Abstract
The industrially important food-yeast Candida utilis is a Crabtree effect-negative yeast used to produce valuable chemicals and recombinant proteins. In the present study, we conducted whole genome sequencing and phylogenetic analysis of C. utilis, which showed that this yeast diverged long before the formation of the CUG and Saccharomyces/Kluyveromyces clades. In addition, we performed comparative genome and transcriptome analyses using next-generation sequencing, which resulted in the identification of genes important for characteristic phenotypes of C. utilis such as those involved in nitrate assimilation, in addition to the gene encoding the functional hexose transporter. We also found that an antisense transcript of the alcohol dehydrogenase gene, which in silico analysis did not predict to be a functional gene, was transcribed in the stationary-phase, suggesting a novel system of repression of ethanol production. These findings should facilitate the development of more sophisticated systems for the production of useful reagents using C. utilis.
Highlights
Candida utilis (Lindnera jadinii) is a Crabtree effect-negative yeast that is currently used to produce several industrially important compounds, such as glutathione and RNA [1,2,3]
Annotation of the C. utilis genome Protein coding genes were predicted using GlimmerM [19] and GeneLook [20] for the 975 supercontigs (Materials and Methods; Figure S1). This resulted in the identification of a total of 8,646 protein coding genes of which 4,041 (46.7%) had at least one homolog in the Saccharomyces genome database (SGD), Candida Genome Database (CGD), and/or SwissProt release 55.6
Each putative 8,864 genes in C. utilis was compared with S. cerevisiae S288C mitochondrial genome (85,779 bp) to reveal that nine orthologous genes in the unmapped chromosome were identified as mitochondrial genes (e-values were each less than 1e-10)
Summary
Candida utilis (Lindnera jadinii) is a Crabtree effect-negative yeast that is currently used to produce several industrially important compounds, such as glutathione and RNA [1,2,3]. C. utilis can grow on inexpensive substrates, such as pulping-waste liquors from the paper industry [4], and high cell density culture and large-scale production are possible under efficient continuous-culture conditions [1]. Since efficient methods of C. utilis transformation have been developed [5,6,7], the yeast has been used for the heterologous production of monellin, a-amylase, carotenoids, and organic acids such as L-lactic acid [8,9,10,11,12]. The whole transcriptome analysis of C. utilis has not yet been reported
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