Harrison SJ, Dickinson JA, Hewlins MJE (2000) An investigation of the metabolism of isoleucine to active amyl alcohol in Saccharomyces cerevisiae. J Biol Chem 275:10937–10942.  https://doi.org/10.1074/jbc.275.15.10937 CrossRefPubMedGoogle Scholar
  14. Donaton MCV, Holsbeeks I, Lagatie O, Van Zeebroeck G, Crauwels M, Winderickx J, Thevelein JM (2003) The Gap1 general amino acid permease acts as an amino acid sensor for activation of protein kinase A targets in the yeast Saccharomyces cerevisiae. Mol Microbiol 50:911–929.  https://doi.org/10.1046/j.1365-2958.2003.03732.x CrossRefPubMedGoogle Scholar
  15. Eden A, Van Nedervelde L, Drukker M, Benvenisty N, Debourg A (2001) Involvement of branched-chain amino acid aminotransferases in the production of fusel alcohols during fermentation in yeast. Appl Microbiol Biotechnol 55:296–300.  https://doi.org/10.1007/s002530000506 CrossRefPubMedGoogle Scholar
  16. Eglinton JM, Heinrich AJ, Pollnitz AP, Langridge P, Henschke PA, de Barros Lopes M (2002) Decreasing acetic acid accumulation by a glycerol overproducing strain of Saccharomyces cerevisiae by deleting the ALD6 aldehyde dehydrogenase gene. Yeast 19:295–301.  https://doi.org/10.1002/yea.834
  17. Georis I, Feller A, Vierendeels F, Dubois E (2009) The yeast GATA factor Gat1 occupies a central position in nitrogen catabolite repression-sensitive gene activation. Mol Cell Biol 29:3803–3815.  https://doi.org/10.1128/MCB.00399-09 CrossRefPubMedPubMedCentralGoogle Scholar
  18. Grauslund M, Didion T, Kielland-Brandt MC, Andersen HA (1995) BAP2, a gene encoding a permease for branched-chain amino acids in Saccharomyces cerevisiae. Biochim Biophys Acta 1269:275–280.  https://doi.org/10.1016/0167-4889(95)00138-8 CrossRefPubMedGoogle Scholar
  19. Guldener U, Heinisch J, Koehler GJ, Voss D, Hegemann JH (2002) A second set of loxP marker cassettes for Cre-mediated multiple gene knockouts in budding yeast. Nucleic Acids Res 30:e23.  https://doi.org/10.1093/nar/30.6.e23
  20. Hall C, Dietrich FS (2007) The reacquisition of biotin prototrophy in Saccharomyces cerevisiae involved horizontal gene transfer, gene duplication and gene clustering. Genetics 177:2293–2307.  https://doi.org/10.1534/genetics.107.074963 CrossRefPubMedPubMedCentralGoogle Scholar
  21. Hamada K, Terashima H, Arisawa M, yabuki N, Kitada K (1999) Amino acid residues in the ω-minus region participate in cellular localization of yeast glycosylphosphatidylinositol-attached proteins. J Bacteriol 181:3886–3889PubMedPubMedCentralGoogle Scholar
  22. Hazelwood LA, Daran JM, Van Maris AJA, Pronk JT, Dickinson JR (2008) The Ehrlich pathway for fusel alcohol production: a century of research on Saccharomyces cerevisiae metabolism. Appl Environ Microbiol 74:2259–2266.  https://doi.org/10.1128/AEM.02625-07
  23. Herzig S, Raemy E, Montessuit S, Veuthey JL, Zamboni N, Westermann B, Kunji ERS, Martinou JC (2012) Identification and functional expression of the mitochondrial pyruvate carrier. Science 337:93–96.  https://doi.org/10.1126/science.1218530 CrossRefPubMedGoogle Scholar
  24. Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12:357–360.  https://doi.org/10.1038/nmeth.3317 CrossRefPubMedPubMedCentralGoogle Scholar
  25. Kitagaki H, Shimoi H, Itoh K (1997) Identification and analysis of a static culture-specific cell wall protein, Tirlp/Srplp in Saccharomyces cerevisiae. Eur J Biochem 249:343–349.  https://doi.org/10.1111/j.1432-1033.1997.t01-1-00343.x CrossRefPubMedGoogle Scholar
  26. Kobayashi M, Shimizu H, Shioya S (2008) Beer volatile compounds and their application to low-malt beer fermentation. J Biosci Bioeng 106:317–323.  https://doi.org/10.1263/jbb.106.317 CrossRefPubMedGoogle Scholar
  27. Landaud S, Latrille E, Corrieu G (2001) Top pressure and temperature control the fusel alcohol/ester ratio through yeast growth in beer fermentation. J I Brewing 107:107–117.  https://doi.org/10.1002/j.2050-0416.2001.tb00083.x CrossRefGoogle Scholar
  28. Li W, Chen SJ, Wang JH, Zhang CY, Shi Y, Guo XW, Chen YF, Xiao DG (2018) Genetic engineering to alter carbon flux for various higher alcohol productions by Saccharomyces cerevisiae for Chinese Baijiu fermentation. Appl Microbiol Biotechnol 102:1783–1795. https://doi.org/10.1007/s00253-017-8715-5
  29. Lilly M, Bauer FF, Styger G, Lambrechts MG, Pretorius IS (2006) The effect of increased branched-chain amino acid transaminase activity in yeast on the production of higher alcohols and on the flavour profiles of wine and distillates. FEMS Yeast Res 6:726–743.  https://doi.org/10.1111/j.1567-1364.2006.00057.x
  30. Liu FZ, Zhang CY, Li W, Liu XQ, Xiao DG (2016) Effects of BAT genetic modification on the yield of higher alcohols from Saccharomyces cerevisiae. Mod Food Sci Technol 32:142–147.  https://doi.org/10.13982/j.mfst.1673-9078.2016.6.023 CrossRefGoogle Scholar
  31. Ma LJ, Huang SY, Du LP, Tang P, Xiao DG (2017) Reduced production of higher alcohols by Saccharomyces cerevisiae in red wine fermentation by simultaneously overexpressing BAT1 and deleting BAT2. J Agric Food Chem 65:6936–6942.  https://doi.org/10.1021/acs.jafc.7b01974 CrossRefPubMedGoogle Scholar
  32. Molina AM, Swiegers JH, Varela C, Pretorius IS, Agosin E (2007) Influence of wine fermentation temperature on the synthesis of yeast-derived volatile aroma compounds. Appl Microbiol Biotechnol 77:675–687.  https://doi.org/10.1007/s00253-007-1194-3 CrossRefPubMedGoogle Scholar
  33. Mouret JR, Camarasa C, Angenieux M, Aguera E, Perez M, Farines V, Sablayrolles JM (2014) Kinetic analysis and gas–liquid balances of the production of fermentative aromas during winemaking fermentations: effect of assimilable nitrogen and temperature. Food Res Int 62:1–10.  https://doi.org/10.1016/j.foodres.2014.02.044 CrossRefGoogle Scholar
  34. Nookaew I, Papini M, Pornputtapong N, Scalcinati G, Fagerberg L, Uhlén M, Nielsen J (2012) A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae. Nucleic Acids Res 40:10084–10097.  https://doi.org/10.1093/nar/gks804 CrossRefPubMedPubMedCentralGoogle Scholar
  35. Park SH, Kim SJ, Hahn JS (2014) Metabolic engineering of Saccharomyces cerevisiae for the production of isobutanol and 3-methyl-1-butanol. Appl Microbiol Biotechnol 98:9139–9147.  https://doi.org/10.1007/s00253-014-6081-0 CrossRefPubMedGoogle Scholar
  36. Phalip V, Kuhn I, Lemoine Y, Jeltsch JM (1999) Characterization of the biotin biosynthesis pathway in Saccharomyces cerevisiae and evidence for a cluster containing BIO5, a novel gene involved in vitamer uptake. Gene 232:43–51.  https://doi.org/10.1016/S0378-1119(99)00117-1 CrossRefPubMedGoogle Scholar
  37. Pires EJ, Teixeira JA, Brányik T, Vicente AA (2014) Yeast: the soul of beer’s aroma--a review of flavour-active esters and higher alcohols produced by the brewing yeast. Appl Microbiol Biotechnol 98:1937–1949.  https://doi.org/10.1007/s00253-013-5470-0
  38. Pizarro FJ, Jewett MC, Nielsen J, Agosin E (2008) Growth temperature exerts differential physiological and transcriptional responses in laboratory and wine strains of Saccharomyces cerevisiae. Appl Environ Microbiol 74:6358–6368.  https://doi.org/10.1128/AEM.00602-08 CrossRefPubMedPubMedCentralGoogle Scholar
  39. Procopio S, Qian F, Becker T (2011) Function and regulation of yeast genes involved in higher alcohol and ester metabolism during beverage fermentation. Eur Food Res Technol 233:721–729.  https://doi.org/10.1007/s00217-011-1567-9 CrossRefGoogle Scholar
  40. Procopio S, Krause D, Hofmann T, Becker T (2013) Significant amino acids in aroma compound profiling during yeast fermentation analyzed by PLS regression. LWT-Food Sci Technol 51:423–432.  https://doi.org/10.1016/j.lwt.2012.11.022 CrossRefGoogle Scholar
  41. Ramos F, Wiame JM (1982) Occurrence of a catabolic L-serine (L-threonine) deaminase in Saccharomyces cerevisiae. Eur J Biochem 123:571–576.  https://doi.org/10.1111/j.1432-1033.1982.tb06570.x
  42. Remize F, Andrieu E, Dequin S (2000) Engineering of the pyruvate dehydrogenase bypass in Saccharomyces cerevisiae: role of the cytosolic Mg2+ and mitochondrial K+ acetaldehyde dehydrogenases Ald6p and Ald4p in acetate formation during alcoholic fermentation. Appl Environ Microbiol 66:3151–3159.  https://doi.org/10.1128/AEM.66.8.3151-3159.2000 CrossRefPubMedPubMedCentralGoogle Scholar
  43. Rollero S, Bloem A, Camarasa C, Sanchez I, Ortiz-Julien A, Sablayrolles JM, Dequin S, Mouret JR (2015) Combined effects of nutrients and temperature on the production of fermentative aromas by Saccharomyces cerevisiae during wine fermentation. Appl Microbiol Biotechnol 99:2291–2304.  https://doi.org/10.1007/s00253-014-6210-9 CrossRefPubMedGoogle Scholar
  44. Saerens SMG, Verbelen PJ, Vanbeneden N, Thevelein JM, Delvaux FR (2008) Monitoring the influence of high-gravity brewing and fermentation temperature on flavour formation by analysis of gene expression levels in brewing yeast. Appl Microbiol Biotechnol 80:1039–1051.  https://doi.org/10.1007/s00253-008-1645-5 CrossRefPubMedGoogle Scholar
  45. Sasano Y, Haitani Y, Hashida K, Ohtsu I, Shima J, Takagi H (2012) Enhancement of the proline and nitric oxide synthetic pathway improves fermentation ability under multiple baking-associated stress conditions in industrial baker’s yeast. Microb Cell Fact 11:40.  https://doi.org/10.1186/1475-2859-11-40 CrossRefPubMedPubMedCentralGoogle Scholar
  46. Schoondermark-Stolk SA, Tabernero M, Chapman J, Ter Schure EG, Verrips CT, Verkleij AJ, Boonstra J (2005) Bat2p is essential in Saccharomyces cerevisiae for fusel alcohol production on the non-fermentable carbon source ethanol. FEMS Yeast Res 5:757–766.  https://doi.org/10.1016/j.femsyr.2005.02.005
  47. Schoondermark-Stolk SA, Jansen M, Verkleij AJ, Verrips CT, Euverink GJW, Dijkhuizen L, Boonstra J (2006a) Genome-wide transcription survey on flavour production in Saccharomyces cerevisiae. World J Microbiol Biotechnol 22:1347–1356.  https://doi.org/10.1007/s11274-006-9182-9 CrossRefGoogle Scholar
  48. Schoondermark-Stolk SA, Jansen M, Veurink JH, Verkleij AJ, Verrips CT, Euverink GJW, Boonstra J, Dijkhuizen L (2006b) Rapid identification of target genes for 3-methyl-1-butanol production in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 70:237-246.  https://doi.org/10.1007/s00253-005-0070-2
  49. Stribny J, Gamero A, Pérez-Torrado R, Querol A (2015) Saccharomyces kudriavzevii and Saccharomyces uvarum differ from Saccharomyces cerevisiae during the production of aroma-active higher alcohols and acetate esters using their amino acidic precursors. Int J Food Microbiol 205:41–46.  https://doi.org/10.1016/j.ijfoodmicro.2015.04.003 CrossRefPubMedGoogle Scholar
  50. Tai SL, Daran-Lapujade P, Luttik MAH, Walsh MC, Diderich JA, Krijger GC, Van Gulik WM, Pronk JT, Daran JM (2007) Control of the glycolytic flux in Saccharomyces cerevisiae grown at low temperature: a multi-level analysis in anaerobic chemostat cultures. J Biol Chem 282:10243–10251.  https://doi.org/10.1074/jbc.M610845200 CrossRefPubMedGoogle Scholar
  51. Takagi H (2008) Proline as a stress protectant in yeast: physiological functions, metabolic regulations, and biotechnological applications. Appl Microbiol Biotechnol 81:211–223.  https://doi.org/10.1007/s00253-008-1698-5 CrossRefPubMedGoogle Scholar
  52. Ter Schure EG, Silljé HHW, Verkleij AJ, Boonstra J, Verrips CT (1995) The concentration of ammonia regulates nitrogen metabolism in Saccharomyces cerevisiae. J Bacteriol 177:6672–6675.  https://doi.org/10.1128/jb.177.22.6672-6675.1995
  53. Tokai M, Kawasaki H, Kikuchi Y, Ouchi K (2000) Cloning and characterization of the CSF1 gene of Saccharomyces cerevisiae, which is required for nutrient uptake at low temperature. J Bacteriol 182:2865–2868.  https://doi.org/10.1021/jp2103066 CrossRefPubMedPubMedCentralGoogle Scholar
  54. Vanderhaegen B, Neven H, Coghe S, Verstrepen KJ, Verachtert H, Derdelinckx G (2003) Evolution of chemical and sensory properties during aging of top-fermented beer. J Agric Food Chem 51:6782–6790.  https://doi.org/10.1021/jf034631z CrossRefPubMedGoogle Scholar
  55. Verbelen PJ, Dekoninck TM, Saerens SM, Van Mulders SE, Thevelein JM, Delvaux FR (2009) Impact of pitching rate on yeast fermentation performance and beer flavour. Appl Microbiol Biotechnol 82:155–167.  https://doi.org/10.1007/s00253-008-1779-5 CrossRefPubMedGoogle Scholar
  56. Wang P, Wang FF, Yang J (2017) De novo assembly and analysis of the Pugionium cornutum (L.) Gaertn. transcriptome and identification of genes involved in the drought response. Gene 626:290–297.  https://doi.org/10.1016/j.gene.2017.05.053 CrossRefPubMedGoogle Scholar
  57. Weider M, Machnik A, Klebl F, Sauer N (2006) Vhr1p, a new transcription factor from budding yeast, regulates biotin-dependent expression of VHT1 and BIO5. J Biol Chem 281:13513–13524.  https://doi.org/10.1074/jbc.M512158200 CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Zhong-Guan Sun
    • 1
    • 2
  • Meng-Qi Wang
    • 1
    • 2
  • Ya-Ping Wang
    • 1
    • 2
  • Shuang Xing
    • 1
    • 2
  • Kun-Qiang Hong
    • 1
    • 2
  • Ye-Fu Chen
    • 1
    • 2
  • Xue-Wu Guo
    • 1
    • 2
    Email author
  • Dong-Guang Xiao
    • 1
    • 2
    Email author
  1. 1.Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of BiotechnologyTianjin University of Science and TechnologyTianjinPeople’s Republic of China
  2. 2.Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process ControlTianjin University of Science and TechnologyTianjinPeople’s Republic of China

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