Data_Sheet_2_Comparative Genomic and Transcriptomic Analysis Reveals Specific Features of Gene Regulation in Kluyveromyces marxianus.DOCX

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.

克鲁维氏酵母（Kluyveromyces marxianus）作为一种极具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物种酿酒酵母（Saccharomyces cerevisiae）的多项优越特性，诸如生长迅速、耐热性及广泛吸收糖类的能力。然而，关于K. marxianus快速生长机制的研究尚显不足。本研究通过对K. marxianus与其他接合菌科物种进行基因组比较分析，发现其在絮凝、铁质运输及生物素生物合成等基因上的拷贝数显著较高。此外，识别出60个K. marxianus特有基因，其中45%在富营养培养基培养过程中上调表达，这些基因可能与葡萄糖运输及线粒体相关功能有关。转录组分析还揭示，在好氧条件下，K. marxianus在延滞期参与三羧酸循环、呼吸链及ATP生物合成的基因标准化水平高于酿酒酵母。与延滞期相比，在培养后期，K. marxianus中高度拷贝基因、参与呼吸链及线粒体组装的基因水平上调，而在酿酒酵母中则无此现象。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。基因表达协同调控的特定特征可能对K. marxianus的快速生长表型产生贡献。本研究强调了在进化过程中转录网络全局重构的重要性。