The ascomycetous yeast Yarrowia lipolytica (formerly Candida, Endomycopsis, or Saccharomyces lipolytica) is one of the more intensively studied 'non-conventional' yeast species. This yeast is quite different from the well-studied yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe with respect to its phylogenetic evolution, physiology, genetics, and molecular biology. However, Y. lipolytica is not only of interest for fundamental research, but also for biotechnological applications. It secretes several metabolites in large amounts (i.e. organic acids, extracellular proteins) and the tools are available for overproduction and secretion of foreign proteins. This review presents a comprehensive overview on the available data on physiology, cell biology, molecular biology and genetics of Y. lipolytica.

Physiology and genetics of the dimorphic fungus Yarrowia lipolytica

The yeast Yarrowia lipolytica secretes high amounts of various organic acids, like citric (CA) and isocitric (ICA) acids, triggered by growth limitation caused by different factors and an excess of carbon source. Depending on the carbon source used, Y. lipolytica strains produce a mixture of CA and ICA in a characteristic ratio. To examine whether the CA/ICA product ratio can be influenced by gene-dose-dependent overexpression or by disruption of the isocitrate lyase (ICL)-encoding gene ICL1, recombinant Y. lipolytica strains were constructed, which harbour multiple ICL1 copies or a defective icl1 allele. The high-level expression of ICL in ICL1 multicopy integrative transformants resulted in a strong shift of the CA/ICA ratio into direction of CA. On glycerol, glucose and sucrose, the ICA proportion decreased from 10–12% to 3–6%, on sunflower oil or hexadecane even from 37–45% to 4–7% without influencing the total amount of acids (CA and ICA) produced. In contrast, the loss of ICL activity in icl1-defective strains resulted in a moderate 2–5% increase in the ICA proportion compared to ICL wild-type strains on glucose or glycerol.

Overexpression of the ICL1 gene changes the product ratio of citric acid production by Yarrowia lipolytica

Four commercial strains and two mutants of the yeast species Yarrowia lipolytica were screened using batch fermentation. Strain Y. lipolytica A-101-1.14 (induced with UV irradiation) was found to be the most suitable for citric acid production from glucose hydrol (39.9% glucose and 2.1% other sugars), a byproduct of glucose production from potato starch. The specific rate of total citric and isocitric acid production was 0.138 g/g.h, the yield on consumed glucose 0.93 g/g, and the productivity achieved was as high as 1.25 g/L.h. All of the tested yeast strains were able to utilize only the glucose from the glucose hydrol medium. Thus, some residual higher oligosaccharides remained in the process effluent.

Comparison of different strains of the yeast Yarrowia lipolytica for citric acid production from glucose hydrol.

The yeast Yarrowia lipolytica secretes high amounts of various organic acids, like citric acid (CA) and isocitric acid (ICA) under an excess of carbon source and several conditions of growth limitation. Depending on the carbon source used, Y. lipolytica strains produce a mixture of CA and ICA in a characteristic ratio. To examine whether this CA/ICA product ratio can be influenced by gene-dose-dependent overexpression of aconitase (ACO)-encoding gene ACO1, a recombinant Y. lipolytica strain was constructed containing multiple copies of ACO1. The high-level expression of ACO in the ACO1 multicopy integrative transformant resulted in a shift of the CA/ICA product pattern into the direction of ICA. On sunflower oil, a striking increase of the ICA proportion from 35-49% to 66-71% was observed compared to wild-type strains without influencing the total amount of acids (CA and ICA) produced. On glycerol, glucose or sucrose, the ICA proportion increased only moderately from 10-12% to 13-17%. This moderate shift into the direction of ICA was also observed in an icl1-defective strain.

Aconitase overexpression changes the product ratio of citric acid production by Yarrowia lipolytica

Variation in synonymous codon usage is abundant across multiple levels of organization: between codons of an amino acid, between genes in a genome, and between genomes of different species. It is now well understood that variation in synonymous codon usage is influenced by mutational bias coupled with both natural selection for translational efficiency and genetic drift, but how these processes shape patterns of codon usage bias across entire lineages remains unexplored. To address this question, we used a rich genomic data set of 327 species that covers nearly one third of the known biodiversity of the budding yeast subphylum Saccharomycotina. We found that, while genome-wide relative synonymous codon usage (RSCU) for all codons was highly correlated with the GC content of the third codon position (GC3), the usage of codons for the amino acids proline, arginine, and glycine was inconsistent with the neutral expectation where mutational bias coupled with genetic drift drive codon usage. Examination between genes' effective numbers of codons and their GC3 contents in individual genomes revealed that nearly a quarter of genes (381,174/1,683,203; 23%), as well as most genomes (308/327; 94%), significantly deviate from the neutral expectation. Finally, by evaluating the imprint of translational selection on codon usage, measured as the degree to which genes' adaptiveness to the tRNA pool were correlated with selective pressure, we show that translational selection is widespread in budding yeast genomes (264/327; 81%). These results suggest that the contribution of translational selection and drift to patterns of synonymous codon usage across budding yeasts varies across codons, genes, and genomes; whereas drift is the primary driver of global codon usage across the subphylum, the codon bias of large numbers of genes in the majority of genomes is influenced by translational selection.

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Variation and selection on codon usage bias across an entire subphylum.

We investigated the excretion of citric and isocitric acids in a strain of Saccharomycopsis lipolytica grown on either n-paraffins, glucose, or glycerol. These acids were excreted in the ratio of 67:33 on n-paraffins and roughly 92:8 on either glucose or glycerol. However, with all the carbon sources used, the relative amount of isocitric acid in the intracellular pool remained below 10%. The assimilation of citric and isocitric acids was prevented when glucose or glycerol were the carbon sources, but not when n-paraffins were used. Citric acid stopped isocitric acid assimilation. These phenomena of selective assimilation and/or uptake might explain the variations observed in the ratio of citric to isocitric acids excreted on different carbon sources.

Excretion of citric and isocitric acids by the yeast Saccharomycopsis lipolytica

Four out of the 24 strains of the yeast Yarrowia lipolytica we have checked for the presence of virus-like particles (VLPs) proved to contain encapsidated double-stranded RNA (dsRNA) molecules, 4.9 kb long. A major VLP polypeptide of MW 80,000 was observed in all 4 cases, and a second one of MW 77,000 in three cases. dsRNA from the VLPs harboring only the larger polypeptide showed little homology with the 3 others. We have found no homology between VLP dsRNAs and host DNA or dsRNAs from Saccharomyces cerevisiae, and no relationship between the presence of VLPs and a possible killer phenomenon in Y. lipolytica.

Virus-like particles from the yeast Yarrowia lipolytica

Curing of the viruslike particles harbored by a strain of the yeast Yarrowia lipolytica was achieved by UV irradiation. The cured strain was found to be able to maintain the viruslike particles after their re-introduction by crossing or by cytoplasmic fusion. The involvement of a UV-induced mutation of a yeast maintenance gene seems therefore unlikely.

Brigitte Treton

Papers

Excretion of citric and isocitric acids by the yeast Saccharomycopsis lipolytica

Virus-like particles from the yeast Yarrowia lipolytica

UV-induced curing of the double-stranded RNA virus of the yeast Yarrowia lipolytica

In vitro RNA synthesis by viruses isolated from the yeast Yarrowia lipolytica