Ascomycetous yeasts from the kingdom fungi inhabit every biome in nature. While filamentous fungi have been studied extensively regarding their enzymatic degradation of the complex polymers comprising lignocellulose, yeasts have been largely overlooked. As yeasts are key organisms used in industry, understanding their enzymatic strategies for biomass conversion is an important factor in developing new and more efficient cell factories. The aim of this study was to identify polysaccharide-degrading yeasts by mining CAZymes in 332 yeast genomes from the phylum Ascomycota. Selected CAZyme-rich yeasts were then characterized in more detail through growth and enzymatic activity assays. The CAZyme analysis revealed a large spread in the number of CAZyme-encoding genes in the ascomycetous yeast genomes. We identified a total of 217 predicted CAZyme families, including several CAZymes likely involved in degradation of plant polysaccharides. Growth characterization of 40 CAZyme-rich yeasts revealed no cellulolytic yeasts, but several species from the Trichomonascaceae and CUG-Ser1 clades were able to grow on xylan, mixed-linkage β-glucan and xyloglucan. Blastobotrys mokoenaii, Sugiyamaella lignohabitans, Spencermartinsiella europaea and several Scheffersomyces species displayed superior growth on xylan and well as high enzymatic activities. These species possess genes for several putative xylanolytic enzymes, including ones from the well-studied xylanase-containing glycoside hydrolase families GH10 and GH30, which appear to be attached to the cell surface. B. mokoenaii was the only species containing a GH11 xylanase, which was shown to be secreted. Surprisingly, no known xylanases were predicted in the xylanolytic species Wickerhamomyces canadensis, suggesting that this yeast possesses novel xylanases. In addition, by examining non-sequenced yeasts closely related to the xylanolytic yeasts, we were able to identify novel species with high xylanolytic capacities. Our approach of combining high-throughput bioinformatic CAZyme-prediction with growth and enzyme characterization proved to be a powerful pipeline for discovery of novel xylan-degrading yeasts and enzymes. The identified yeasts display diverse profiles in terms of growth, enzymatic activities and xylan substrate preferences, pointing towards different strategies for degradation and utilization of xylan. Together, the results provide novel insights into how yeast degrade xylan, which can be used to improve cell factory design and industrial bioconversion processes.

中文翻译：

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子囊菌酵母基因组中的 CAZyme 预测指导发现具有不同半纤维素水解能力的新型木聚糖分解物种

来自真菌界的子囊菌酵母栖息在自然界的每一个生物群落中。虽然已经广泛研究了丝状真菌对包含木质纤维素的复杂聚合物的酶促降解，但酵母在很大程度上被忽视了。由于酵母是工业中使用的关键生物，因此了解它们用于生物质转化的酶促策略是开发新的、更高效的细胞工厂的重要因素。本研究的目的是通过挖掘来自子囊菌门的 332 个酵母基因组中的 CAZymes 来鉴定多糖降解酵母。然后通过生长和酶活性测定更详细地表征选定的富含 CAZyme 的酵母。CAZyme 分析显示子囊菌酵母基因组中 CAZyme 编码基因的数量有很大的分布。我们总共确定了 217 个预测的 CAZyme 家族，包括几个可能参与植物多糖降解的 CAZymes。40 种富含 CAZyme 的酵母的生长特征显示没有纤维素分解酵母，但来自毛滴虫科和 CUG-Ser1 进化枝的几个物种能够在木聚糖、混合连锁 β-葡聚糖和木葡聚糖上生长。Blastobotrys mokoenaii、Sugiyamaella lignohabitans、Spencermartinsiella europaea 和几种 Scheffersomyces 物种在木聚糖上表现出优异的生长和高酶活性。这些物种拥有几种假定的木聚糖分解酶的基因，包括来自经过充分研究的含木聚糖酶的糖苷水解酶家族 GH10 和 GH30 的基因，它们似乎附着在细胞表面。B. mokoenaii 是唯一含有 GH11 木聚糖酶的物种，其被证明是分泌的。令人惊讶的是，在木聚糖分解物种 Wickerhamomyces canadensis 中没有预测到已知的木聚糖酶，这表明该酵母具有新的木聚糖酶。此外，通过检查与木聚糖分解酵母密切相关的未测序酵母，我们能够鉴定出具有高木聚糖分解能力的新物种。我们将高通量生物信息学 CAZyme 预测与生长和酶表征相结合的方法被证明是发现新型木聚糖降解酵母和酶的有力途径。已鉴定的酵母在生长、酶活性和木聚糖底物偏好方面表现出不同的特征，表明木聚糖降解和利用的不同策略。总之，这些结果为酵母如何降解木聚糖提供了新的见解，