Skip to main content
SpringerLink
Log in

Investigating the underlying mechanism of Saccharomyces cerevisiae in response to ethanol stress employing RNA-seq analysis

  • Original Paper
  • Published:
World Journal of Microbiology and Biotechnology Aims and scope Submit manuscript

Abstract

Saccharomyces cerevisiae has been widely used for wine fermentation and bio-fuels production. A S. cerevisiae strain Sc131 isolated from tropical fruit shows good fermentation properties and ethanol tolerance, exhibiting significant potential in Chinese bayberry wine fermentation. In this study, RNA-sequence and RT-qPCR was used to investigate the transcriptome profile of Sc131 in response to ethanol stress. Scanning Electron Microscopy were carried out to observe surface morphology of yeast cells. Totally, 937 genes were identified differential expressed, including 587 up-regulated and 350 down-regulated genes, after 4-h ethanol stress (10% v/v). Transcriptomic analysis revealed that, most genes involved in regulating filamentous growth or pseudohyphal growth were significantly up-regulated in response to ethanol stress. The complex protein quality control machineries, Hsp90/Hsp70 and Hsp104/Hsp70/Hsp40 based chaperone system combining with ubiquitin–proteasome proteolytic pathway were both activated to recognize and degrade misfolding proteins. Genes related to biosynthesis and metabolism of two well-known stress-responsive substances trehalose and ergosterol were generally up-regulated, while genes associated with amino acids biosynthesis and metabolism processes were differentially expressed. Moreover, thiamine was also important in response to ethanol stress. This research may promote the potential applications of Sc131 in the fermentation of Chinese bayberry wine.

Graphical Abstract

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

References

  • Amm I, Sommer T, Wolf DH (2014) Protein quality control and elimination of protein waste: the role of the ubiquitin-proteasome system. Biochim Biophys Acta 1843:182–196

    Article  CAS  Google Scholar 

  • Behnke J, Hendershot LM (2014) The large hsp70 grp170 binds to unfolded protein substrates in vivo with a regulation distinct from conventional hsp70s. J Biol Chem 289:2899–2907

    Article  CAS  Google Scholar 

  • Benjaphokee S, Hasegawa D, Yokota D, Asvarak T, Auesukaree C, Sugiyama M, Kaneko Y, Boonchird C, Harashima S (2012) Highly efficient bioethanol production by a Saccharomyces cerevisiae strain with multiple stress tolerance to high temperature, acid and ethanol. New Biotechnol 29:379–386

    Article  CAS  Google Scholar 

  • Berndsen CE, Wolberger C (2014) New insights into ubiquitin E3 ligase mechanism. Nat Struct Mol Biol 21:301–307

    Article  CAS  Google Scholar 

  • Cain CW, Lohse MB, Homann OR, Sil A, Johnson AD (2012) A conserved transcriptional regulator governs fungal morphology in widely diverged species. Genetics 190:511–521

    Article  CAS  Google Scholar 

  • Chen YY, Zhang ZH, Zhong CY, Song XM, Lin QH, Huang CM, Huang RH, Chen W (2016) Functional analysis of differentially expressed proteins in Chinese bayberry (Myrica rubra sieb. et Zucc.) fruits during ripening. Food Chem 190:763–770

    Article  CAS  Google Scholar 

  • Dimauro S, Tanji K, Schon EA (2012) The many clinical faces of cytochrome c oxidase deficiency. Adv Exp Med Biol 748:341–357

    Article  CAS  Google Scholar 

  • Doğan A, Demirci S, Aytekin AÖ, Şahin F (2014) Improvements of tolerance to stress conditions by genetic engineering in Saccharomyces cerevisiae, during ethanol production. Appl Biochem Biotechnol 174:28–42

    Article  Google Scholar 

  • Du J, Han F, Yu P, Li J, Fan L (2016) Optimization of fermentation conditions for Chinese bayberry wine by response surface methodology and its qualities. J Inst Brew 122:763–771

    Article  CAS  Google Scholar 

  • Fraser HB (2011) Genome-wide approaches to the study of adaptive gene expression evolution: systematic studies of evolutionary adaptations involving gene expression will allow many fundamental questions in evolutionary biology to be addressed. Bioessays 33:469–477

    Article  CAS  Google Scholar 

  • Fujita K, Matsuyama A, Kobayashi Y, Iwahashi H (2004) Comprehensive gene expression analysis of the response to straight-chain alcohols in Saccharomyces cerevisiae using cDNA microarray. J Appl Microbiol 97:57–67

    Article  CAS  Google Scholar 

  • Garny K, Neu TR, Horn H (2009) Sloughing and limited substrate conditions trigger filamentous growth in heterotrophic biofilms—measurements in flow-through tube reactor. Chem Eng Sci 64:2723–2732

    Article  CAS  Google Scholar 

  • Glover JR, Lindquist S (1998) Hsp104, hsp70, and hsp40: a novel chaperone system that rescues previously aggregated proteins. Cell 94:73–82

    Article  CAS  Google Scholar 

  • Good M, Tang G, Singleton J, Reményi A, Lim WA (2009) The ste5 scaffold directs mating signaling by catalytically unlocking the fus3 map kinase for activation. Cell 136:1085–1097

    Article  CAS  Google Scholar 

  • Guo S, Zheng Y, Joung JG, Liu SQ, Zhang ZH, Crasta OR, Sobral BW, Xu Y, Huan SW, Fei ZJ (2010) Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types. BMC Genomics 11:384

    Article  Google Scholar 

  • Han XJ, Wang YD, Chen YC, Lin LY, Wu QK (2013) Transcriptome sequencing and expression analysis of terpenoid biosynthesis genes in litsea cubeba. PLoS ONE 8:e76890

    Article  CAS  Google Scholar 

  • Jin H, Komita M, Aoe T (2017) The role of BiP retrieval by the KDEL receptor in the early secretory pathway and its effect on protein quality control and neurodegeneration. Front Mol Neurosci 10:222

    Article  Google Scholar 

  • Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori AM (2004) The kegg resource for deciphering the genome. Nucleic Acids Res 32:277–280

    Article  Google Scholar 

  • Kasavi C, Eraslan S, Oner ET, Kirdar B (2016) An integrative analysis of transcriptomic response of ethanol tolerant strains to ethanol in Saccharomyces cerevisiae. Mol Biosyst 12:464–476

    Article  CAS  Google Scholar 

  • Kempf C, Lengeler K, Wendland J (2017) Differential stress response of saccharomyces hybrids revealed by monitoring hsp104 aggregation and disaggregation. Microbiol Res 200:53–63

    Article  CAS  Google Scholar 

  • Kimura T, Hosoda Y, Sato Y, Kitamura Y, Ikeda T, Horibe T, Kikuchi M (2005) Interactions among yeast protein-disulfide isomerase proteins and endoplasmic reticulum chaperone proteins influence their activities. J Biol Chem 280:31438–31441

    Article  CAS  Google Scholar 

  • Lam FH, Ghaderi A, Fink GR, Stephanopoulos G (2014) Engineering alcohol tolerance in yeast. Science 346:71–75

    Article  CAS  Google Scholar 

  • Lee D, Kim M, Cho KH (2014) A design principle underlying the paradoxical roles of E3 ubiquitin ligases. Sci Rep 4:5573

    Article  CAS  Google Scholar 

  • Li J, Soroka J, Buchner J (2012) The hsp90 chaperone machinery: conformational dynamics and regulation by co-chaperones ☆. Biochim Biophys Acta 1823:624–635

    Article  CAS  Google Scholar 

  • Lorenz MC, Cutler NS, Heitman J (2000) Characterization of alcohol-induced filamentous growth in Saccharomyces cerevisiae. Mol Biol Cell 11:183–199

    Article  CAS  Google Scholar 

  • Ma M, Liu ZL (2010) Mechanisms of ethanol tolerance in Saccharomyces cerevisiae. Appl. Microbiol Biotechnol 87:829–845

    Article  CAS  Google Scholar 

  • Martínezmontañés F, Rienzo A, Povedahuertes D, Pascualahuir A, Proft M (2013) Activator and repressor functions of the Mot3 transcription factor in the osmostress response of Saccharomyces cerevisiae. Eukaryot Cell 12:636–647

    Article  Google Scholar 

  • Martos GI, Minahk CJ, Valdez GFD, Morero R (2007) Effects of protective agents on membrane fluidity of freeze-dried Lactobacillus delbrueckii ssp. bulgaricus. Lett Appl Microbiol 45:282–288

    Article  CAS  Google Scholar 

  • Mourier A, Larsson N (2011) Tracing the trail of protons through complex I of the mitochondrial respiratory chain. PLoS Biol 9:e1001129

    Article  CAS  Google Scholar 

  • Müller CA, Hawkins M, Retkute R, Malla S, Wilson R, Blythe MJ, Nakato R, Komata M, Shirahige K, Moura APSD, Nieduszynski CA (2014) The dynamics of genome replication using deep sequencing. Nucleic Acids Res 42:e3

    Article  Google Scholar 

  • Nagae M, Parniske M, Kawaguchi M, Takeda N (2016) The thiamine biosynthesis gene THI1 promotes nodule growth and seed maturation. Plant Physiol 172:2033–2043

    Article  CAS  Google Scholar 

  • Nillegoda NB, Theodoraki MA, Mandal AK, Mayo KJ, Ren HY, Sultana R, Wu K, Johnson J, Cyr DM, Caplan AJ (2010) Ubr1 and Ubr2 function in a quality control pathway for degradation of unfolded cytosolic proteins. Mol Biol Cell 21:2102–2116

    Article  CAS  Google Scholar 

  • Patterson JC, Klimenko ES, Thorner J (2010) Single-cell analysis reveals that insulation maintains signaling specificity between two yeast mapk pathways with common components. Sci Signal 3:625–638

    Article  Google Scholar 

  • Ranganathan S, Bai G, Lyubetskaya A, Knapp GS, Peterson MW, Gazdik M, Gomes ALC, Galagan JE, McDonough KA (2015) Characterization of a cAMP responsive transcription factor, Cmr (Rv1675c), in TB complex mycobacteria reveals overlap with the DosR (Devr) dormancy regulon. Nucleic Acids Res 44:134–151

    Article  Google Scholar 

  • Ren B, Dai HQ, Pei G, Tong YJ, Zhuo Y, Yang N, Su MY, Huang P, Yang YZ, Zhang LX (2014) ABC transporters coupled with the elevated ergosterol contents contribute to the azole resistance and amphotericin B susceptibility. Appl Microbiol Biot 98:2609–2616

    Article  CAS  Google Scholar 

  • Schröder M, Chang JS, Kaufman RJ (2000) The unfolded protein response represses nitrogen-starvation induced developmental differentiation in yeast. Gene Dev 14:2962–2975

    Article  Google Scholar 

  • Schuierer S, Carbone W, Knehr J, Petitjean V, Fernandez A, Sultan M (2017) A comprehensive assessment of RNA-seq protocols for degraded and low-quantity samples. BMC Genomics 18:442

    Article  Google Scholar 

  • Snoek T, Nicolino MP, Bremt SVD, Mertens S, Saels V, Verplaetse A, Steensels J, Verstrepen KJ (2015) Large-scale robot-assisted genome shuffling yields industrial Saccharomyces cerevisiae yeasts with increased ethanol tolerance. Biotechnol Biofuels 8:32

    Article  Google Scholar 

  • Stanley D, Bandara A, Fraser S, Chambers PJ, Stanley GA (2010) The ethanol stress response and ethanol tolerance of Saccharomyces cerevisiae. J Appl Microbiol 109:13–24

    CAS  Google Scholar 

  • Teixeira MC, Raposo LR, Mira NP, Lourenço AB, Sá-Correia I (2009) Genome-wide identification of Saccharomyces cerevisiae genes required for maximal tolerance to ethanol. Appl Environ Microbiol 75:5761–5772

    Article  CAS  Google Scholar 

  • Tesnière C, Brice C, Blondin B (2015) Responses of Saccharomyces cerevisiae, to nitrogen starvation in wine alcoholic fermentation. Appl Microbiol Biotechnol 99:7025–7034

    Article  Google Scholar 

  • Teste MA, Duquenne M, François JM, Parrou JL (2009) Validation of reference genes for quantitative expression analysis by real-time RT-PCR in Saccharomyces cerevisiae. BMC Mol Biol 10:99

    Article  Google Scholar 

  • Valnot I, Osmond S, Gigarel N (2000) Mutations of the sco1 gene in mitochondrial cytochrome c oxidase deficiency with neonatal-onset hepatic failure and encephalopathy. Am J Hum Genet 67:1104–1109

    CAS  Google Scholar 

  • Wolak N, Kowalska E, Kozik A, Rapala-Kozik M (2014) Thiamine increases the resistance of baker’s yeast Saccharomyces cerevisiae against oxidative, osmotic and thermal stress, through mechanisms partly independent of thiamine diphosphate-bound enzymes. FEMS Yeast Res 14:1249–1262

    Article  CAS  Google Scholar 

  • Yoshikawa K, Tanaka T, Furusawa C, Nagahisa K, Hirasawa T, Shimizu H (2009) Comprehensive phenotypic analysis for identification of genes affecting growth under ethanol stress in Saccharomyces cerevisiae. FEMS Yeast Res 9:32–44

    Article  CAS  Google Scholar 

Download references

Acknowledgements

Authors gratefully acknowledge the financial support of National Natural Science Foundation of China (NNSF No. 31471709), K. C. Wong Magna Fund in Ningbo University and the Scientific Research Foundation of Graduate School of Ningbo University.

Author information

Authors and Affiliations

  1. Department of Food Science and Engineering, School of Marine Sciences, Ningbo University, Ningbo, 315211, People’s Republic of China

    Ruoyun Li, Guotong Xiong, Shukun Yuan, Zufang Wu, Yingjie Miao & Peifang Weng

  2. Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, People’s Republic of China

    Zufang Wu

Authors
  1. Ruoyun Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Guotong Xiong
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Shukun Yuan
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Zufang Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yingjie Miao
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Peifang Weng
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Zufang Wu.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Li, R., Xiong, G., Yuan, S. et al. Investigating the underlying mechanism of Saccharomyces cerevisiae in response to ethanol stress employing RNA-seq analysis. World J Microbiol Biotechnol 33, 206 (2017). https://doi.org/10.1007/s11274-017-2376-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s11274-017-2376-5

Keywords

Search

Navigation