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中国生物工程杂志

CHINA BIOTECHNOLOGY
中国生物工程杂志
中国生物工程杂志  2023, Vol. 43 Issue (9): 77-92    DOI: 10.13523/j.cb.2302036
综述     
面向生物乙醇生产的酿酒酵母比较基因组序列分析研究进展*
许建韧1,2,3,**(),王岚4,马海军1,2
1 北方民族大学生物科学与工程学院 银川 750021
2 北方民族大学宁夏葡萄与葡萄酒技术创新中心 银川 750021
3 北方民族大学宁夏特殊生境微生物资源开发与利用重点实验室 银川 750021
4 宁夏大学葡萄酒与园艺学院 银川 750021
Research Progress of Sequence Analysis of Comparative Genomes in Saccharomyces cerevisiae for Bioethanol Production
XU Jian-ren1,2,3,**(),WANG Lan4,MA Hai-jun1,2
1 College of Bioscience and Engineering, North Minzu University, Yinchuan 750021, China
2 Ningxia Grape and Wine Technology Innovation Center, North Minzu University, Yinchuan 750021, China
3 Ningxia Key Laboratory for the Development and Application of Microbial Resources in Extreme Environments, North Minzu University, Yinchuan 750021, China
4 School of Food and Wine, Ningxia University, Yinchuan 750021, China
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摘要：

酿酒酵母是生物乙醇领域应用和研究的常用菌。综述了酿酒酵母基因组序列比较在提高基因功能注释准确性、发现不同菌株间分子结构变异、提供遗传育种潜在靶标基因等的相关研究,以及揭示酵母种间遗传进化关系,探究基因型与表型之间关联的研究进展。探讨了面向生物乙醇生产的酵母遗传育种,以满足工业生产需求。展望了随着测序菌株数量增多,酿酒酵母基因组的资源挖掘、重要价值和研究前景。
关键词： 酿酒酵母;  比较基因组;  序列分析;  遗传进化;  生物乙醇    
Abstract:

Saccharomyces cerevisiae is a common strain used in the field of bioethanol production. This paper reviews recent progress of comparative studies on S. cerevisiae genomic sequences in improving the accuracy of gene functional annotation, discovering molecular variation among different strains, providing potential target genes for genetic breeding, as well as revealing interspecific genetic evolution of yeasts, and exploring the correlation between genotypes and phenotypes. Moreover, yeast genetic breeding for bioethanol production to meet the requirements of industrial production was further discussed, and some insightful views on the bioresource mining of the genome of Saccharomyces cerevisiae with the increasing number of genome-sequenced strains, its important value, and research prospects were also provided.
Key words: Saccharomyces cerevisiae    Comparative genomics    Sequence analysis    Genetic evolution    Bioethanol
收稿日期: 2023-02-21 出版日期: 2023-10-08
ZTFLH:  Q815  
基金资助: * 宁夏重点研发计划(2020BEB04013);宁夏自然科学基金(2021AAC03182)
通讯作者: ** 电子信箱:xujianren@nmu.edu.cn   
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许建韧
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引用本文:

许建韧, 王岚, 马海军. 面向生物乙醇生产的酿酒酵母比较基因组序列分析研究进展*[J]. 中国生物工程杂志, 2023, 43(9): 77-92.

XU Jian-ren, WANG Lan, MA Hai-jun. Research Progress of Sequence Analysis of Comparative Genomes in Saccharomyces cerevisiae for Bioethanol Production. China Biotechnology, 2023, 43(9): 77-92.

链接本文:

https://manu60.magtech.com.cn/biotech/CN/10.13523/j.cb.2302036    或    https://manu60.magtech.com.cn/biotech/CN/Y2023/V43/I9/77

菌株名称 基因组大小
/Mb		 描述说明 国家 年份 文献
VIN7 23.4 一株释放硫醇的商业葡萄酒酵母种间杂交菌 澳大利亚 2011 [4]
W303-K6001 11.8 一株W303的变种、用以研究衰老机制的模式酵母 英国 2012 [5]
CEN.PK113-7D 11.6 一株实验室常用以代谢改造的菌株,具有工业菌株特征 荷兰 2012 [6]
YJS329 11.5 从土壤样品中分离得到,河南天冠集团用于生物乙醇生产 中国 2012 [7]
CAT-1 约12 一株巴西甘蔗工业的主要燃料乙醇生产菌株 巴西 2012 [8]
M3707 11.5 从蒸馏样本中分离,具有联合生物加工生物燃料潜力 美国 2013 [9]
NAM34-4C 11.5 源自工业酵母菌株KF-7,用于生物乙醇生产 日本 2014 [10]
YHJ7 11.5 一株从中国黄酒(传统酒精饮料)中分离出来菌株 中国 2014 [11]
IR-2 11.4 一株高效生产生物乙醇的工业菌株 日本 2014 [12]
MT1 11.6 一株从复杂的中国茅台白酒酿造环境中分离的菌株 中国 2015 [13]
NCIM3107 11.8 从Microbial Type Culture Collection (MTCC)保藏机构获得,
用于生物乙醇生产		 印度 2015 [14]
NCIM3186 11.9 从MTCC机构获得,用于甜高粱为底物的生物乙醇生产 印度 2015 [15]
GSY2239 11.5 一株由工业酿造菌株Wyeast1388衍生来的啤酒发酵菌株 美国 2015 [16]
EBY.VW4000 11.4 一株常见的己糖转运缺乏(研究糖转运功能)酵母菌株 荷兰 2015 [17]
202-3 11.9 从哥伦比亚分离,用于从甘蔗渣水解液来生产生物乙醇 哥伦比亚 2015 [18]
15V-P4 (et al.) 11.6 从Peterhof Genetic Collection (PGC)保存机构获得 俄罗斯 2016 [19]
GLBRCY22-3 12.3 衍生于生物能源领域的一株胁迫耐受野生菌NRRL YB-210 美国 2016 [20]
Kagoshima No. 2 12.3 一株用于日本蒸馏酒(烧酒)酿造工艺的酵母菌 日本 2017 [21]
BG-1 11.7 广泛用于甘蔗乙醇生产的一株巴西工业菌 巴西 2017 [22]
NY1308 11.5 一株用于乙醇发酵工业已有50多年历史的菌种 中国 2018 [23]
N85 12.7 一株用于米酒(传统酒精饮料)生产的工业菌株 中国 2018 [24]
I-328 11.6 用于类似雪利酒的葡萄酒酿造 俄罗斯 2018 [25]
SPSC01 13.5 一株应用于超高浓度乙醇发酵(VHG)的絮凝工业菌株 中国 2018 [26]
FMY097 11.6 从巴西乙醇厂分离到的SA1衍生的单倍体菌株 巴西 2019 [27]
Pf-1 12.4 从梅子中分离,用于生产独特风味的清酒 日本 2019 [28]
BT0510 约12 一株高渗透和乙醇/热胁迫的耐性菌株,用于生产甘蔗烈酒 巴西 2021 [29]
AW101 11.5 一种用于生产蒸馏酒精饮料(泡盛)的工业菌种 日本 2021 [30]
PE-2 (H3 & H4) 11.8 生产甘蔗乙醇优势菌株PE-2的两个单孢分离株H3和H4 巴西 2021 [31]
NYR20 11.5 一株清酒发酵过程中分泌红色素的腺嘌呤营养缺陷突变体 日本 2021 [32]
IMDO 050523 12.1 从可可堆自然发酵过程中分离 比利时 2022 [33]
DJJ01 8.3 从道成寺分离,用于酿造清酒 日本 2022 [34]
表1  2011年至今已完成基因组测序的酿酒酵母菌株
图1  酿酒酵母菌株比较基因组学领域的主要研究路径
测序菌株数
(基因组数)		 来源 方法或策略 结果与分析 意义 国家
(年份)		 文献
63株 不同大陆位置或不同生境 基因组DNA杂交全基因组平铺微阵列 鉴定出超10万个不同分离位点上189万个SNPs和近4 000个(>200 bp)的序列删除 明晰系统发育关系,了解多重驯化事件,支持种群溯源 美国
(2009)		 [40]
超70株 不同地理位置和发酵用途的酿酒酵母及其近亲酵母 基因组测序与变异分析 鉴定出大量SNPs、Indels、CNVs及Ty元件和基因含量变化 酵母种群结构由地理上孤立的明确谱系组成;人类活动影响菌株杂交而产生新变异 英国
(2009)		 [41]
83株 来自葡萄酒酿造、工业或自然环境 阵列-比较基因组杂交与全基因组测序 发现种间杂交事件、基因渐渗,CNVs在全部菌株中普遍分布 表明野生菌株和工业菌株存在广泛杂交 美国
(2012)		 [42]
102株
(99个基因组)		 不同生态或地理环境(数据库SGRP) DNA测序、分子系统发育分析、群落结构分析 中国分离株表现出强大群体结构,综合遗传变异几乎为世界其他地区分离株的2倍 原始森林的酿酒酵母种群早于和独立于驯化菌落,欧洲/葡萄酒菌群可能起源于亚洲 中国
(2012)		 [43]
262株 从广泛的地理位置和环境生态位分离 每株菌取1%基因组序列进行简化测序 多序列比对发现菌株的多样性由地理区分 各种发酵菌株表现出高度杂合性,构建起地理分化模型 美国
(2013)		 [44]
90株 测序分离菌(数据库NCBI与SGRP) 基因组测序、分子多态性和全基因组系统发育分析 鉴定到工业变异和新的地理划分酵母种群,含一个新的地中海橡树种群 地中海橡树拥有驯化葡萄酒酿造酵母的野生基因库 葡萄牙
(2015)		 [45]
100株 采自多个地理环境 基因组测序、种群结构分析、分化表型分析 鉴定出多种类型的序列变异,如染色体重排、CNVs、基因渐渗、重组事件和种群结构等 大多数表型变异是可定量的,可用于鉴定种群和鉴别基因型和表型的关联 美国
(2015)		 [46]
212株 葡萄酒酿造分离株 泛基因组比较分析 发现商业菌株和葡萄酒酿造菌株在遗传水平上相似,近亲杂交水平很高 用于葡萄酒酿造的商业酿酒酵母种系群体中有效遗传变异极限正接近饱和 澳大利亚
(2016)		 [47]
1 011株 全球收集 基因组深度测序与比较分析 获得物种表型相关的基因组变异进化图;鉴定出某单一起源的几次独立驯化事件 基因组进化由SNPs积累驱动,但CNVs比SNPs具有更强的多样性表型效应 法国
(2018)		 [48]
266株 106株野生分离菌和160株发酵菌 基因组重测序、系统基因组学分析 发现一致的基因扩张和收缩,及适应不同环境的谱系特异性基因组变异 揭示中国/远东地区或是酿酒酵母驯化种群起源中心 中国
(2018)		 [49]
(239个基因组) 2株PE-2单孢分离菌/42株甘蔗发酵菌及其他195株菌 全基因组序列对比分析 酵母基因组均扩增了维生素B1/B6生物合成SNO2(3)/SNZ2(3)基因簇,醌氧化还原酶、水通道蛋白等编码基因 证明巴西生物燃料生产菌可能筛选于预先适应了甘蔗乙醇发酵过程(朗姆酒)的酵母 巴西
(2021)		 [31]
126株 64株来自非洲/52株(白酒)和10株(黄酒)来自中国 基因组重测序、群体基因组比较分析 具有群体特异性等位基因分布模式的基因多富集在功能相似或相关基础代谢过程 说明酵母在非洲有很长的驯化历史 中国
(2021)		 [50]
104株
(450个基因组)		 新西兰(数据库
SGRP)		 基因组测序与序列变异比较 菌种适应性进化与特异性基因拷贝数(CNVs)变化有关,如HXT家族 揭示新西兰酿酒酵母是欧洲/葡萄酒分支的一个亚群 英国
(2021)		 [51]
(1 011个
基因组)		 全球收集(1002酵母基因组计划) 基因组测序、分析、编辑 基因缺失、CNVs和SNPs等是可关联及追踪酵母驯化和起源的遗传标记 驯化影响酵母发酵、繁殖和胁迫耐受,但世代寿命不受驯化影响,而由进化决定 法国
(2022)		 [52]
表2  酿酒酵母菌株的比较(群体)基因组分析典型实例
图2  通过基因组测序分析和基因组工程改造开展酿酒酵母遗传育种研究
名称 载体或策略 底盘菌株 靶向基因 具体方式 实验结果 年份 文献
CRISPRi Cas9介导的
双链断裂(DSBs)		 Y1H ADH2 完全敲除
移码突变		 乙醇产量
提高74.7%		 2018 [95]
CRISPRi Cas9介导的
单步多基因敲除		 Y1H ADH2
GPD1
ALD4		 单独敲除
组合敲除		 乙醇产量
提高1.41倍		 2019 [96]
CRISPRa Cas9-TRK1-
crRNA-pRS423		 CEN.PK113-7D TRK1 基因突变 增强菌株
丙酸耐受性		 2019 [97]
CRISPRa dCas9-VP64 TSH3 OLE1 基因激活
文库筛选		 过量表达增强
菌株高温耐性		 2019 [98]
CRISPR-Cas DSBs和
基因组重排		 YPH499 δ序列 突变株
筛选		 突变株耐受性提高
(39℃、低pH和
高浓度乙醇)		 2019 [99]
CRSPRa/i dCas9
dCas9-Mxi1
dCas9-VP64
dCas9-VPR		 KE6-12 HRK1
SSK2
ISC1
BDH2		 基因激活
基因抑制		 增强菌株的木质
纤维素水解液
抑制耐受性		 2020 [100]
CRISPRi dCas9-Mxi1 9 078株
酿酒酵母		 必需基因
和呼吸生长
相关基因		 文库筛选 增强菌株
乙酸耐受性		 2021 [101]
CRISPRi dCas9-Mxi1 BY4743 YAP1
HAA1
DOT6		 基因敲除 改变木质纤维素
水解液中菌株
生长耐受性		 2021 [102]
CRISPRi Cas9线性化
共转化载体		 EC1118 ECM33 基因敲除 限氮和足氮条件下
发酵速率显著加快		 2021 [103]
CRSPRa nCas9(D10A)-
PmCDA1		 BY4741
BY4741a		 SPT15 基因突变 突变株耐受性提高(高
渗、高温和乙醇胁迫)且
发酵性能增强1.5倍以上		 2021 [104]
CRISPRi Cas9-NTC 野生型
酿酒酵母		 GPD2
FPS1
GDH2		 基因敲除 乙醇生产
性能提高		 2022 [105]
CRISPRi Cas9-NTC S288c ADH2
FPS1
GPD2
DLD3		 基因敲除 乙醇产量提高,副产物
(甘油、乙酸和乳酸)
含量减少		 2022 [106]
表3  CRISPR/Cas9基因编辑提高酿酒酵母乙醇产量或耐受性的研究
图3  酵母比较基因组序列分析呈现不同层次的研究维度
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