QTL analysis reveals genomic variants linked to high-temperature fermentation performance in the industrial yeast

被引:29
作者
Wang, Zhen [1 ,2 ]
Qi, Qi [1 ,2 ]
Lin, Yuping [1 ]
Guo, Yufeng [1 ]
Liu, Yanfang [1 ,2 ]
Wang, Qinhong [1 ]
机构
[1] Chinese Acad Sci, Tianjin Inst Ind Biotechnol, Key Lab Syst Microbial Biotechnol, Tianjin 300308, Peoples R China
[2] Univ Chinese Acad Sci, Beijing 100049, Peoples R China
基金
美国国家科学基金会;
关键词
High-temperature fermentation (HTF); Pooled-segregant whole-genome sequence analysis; QTL mapping; Reciprocal hemizygosity analysis; Allele replacement; Saccharomyces cerevisiae; SACCHAROMYCES-CEREVISIAE; ETHANOL-PRODUCTION; GENE; TOLERANCE; VACUOLE; PROTEIN; TRAIT; FRUCTOSE-1,6-BISPHOSPHATASE; IDENTIFICATION; FRAMEWORK;
D O I
10.1186/s13068-019-1398-7
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
BackgroundHigh-temperature fermentation is desirable for the industrial production of ethanol, which requires thermotolerant yeast strains. However, yeast thermotolerance is a complicated quantitative trait. The understanding of genetic basis behind high-temperature fermentation performance is still limited. Quantitative trait locus (QTL) mapping by pooled-segregant whole genome sequencing has been proved to be a powerful and reliable approach to identify the loci, genes and single nucleotide polymorphism (SNP) variants linked to quantitative traits of yeast.ResultsOne superior thermotolerant industrial strain and one inferior thermosensitive natural strain with distinct high-temperature fermentation performances were screened from 124 Saccharomyces cerevisiae strains as parent strains for crossing and segregant isolation. Based on QTL mapping by pooled-segregant whole genome sequencing as well as the subsequent reciprocal hemizygosity analysis (RHA) and allele replacement analysis, we identified and validated total eight causative genes in four QTLs that linked to high-temperature fermentation of yeast. Interestingly, loss of heterozygosity in five of the eight causative genes including RXT2, ECM24, CSC1, IRA2 and AVO1 exhibited positive effects on high-temperature fermentation. Principal component analysis (PCA) of high-temperature fermentation data from all the RHA and allele replacement strains of those eight genes distinguished three superior parent alleles including VPS34, VID24 and DAP1 to be greatly beneficial to high-temperature fermentation in contrast to their inferior parent alleles. Strikingly, physiological impacts of the superior parent alleles of VPS34, VID24 and DAP1 converged on cell membrane by increasing trehalose accumulation or reducing membrane fluidity.ConclusionsThis work revealed eight novel causative genes and SNP variants closely associated with high-temperature fermentation performance. Among these genes, VPS34 and DAP1 would be good targets for improving high-temperature fermentation of the industrial yeast. It also showed that loss of heterozygosity of causative genes could contribute to the improvement of high-temperature fermentation capacities. Our findings would provide guides to develop more robust and thermotolerant strains for the industrial production of ethanol.
引用
收藏
页数:18
相关论文
共 64 条
[1]   High-temperature fermentation: how can processes for ethanol production at high temperatures become superior to the traditional process using mesophilic yeast? [J].
Abdel-Banat, Babiker M. A. ;
Hoshida, Hisashi ;
Ano, Akihiko ;
Nonklang, Sanom ;
Akada, Rinji .
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 2010, 85 (04) :861-867
[2]   Mechanistic role of ergosterol in membrane rigidity and cycloheximide resistance in Saccharomyces cerevisiae [J].
Abe, Fumiyoshi ;
Hiraki, Toshiki .
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 2009, 1788 (03) :743-752
[3]   Vps34p Is Required for the Decline of Extracellular Fructose-1,6-bisphosphatase in the Vacuole Import and Degradation Pathway [J].
Alibhoy, Abbas A. ;
Giardina, Bennett J. ;
Dunton, Danielle D. ;
Chiang, Hui-Ling .
JOURNAL OF BIOLOGICAL CHEMISTRY, 2012, 287 (39) :33080-33093
[4]   A genetic screen for increased loss of heterozygosity in Saccharomyces cerevisiae [J].
Andersen, Marguerite R. ;
Nelson, Zara W. ;
Hetrick, Elizabeth D. ;
Gottschling, Daniel E. .
GENETICS, 2008, 179 (03) :1179-1195
[5]  
[Anonymous], STAT
[6]  
[Anonymous], J CHEM BIOL
[7]   Genome-wide identification of genes involved in tolerance to various environmental stresses in Saccharomyces cerevisiae [J].
Auesukaree, C. ;
Damnernsawad, A. ;
Kruatrachue, M. ;
Pokethitiyook, P. ;
Boonchird, C. ;
Kaneko, Y. ;
Harashima, S. .
JOURNAL OF APPLIED GENETICS, 2009, 50 (03) :301-310
[8]  
BECKER DM, 1991, METHOD ENZYMOL, V194, P182
[9]   The Vacuole Import and Degradation Pathway Utilizes Early Steps of Endocytosis and Actin Polymerization to Deliver Cargo Proteins to the Vacuole for Degradation [J].
Brown, C. Randell ;
Dunton, Danielle ;
Chiang, Hui-Ling .
JOURNAL OF BIOLOGICAL CHEMISTRY, 2010, 285 (02) :1516-1528
[10]   Epistasis:: too often neglected in complex trait studies? [J].
Carlborg, Ö ;
Haley, CS .
NATURE REVIEWS GENETICS, 2004, 5 (08) :618-U4