Development of the genetic map of the yeast Saccharomycopsis lipolytica

Identification of the transcription factor Znc1p, which regulates the yeast-to-hypha transition in the dimorphic yeast Yarrowia lipolytica

The dimorphic yeast Yarrowia lipolytica is used as a model to study fungal differentiation because it grows as yeast-like cells or forms hyphal cells in response to changes in environmental conditions. Here, we report the isolation and characterization of a gene, ZNC1, involved in the dimorphic transition in Y. lipolytica. The ZNC1 gene encodes a 782 amino acid protein that contains a Zn(II)2C6 fungal-type zinc finger DNA-binding domain and a leucine zipper domain. ZNC1 transcription is elevated during yeast growth and decreases during the formation of mycelium. Cells in which ZNC1 has been deleted show increased hyphal cell formation. Znc1p-GFP localizes to the nucleus, but mutations within the leucine zipper domain of Znc1p, and to a lesser extent within the Zn(II)2C6 domain, result in a mislocalization of Znc1p to the cytoplasm. Microarrays comparing gene expression between znc1::URA3 and wild-type cells during both exponential growth and the induction of the yeast-to-hypha transition revealed 1,214 genes whose expression was changed by 2-fold or more under at least one of the conditions analyzed. Our results suggest that Znc1p acts as a transcription factor repressing hyphal cell formation and functions as part of a complex network regulating mycelial growth in Y. lipolytica.

Genomic exploration of the hemiascomycetous yeasts: 17. Yarrowia lipolytica

A total of 4940 random sequence tags of the dimorphic yeast Yarrowia lipolytica, totalling 4.9 Mb, were analyzed. BLASTX comparisons revealed at least 1229 novel Y. lipolytica genes 1083 genes having homology with Saccharomyces cerevisiae genes and 146 with genes from various other genomes. This confirms the rapid sequence evolution assumed for Y. lipolytica. Functional analysis of newly discovered genes revealed that several enzymatic activities were increased compared to S. cerevisiae, in particular, transport activities, ion homeostasis, and various metabolism pathways. Most of the mitochondrial genes were identified in contigs spanning more than 47 kb. Matches to retrotransposons were observed, including a S. cerevisiae Ty3 and a LINE element. The sequences have been deposited with EMBL under the accession numbers AL409956-AL414895.

Sequence analysis of SLA2 of the dimorphic yeasts Candida albicans and Yarrowia lipolytica

We report the complete nucleotide sequence of SLA2 of the dimorphic yeasts Candida albicans and Yarrowia lipolytica. In Saccharomyces cerevisiae, SLA2 codes for an actin binding protein. The deduced amino acid (aa) sequences of C. albicans CaSla2p and Y. lipolytica YlSla2p consist of 1063 and 1054 aa, respectively. The alignment of the deduced proteins of Saccharomyces cerevisiae, Y. lipolytica and C. albicans shows regions of identity in the N-terminal part of the proteins, which are essential for growth at 37 degrees C, endocytosis and actin organization in S. cerevisiae. The Sla2p proteins have also several conserved regions in the C-terminal moiety, the I/LWEQ boxes, displaying homology to the talin protein of mouse, Dictyostelium discoideum, Caenorhabditis elegans and to human huntingtin interacting protein (Hip 1p). The sequence data of C. albicans SLA2 are registered in the EMBL database (AJ009556), and for the Y. lipolytica gene in GenBank (U65409).

Distribution of the actin cytoskeleton during the cell cycle of Yarrowia lipolytica and the visualization of the tubulin cytoskeleton by immunofluorescence

Actin distribution was examined during the cell cycle of the dimorphic yeast Yarrowia lipolytica, showing the correlation between bud growth, nuclear migration and rearrangement of the actin cytoskeleton. The results correspond with observations made in cells of Saccharomyces cerevisiae, S. uvarum and Candida albicans. Localization of actin was also determined in hyphal cells, where actin is stained predominantly in the tip and also at the septum of hyphae. The standard methods used for tubulin immunostaining in S. cerevisiae and C. albicans cells were adapted for application in Y. lipolytica.

A novel cell wall protein specific to the mycelial form of Yarrowia lipolytica

A cDNA clone specifying a cell wall protein was isolated from a Yarrowia lipolytica cDNA library. The cDNA library was constructed in the expression vector lambda gt 11, with the RNA isolated from actively growing mycelial cells. The deduced amino acid sequence shows that the encoded protein contains an N-terminal hydrophobic signal peptide. We have designated this protein YWP1 for Yarrowia lipolytica cell Wall Protein. Northern hybridization identified YWP1 transcript only when Y. lipolytica was growing in the mycelial form. The encoded protein seems to be covalently bound to the glucan cell wall since it is not released from the cell walls by sodium dodecyl sulphate extraction, but it is solubilized following partial degradation of beta-glucan by Zymolyase digestion. The protein is localized in the outer surface on the tip of the growing mycelial cells and is found partially cryptic in sub-apical locations, suggesting that it participates directly in the mycelial wall architecture.

Chromosomal polymorphism of the yeast Yarrowia lipolytica and related species: electrophoretic karyotyping and hybridization with cloned genes

Significant differences in electrophoretic karyotyping patterns were found among 27 strains of Y. lipolytica. Twenty-one of these strains were classified into four groups of similar karyotypes while six strains showed unique karyotypes. Chromosomal DNAs of different strains were hybridized with cloned genes of Y. lipolytica (URA3, LEU2, ARS18 and ARS68), which revealed four different bands in most strains. We conclude that the haploid chromosome number of Y. lipolytica is at least four, and possibly five or six. Electrophoretic karyotyping and hybridization with cloned genes of Y. lipolytica provided evidence of a large divergence between Y. lipolytica and related species of Saccharomycopsis, Endomycopsella and Endomyces.

The production of organic acids

The production of organic acids covers two aspects: first, the metabolic pathways involved in the biosynthesis, and, second, the industrial process strategy adopted. The review seeks to show the underlying biochemical similarities in the biosynthesis of organic acids and the resulting similarities in the commercial processes. Two groups of acids are defined, those with a "long" biosynthetic path from glucose, involving much of the glycolytic pathway and the tricarboxylic acid cycle, and those acids with a "short pathway", essentially a biotransformation of glucose. The regulation of the pathways and the future developments in metabolic control theory and genetic manipulations relating to them are considered. The organisms used industrially are also limited, Aspergillus sp. and Candida yeasts; again the underlying metabolic similarities lead to similar strategies for all the acids discussed.

Development of genetic maps of non-conventional yeasts

Numerous methods based on classical genetics have been developed for the genetic mapping of yeasts. Recombinant DNA technology and technology for electrophoretic separation of chromosomes make new approaches possible. The state-of-the-art in genetic mapping of Saccharomyces cerevisiae will be briefly reviewed. Then the availability and application of genetic mapping methods to non-conventional yeasts will be surveyed. Development of the genetic maps of the asexual diploid Candida albicans and of the heterothallic yeast Yarrowia lipolytica will be discussed in more detail.

Nonconventional yeasts: their genetics and biotechnological applications

To date, more than 500 species of yeasts have been described. Most of the genetic and biochemical studies have, however, been carried out with Saccharomyces cerevisiae. Although a considerable amount of knowledge has been accumulated on fundamental processes and biotechnological applications of this industrially important yeast, the large variety of other yeast genera and species may offer various advantages for experimental study as well as for product formation in biotechnology. The genetic investigation of these so-called unconventional yeasts is poorly developed and information about corresponding data is dispersed. It is the aim of this review to summarize and discuss the main results of genetic studies and biotechnological applications of unconventional yeasts and to serve as a guide for scientists who wish to enter this field or are interested in only some aspects of these yeasts.

Spontaneous haploidization in early zygote progeny and its use for mapping in the yeast Yarrowia lipolytica

By means of spontaneous haploidization immediately after conjugation, it is possible to map genes in Y. lipolytica. The already known linkages argA--leuA and metA--lysA were confirmed by means of this method. The mating type locus (MAT) is located on the same chromosome as argA--leuA.

Heterogeneity in the ribosomal family of the yeast Yarrowia lipolytica: genomic organization and segregation studies

The cloned r-DNA units of Yarrowia lipolytica [Van Heerikhuizen et al., 39 (1985) 213-222] and their restriction fragments have been used to probe blots of genomic DNA of this yeast. Wild-type and laboratory strains were shown to contain two-to-five types of repeated units, each strain displaying a specific pattern. By comparing their restriction patterns, we could localize the differences between units within their spacer region. Tetrad analysis strongly suggested a clustered organization of each type of repeat as well as the occurrence of meiotic exchanges within the r-DNA family. Chromosome loss was induced by benomyl and allowed to map several r-DNA clusters on the same chromosome. All those results indicate that the Y. lipolytica r-DNA gene family is quite different from other yeasts.

Parasexual process in the yeast Yarrowia lipolytica

Genetic studies of several events of the life cycle of Y. lipolytica demonstrated that diploid strains were unstable and produced mitotic segregants by haploidization. A screening system was developed which enabled us to show that parasexual processes can take place in addition to the sexual life cycle. This haploidization occurred through aneuploid intermediates as was proven statistically by the deviations from the segregation pattern as well as by the segregation data of the clones. The direction of the cross, was--with respect to the resistance to 2-deoxyglucose of A- or B-strain--not important for selection of mitotic segregants.

Improvement of sporulation in the yeast Yarrowia lipolytica

Strains of Yarrowia lipolytica forming exclusively spherical ascospores were developed through inbreeding. These strains are more suitable for micromanipulation than other inbred strains forming helm-shaped ascospores. External factors affecting sporulation frequency and tetrad formation in this yeast were investigated. Optimal formation of complete tetrads occurred at a narrow range of pH values around 6.0. Citrate was found to stimulate sporulation strongly. A synthetic medium containing citrate was developed to obtain standard conditions for maximum sporulation.