An economically viable production of biofuels and biochemicals from lignocellulose requires microorganisms that can readily convert both the cellulosic and hemicellulosic fractions into product. The yeast Candida intermedia displays a high capacity for uptake and conversion of several lignocellulosic sugars including the abundant pentose d-xylose, an underutilized carbon source since most industrially relevant microorganisms cannot naturally ferment it. Thus, C. intermedia constitutes an important source of knowledge and genetic information that could be transferred to industrial microorganisms such as Saccharomyces cerevisiae to improve their capacity to ferment lignocellulose-derived xylose. To understand the genetic determinants that underlie the metabolic properties of C. intermedia, we sequenced the genomes of both the in-house-isolated strain CBS 141442 and the reference strain PYCC 4715. De novo genome assembly and subsequent analysis revealed C. intermedia to be a haploid species belonging to the CTG clade of ascomycetous yeasts. The two strains have highly similar genome sizes and number of protein-encoding genes, but they differ on the chromosomal level due to numerous translocations of large and small genomic segments. The transcriptional profiles for CBS 141442 grown in medium with either high or low concentrations of glucose and xylose were determined through RNA-sequencing analysis, revealing distinct clusters of co-regulated genes in response to different specific growth rates, carbon sources and osmotic stress. Analysis of the genomic and transcriptomic data also identified multiple xylose reductases, one of which displayed dual NADH/NADPH co-factor specificity that likely plays an important role for co-factor recycling during xylose fermentation. In the present study, we performed the first genomic and transcriptomic analysis of C. intermedia and identified several novel genes for conversion of xylose. Together the results provide insights into the mechanisms underlying saccharide utilization in C. intermedia and reveal potential target genes to aid in xylose fermentation in S. cerevisiae.

中文翻译：

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中间念珠菌的基因组和转录组分析揭示了其木糖转化能力的遗传决定因素

由木质纤维素经济可行地生产生物燃料和生化产品需要能够容易地将纤维素和半纤维素部分转化为产品的微生物。酵母中间念珠菌显示出吸收和转化几种木质纤维素糖的高能力，包括丰富的戊糖 d-木糖，这是一种未被充分利用的碳源，因为大多数工业相关微生物不能自然发酵它。因此，C. intermedia 构成了重要的知识和遗传信息来源，可以将其转移到工业微生物（如酿酒酵母）以提高其发酵木质纤维素衍生木糖的能力。为了解构成 C. intermedia 代谢特性的遗传决定因素，我们对内部分离菌株 CBS 141442 和参考菌株 PYCC 4715 的基因组进行了测序。从头基因组组装和随后的分析表明，中间梭菌是属于子囊酵母 CTG 进化枝的单倍体物种。这两个菌株具有高度相似的基因组大小和蛋白质编码基因的数量，但由于大小基因组片段的大量易位，它们在染色体水平上存在差异。通过 RNA 测序分析确定了在具有高或低浓度葡萄糖和木糖的培养基中生长的 CBS 141442 的转录谱，揭示了响应不同特定生长速率、碳源和渗透胁迫的不同共调节基因簇。基因组和转录组数据的分析还确定了多种木糖还原酶，其中一个显示出双重 NADH/NADPH 辅因子特异性，这可能在木糖发酵过程中对辅因子循环发挥重要作用。在本研究中，我们对 C. intermedia 进行了首次基因组和转录组学分析，并鉴定了几个用于木糖转化的新基因。这些结果共同提供了对中间酵母中糖利用的潜在机制的见解，并揭示了有助于酿酒酵母中木糖发酵的潜在靶基因。