Comparative genomic analysis reveals metabolic mechanisms for Kluyveromyces marxianus’ fast growth during evolution

Abstract

Background Using yeast fermentation to produce bioethanol, is an economic and renewable way to tackle the rapid increase in fuel consumption. Faster cell growth rate guarantees the superior result of fermentation course. The “non-conventional” yeast Kluyveromyces marxianus is the known fastest-growing eukaryote on the earth. Although its wide application in industry, the molecular mechanisms for its fast growth have seldom been discovered.Results We first carried out a comparative genome content analysis for K. marxianus evolution in Saccharomycetaceae and identified the gain/lost genes as well as highly copied genes during K. marxianus speciation. Then RNA-seq analyses for K. marxianus and S. cerevisiae at different time points along cultivation were performed, to infer the function of K. marxianus-specific genes and to find out the difference in homologous gene expression patterns between the two species. RNA-seq results were further validated with RT-qPCR analysis. Genome content analysis shows the highly intense events of genes’ gain/loss happened at the occurrence of Saccharomycetaceae and Kluyveromyces, and K. marxianus has particularly high copy numbers of genes participating in iron transport and biotin biosynthesis. The RNA-seq analysis reveals 40% of K. marxianus-specific genes were up-regulated and may participate in glucose transport and mitochondrial function. Furthermore, compared to S. cerevisiae, K. marxianus has developed two features in homologous gene expressions to ensure its fast growth: (1) enhanced fundamental expressions of TCA cycle and respiratory chain genes at the beginning of cultivation; (2) tightly co-up-regulated expressions of respiratory chain, F0F1 ATPase, and glucose transporter genes at its fastest growth phase. Those co-expressions are mainly ascribed to the higher number of significant motifs in the upstream sequences of involved genes in K. marxianus than in S. cerevisiae, indicating the importance of transcriptional network remodelling during evolution.Conclusions This study gives insights into the possible mechanisms of K. marxianus’ fast growth trait, via efficiently supplying sufficient energy for cell growth, meanwhile reinforcing glucose transport to guarantee the competition for environmental resources. Our findings present a theoretical support for K. marxianus’ prospective application in industry, and give clues for further rational construction of fast-growing yeast strains.

Bioprospecting Kluyveromyces marxianus as a Robust Host for Industrial Biotechnology

“…Simultaneous saccharification and fermentation of lignocellulosic and other polysaccharide-based feedstocks at higher temperature can augment the enzyme efficacy and reducing the enzymes-associated costs. All these desired traits, such as fastest growth, thermotolerance, and broad substrate spectrum (i.e., hemi-cellulose hydrolysates, xylose, l -arabinose, d -mannose, galactose, maltose, sugar syrup molasses, cellobiose, dairy industry waste, such as cheese whey, lactose, and galactose) constitutes K. marxianus , a versatile host for applications in the food, feed, and pharmaceutical industries ( Löser et al, 2013 ; Morrissey et al, 2015 ; Mo et al, 2019a ; Mo et al, 2019b ; Lyu et al, 2021 ).…”