Comparative functional genomics to reveal the molecular basis of phenotypic diversities and guide the genetic breeding of industrial yeast strains

Applied Microbiology and Biotechnology

Volumn 97, Issue 5, 2013, Pages 2067-2076

  Zheng, Dao Qiong ^a   Liu, Tian Zhe ^a   Chen, Jie ^a   Zhang, Ke ^a   Li, Ou ^a   Zhu, Liang ^a   Zhao, Yu Hua ^a   Wu, Xue Chang ^a   Wang, Pin Mei ^a  

^a ZHEJIANG UNIVERSITY   (China)

Author keywords

Bioethanol; Genetic breeding; RNA Seq; Saccharomyces cerevisiae; Stress

Indexed keywords

ACID TOLERANCE; ANTIOXIDATIVE; CENTRAL CARBON METABOLISMS; ETHANOL FERMENTATION; EXPRESSED GENES; FUNCTIONAL GENOMICS; GENETIC BASIS; GENETIC BREEDING; GENETIC INFORMATION; INDUSTRIAL YEAST; MEMBRANE COMPOSITION; MOLECULAR BASIS; PHENOTYPIC DIVERSITY; PHENOTYPIC VARIATIONS; RNA-SEQ; SACCHAROMYCES CEREVISIAE STRAINS; STRESS TOLERANCE; STRUCTURAL VARIATIONS; YEAST STRAIN;

ACETIC ACID; BIOETHANOL; CELL MEMBRANES; ETHANOL; FERMENTATION; GENE EXPRESSION; OLEIC ACID; RNA; STRESSES;

YEAST;

ANTIOXIDANT; FATTY ACID; OLEIC ACID; STEROL;

BREEDING; ETHANOL; FERMENTATION; GENE; GENETIC ANALYSIS; GENETIC VARIATION; GENOMICS; MEMBRANE; METABOLISM; PHENOTYPE; PLASMA; YEAST;

ACID TOLERANCE; ALCOHOL PRODUCTION; ARTICLE; BACTERIUM CONTAMINATION; BREEDING METHOD; CARBON METABOLISM; CONTROLLED STUDY; COPY NUMBER VARIATION; FATTY ACID METABOLISM; FATTY ACID OXIDATION; FATTY ACID SYNTHESIS; FERMENTATION TECHNIQUE; FUNCTIONAL GENOMICS; GENE MAPPING; GENE OVEREXPRESSION; GENE STRUCTURE; GENETIC MANIPULATION; GENETIC TRAIT; GENETIC VARIABILITY; MEMBRANE FORMATION; NONHUMAN; NUCLEOTIDE SEQUENCE; OSMOTIC PRESSURE; OXIDATIVE STRESS; PHENOTYPIC VARIATION; RNA SEQUENCE; SACCHAROMYCES CEREVISIAE; STEROL METABOLISM; STRESS; SYNTHESIS; YEAST;

DNA SHUFFLING; ETHANOL; GENE EXPRESSION PROFILING; GENOMICS; INDUSTRIAL MICROBIOLOGY; METABOLIC ENGINEERING; METABOLIC NETWORKS AND PATHWAYS; SACCHAROMYCES CEREVISIAE;

SACCHAROMYCES CEREVISIAE;

EID: 84874118739     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-013-4698-z     Document Type: Article

References (37)

1. Akache B, Wu KQ, Turcotte B (2001) Phenotypic analysis of genes encoding yeast zinc cluster proteins. Nucleic Acids Res 29(10):2181-2190
2. Akao T, Yashiro I, Hosoyama A, Kitagaki H, Horikawa H, Watanabe D, Akada R, Ando Y, Harashima S, Inoue T, Inoue Y, Kajiwara S, Kitamoto K, Kitamoto N, Kobayashi O, Kuhara S, Masubuchi T, Mizoguchi H, Nakao Y, Nakazato A, Namise M, Oba T, Ogata T, Ohta A, Sato M, Shibasaki S, Takatsume Y, Tanimoto S, Tsuboi H, Nishimura A, Yoda K, Ishikawa T, Iwashita K, Fujita N, Shimoi H (2011) Whole-genome sequencing of sake yeast Saccharomyces cerevisiae kyokai no. 7. DNA Res 18(6):423-434
3. Anderson MJ, Barker SL, Boone C, Measday V (2012) Identification of RCN1 and RSA3 as ethanol-tolerant genes in Saccharomyces cerevisiae using a high copy barcoded library. FEMS Yeast Res 12(1):48-60
4. Argueso JL, Carazzolle MF, Mieczkowski PA, Duarte FM, Netto OV, Missawa SK, Galzerani F, Costa GG, Vidal RO, Noronha MF, Dominska M, Andrietta MG, Andrietta SR, Cunha AF, Gomes LH, Tavares FC, Alcarde AR, Dietrich FS, McCusker JH, Petes TD, Pereira GA (2009) Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production. Genome Res 19(12):2258-2270
5. Auesukaree C, Damnernsawad A, Kruatrachue M, Pokethitiyook P, Boonchird C, Kaneko Y, Harashima S (2009) Genome-wide identification of genes involved in tolerance to various environmental stresses in Saccharomyces cerevisiae. J Appl Genet 50(3):301-310
6. 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. N Biotechnol 29(3):379-386
7. Borneman AR, Desany BA, Riches D, Affourtit JP, Forgan AH, Pretorius IS, Egholm M, Chambers PJ (2011) Whole-genome comparison reveals novel genetic elements that characterize the genome of industrial strains of Saccharomyces cerevisiae. PLoS Genet 7(2):e1001287
8. Causton HC, Ren B, Koh SS, Harbison CT, Kanin E, Jennings EG, Lee TI, True HL, Lander ES, Young RA (2001) Remodeling of yeast genome expression in response to environmental changes. Mol Biol Cell 12(2):323-337
9. Dunn B, Richter C, Kvitek DJ, Pugh T, Sherlock G (2012) Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments. Genome Res 22(5):908-924
10. Estruch F (2000) Stress-controlled transcription factors, stress-induced genes and stress tolerance in budding yeast. FEMS Microbiol Rev 24(4):469-486
11. Fujita K, Matsuyama A, Kobayashi Y, Iwahashi H (2006) The genome-wide screening of yeast deletion mutants to identify the genes required for tolerance to ethanol and other alcohols. FEMS Yeast Res 6(5):744-750
12. Hirasawa T, Yamada K, Nagahisa K, Dinh TN, Furusawa C, Katakura Y, Shioya S, Shimizu H (2009) Proteomic analysis of responses to osmotic stress in laboratory and sake-brewing strains of Saccharomyces cerevisiae. Process Biochem 44(6):647-653
13. Jamieson DJ (1998) Oxidative stress responses of the yeast Saccharomyces cerevisiae. Yeast 14(16):1511-1527
14. Kvitek DJ, Will JL, Gasch AP (2008) Variations in stress sensitivity and genomic expression in diverse S. cerevisiae isolates. PLoS Genet 4(10):e1000223
15. 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(3):229-235
16. Lewis JA, Elkon IM, McGee MA, Higbee AJ, Gasch AP (2010) Exploiting natural variation in Saccharomyces cerevisiae to identify genes for increased ethanol resistance. Genetics 186(4):1197-1205
17. Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25(15):1966-1967
18. Mahmud SA, Hirasawa T, Shimizu H (2010) Differential importance of trehalose accumulation in Saccharomyces cerevisiae in response to various environmental stresses. J Biosci Bioeng 109(3):262-266
19. Melamed D, Pnueli L, Arava Y (2008) Yeast translational response to high salinity: global analysis reveals regulation at multiple levels. RNA 14(7):1337-1351
20. Mira NP, Palma M, Guerreiro JF, Sa-Correia I (2010) Genome-wide identification of Saccharomyces cerevisiae genes required for tolerance to acetic acid. Microb Cell Factories 9:79
21. Mira NP, Henriques SF, Keller G, Teixeira MC, Matos RG, Arraiano CM, Winge DR, Sa-Correia I (2011) Identification of a DNA-binding site for the transcription factor Haa1, required for Saccharomyces cerevisiae response to acetic acid stress. Nucleic Acids Res 39(16):6896-6907
22. Mulford KE, Fassler JS (2011) Association of the Skn7 and Yap1 transcription factors in the Saccharomyces cerevisiae oxidative stress response. Eukaryot Cell 10(6):761-769
23. Pavelka N, Rancati G, Zhu J, Bradford WD, Saraf A, Florens L, Sanderson BW, Hattem GL, Li R (2010) Aneuploidy confers quantitative proteome changes and phenotypic variation in budding yeast. Nature 468(7321):321-325
24. Redón M, Guillamón JM, Mas A, Rozès N (2011) Effect of growth temperature on yeast lipid composition and alcoholic fermentation at low temperature. Eur Food Res Technol 232(3):517-527
25. 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(20):6600-6612
26. Sanda T, Hasunuma T, Matsuda F, Kondo A (2011) Repeated-batch fermentation of lignocellulosic hydrolysate to ethanol using a hybrid Saccharomyces cerevisiae strain metabolically engineered for tolerance to acetic and formic acids. Bioresour Technol 102(17):7917-7924
27. Tao X, Zheng D, Liu T, Wang P, Zhao W, Zhu M, Jiang X, Zhao Y, Wu X (2012) A novel strategy to construct yeast Saccharomyces cerevisiae strains for very high gravity fermentation. PLoS One 7(2):e31235
28. Teixeira MC, Raposo LR, Mira NP, Lourenco AB, Sa-Correia I (2009) Genome-wide identification of Saccharomyces cerevisiae genes required for maximal tolerance to ethanol. Appl Environ Microbiol 75(18):5761-5772
29. Teste MA, Duquenne M, François J, Parrou JL (2009) Validation of reference genes for quantitative expression analysis by real-time RT-PCR in Saccharomyces cerevisiae. BMC Mol Biol 10:99
30. Torres EM, Sokolsky T, Tucker CM, Chan LY, Boselli M, Dunham MJ, Amon A (2007) Effects of aneuploidy on cellular physiology and cell division in haploid yeast. Science 317(5840):916-924
31. Wang B, Guo G, Wang C, Lin Y, Wang X, Zhao M, Guo Y, He M, Zhang Y, Pan L (2010) Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing. Nucleic Acids Res 38(15):5075-5087
32. Wang PM, Zheng DQ, Liu TZ, Tao XL, Feng MG, Min H, Jiang XH, Wu XC (2012) The combination of glycerol metabolic engineering and drug resistance marker-aided genome shuffling to improve very-high-gravity fermentation performances of industrial Saccharomyces cerevisiae. Bioresour Technol 108:203-210
33. Yang J, Bae JY, Lee YM, Kwon H, Moon HY, Kang HA, Yee S, Kim W, Choi W (2011) Construction of Saccharomyces cerevisiae strains with enhanced ethanol tolerance by mutagenesis of the TATA-binding protein gene and identification of novel genes associated with ethanol tolerance. Biotechnol Bioeng 108(8):1776-1787
34. Yazawa H, Kamisaka Y, Kimura K, Yamaoka M, Uemura H (2011) Efficient accumulation of oleic acid in Saccharomyces cerevisiae caused by expression of rat elongase 2 gene (rELO2) and its contribution to tolerance to alcohols. Appl Microbiol Biotechnol 91(6):1593-1600
35. You KM, Rosenfield CL, Knipple DC (2003) Ethanol tolerance in the yeast Saccharomyces cerevisiae is dependent on cellular oleic acid content. Appl Environ Microbiol 69(3):1499-1503
36. Zheng DQ, Wu XC, Tao XL, Wang PM, Li P, Chi XQ, Li YD, Yan QF, Zhao YH (2011) Screening and construction of Saccharomyces cerevisiae strains with improved multi-tolerance and bioethanol fermentation performance. Bioresour Technol 102(3):3020-3027
37. Zheng DQ, Wang PM, Chen J, Zhang K, Liu TZ, Wu XC, Li YD, Zhao YH (2012) Genome sequencing and genetic breeding of a bioethanol Saccharomyces cerevisiae strain YJS329. BMC Genomics 13(1):479