Chromosomal Copy Number Variation in Saccharomyces pastorianus Is Evidence for Extensive Genome Dynamics in Industrial Lager Brewing Strains.
Chromosomal Copy Number Variation in Saccharomyces pastorianus Is Evidence for Extensive Genome Dynamics in Industrial Lager Brewing Strains.
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DOI：
10.1128/aem.01263-15
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发表时间：
2015-09
影响因子：
4.4
通讯作者：
Daran JM
中科院分区：
文献类型：
--
作者：
van den Broek M;Bolat I;Nijkamp JF;Ramos E;Luttik MA;Koopman F;Geertman JM;de Ridder D;Pronk JT;Daran JM
巴斯德酵母（Saccharomyces pastorianus）是酿酒酵母（Saccharomyces cerevisiae）和真巴亚酵母（Saccharomyces eubayanus）自然杂交产生的天然种间杂种。在过去的500年里，S。巴斯德菌已被驯化成为最重要的工业微生物之一。拉格型啤酒的生产需要一组基本的表型，包括在低温下发酵麦芽糖和麦芽三糖的能力，风味和香气的产生以及絮凝的能力。了解复杂的酿造相关表型性状的分子基础是合理的菌株改良的先决条件。虽然基因组序列已被报道，变异性和动力学的S。巴斯德菌的基因组尚未得到详细研究。在这里，使用深度测序和染色体拷贝数分析，我们表明S. pastorianus菌株CBS1483表现出广泛的非整倍性。这通过定量PCR和流式细胞术证实。作为这种非整倍性的直接结果，鉴定了大量的序列变体，导致S中至少1，800个额外的蛋白变体。巴斯德菌CBS1483。分析了8个额外的S。pastorianus菌株显示，先前定义的组I菌株显示可比较的核型，而组II菌株显示大的菌株间核型变异性。三个菌株几乎相同的基因组序列的比较显示大量的染色体拷贝数的变化，这可能有助于菌株特异性的表型性状。所观察到的啤酒酵母基因组的变异性表明，基因型与表型的系统性联系需要三维基因组分析，包括物理染色体结构、单个染色体或染色体区域的拷贝数以及单个基因拷贝的等位基因变异。
Lager brewing strains of Saccharomyces pastorianus are natural interspecific hybrids originating from the spontaneous hybridization of Saccharomyces cerevisiae and Saccharomyces eubayanus. Over the past 500 years, S. pastorianus has been domesticated to become one of the most important industrial microorganisms. Production of lager-type beers requires a set of essential phenotypes, including the ability to ferment maltose and maltotriose at low temperature, the production of flavors and aromas, and the ability to flocculate. Understanding of the molecular basis of complex brewing-related phenotypic traits is a prerequisite for rational strain improvement. While genome sequences have been reported, the variability and dynamics of S. pastorianus genomes have not been investigated in detail. Here, using deep sequencing and chromosome copy number analysis, we showed that S. pastorianus strain CBS1483 exhibited extensive aneuploidy. This was confirmed by quantitative PCR and by flow cytometry. As a direct consequence of this aneuploidy, a massive number of sequence variants was identified, leading to at least 1,800 additional protein variants in S. pastorianus CBS1483. Analysis of eight additional S. pastorianus strains revealed that the previously defined group I strains showed comparable karyotypes, while group II strains showed large interstrain karyotypic variability. Comparison of three strains with nearly identical genome sequences revealed substantial chromosome copy number variation, which may contribute to strain-specific phenotypic traits. The observed variability of lager yeast genomes demonstrates that systematic linking of genotype to phenotype requires a three-dimensional genome analysis encompassing physical chromosomal structures, the copy number of individual chromosomes or chromosomal regions, and the allelic variation of copies of individual genes.