Data_Sheet_3_Comparative Genomic and Transcriptomic Analysis Reveals Specific Features of Gene Regulation in Kluyveromyces marxianus.XLSX

Kluyveromyces marxianus is a promising host for producing bioethanol and heterologous proteins. It displays many superior traits to a conventional industrial yeast species, Saccharomyces cerevisiae, including fast growth, thermotolerance and the capacity to assimilate a wider variety of sugars. However, little is known about the mechanisms underlying the fast-growing feature of K. marxianus. In this study, we performed a comparative genomic analysis between K. marxianus and other Saccharomycetaceae species. Genes involved in flocculation, iron transport, and biotin biosynthesis have particularly high copies in K. marxianus. In addition, 60 K. marxianus specific genes were identified, 45% of which were upregulated during cultivation in rich medium and these genes may participate in glucose transport and mitochondrion related functions. Furthermore, the transcriptomic analysis revealed that under aerobic condition, normalized levels of genes participating in TCA cycles, respiration chain and ATP biosynthesis in the lag phase were higher in K. marxianus than those in S. cerevisiae. Levels of highly copied genes, genes involved in the respiratory chain and mitochondrion assembly, were upregulated in K. marxianus, but not in S. cerevisiae, in later time points during cultivation compared with those in the lag phase. Notably, during the fast-growing phase, genes involved in the respiratory chain, ATP synthesis and glucose transport were co-upregulated in K. marxianus. A few shared motifs in upstream sequences of relevant genes might result in the co-upregulation. Specific features in the co-regulations of gene expressions might contribute to the fast-growing phenotype of K. marxianus. Our study underscores the importance of genome-wide rewiring of the transcriptional network during evolution.

克卢维酵母（Kluyveromyces marxianus）作为一种具有潜力的生物乙醇及异源蛋白生产宿主，展现出相较于传统工业酵母（Saccharomyces cerevisiae）诸多卓越特性，诸如快速生长、耐热性以及广泛糖类同化能力。然而，关于K. marxianus快速生长机制的了解尚显不足。本研究通过对K. marxianus与其他酿酒酵母科物种的基因组进行对比分析，发现其在絮凝、铁质运输及生物素生物合成相关基因拷贝数显著。此外，共鉴定出60个K. marxianus特有基因，其中45%在富营养培养基培养过程中表达上调，这些基因可能参与葡萄糖运输及线粒体相关功能。进一步地，转录组分析揭示，在有氧条件下，K. marxianus在滞后期参与三羧酸循环、呼吸链及ATP生物合成的基因标准化水平高于S. cerevisiae。与滞后期相比，K. marxianus在培养后期的高拷贝基因、参与呼吸链及线粒体组装的基因表达水平上调，而S. cerevisiae则不然。值得注意的是，在快速生长阶段，K. marxianus中参与呼吸链、ATP合成及葡萄糖运输的基因协同上调。相关基因上游序列中的一些共有基序可能导致了这种协同上调。基因表达共调节的特定特征可能有助于K. marxianus快速生长表型的形成。本研究强调了转录网络全局重构在进化过程中的重要性。