Multiple-copy integration in the yeast Yarrowia lipolytica

Using an EcoRI-BglII fragment of the G unit of the rDNA of Y. lipolytica and a set of 11 deletions in the URA3 promoter, we have constructed several plasmids to test gene amplification in the rDNA. These plasmids contain the rDNA fragment for integration, defective versions of the URA3 gene, the XPR2 gene encoding alkaline extracellular protease (AEP) as a reporter gene, and part of the pBR322 plasmid for selection and replication in E. coli. Among these plasmids, one corresponds to a deletion which allows multiple integration into the rDNA (plasmid pINA773). Two other plasmids (pINA767 and pINA772) give multiple integration only with a mutated URA3 gene. Transformants carrying these three plasmids were tested for copy number, stability, chromosomal localization and AEP secretion. Transformants containing plasmids pINA767, 772 and 773 displayed an average copy number of 5, 12 and 25–60 copies respectively of the plasmid, as estimated by PCR and DNA hybridization. Integrations occurred in only one chromosome except for transformants containing 60 copies where copies were observed at least in two different chromosomes. Multiple integrations were found both as tandem repeats and as dispersed copies. Plasmid copy number was stable in both minimum and rich media, for strains containing less than ten copies per cells. However, for higher copy number, multiple integrations were stable only when AEP synthesis was not induced, while in inducing medium stability of the multiple integrations was dramatically affected.     

Virus-like particles from the yeast Yarrowia lipolytica

Summary 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.     

Integrative transformation of the yeast Yarrowia lipolytica

Summary An EcoR1 shotgun of Yarrowia lipolytica DNA was inserted into the plasmid YIp333 which carries the LYS2 gene of S. cerevisiae. The resulting plasmid pool was transformed in both S. cerevisiae and Y. lipolytica. Whereas numerous replicating plasmids could be isolated from the S. cerevisiae Lys⁺ transformants, all transformants of Y. lipolytica so far analyzed were found to result from integrative transformation. This occurred at a frequency of 1 to 10 transformants per g of input DNA. Co-transformation occurred at high frequency and resulted in tandem integration of 2 to 10 copies of the incoming DNA. Structural and segregational stability of the transforming DNA were both high.     

Cloning and characterisation of the ribosomal RNA genes of the dimorphic yeast,Yarrowia lipolytica

Summary The ribosomal RNA genes of Yarrowia lipolytica have been identified, both in restriction digests of total genomic DNA and in a pBR322 gene bank, by hybridisation with cloned Saccharomyces cerevisiae rDNA. The Y. lipolytica rDNA repeat unit is 8.9 kb in size and contains the genes for the 25S and 18S, but not the 5S, rRNA species. The number of copies of these repeat units is approx. 50 per haploid genome. Several clones were found which did not conform to the standard restriction map due to differences outside the coding region. It appears that there is either heterogeneity of the spacer sequence within a strain or that the Y. lipolytica rDNA genes may be present as a number of separate clusters within this yeast's genome.     

Gene-protein assignments within the yeast Yarrowia lipolytica dsRNA viral genome

Summary Some strains of the yeast Yarrowia lipolytica possess virus-like particles (VLPs) which encapsidate a double-stranded RNA (dsRNA) genome designated L_y. We report here that these VLPs have two associated polypeptides of molecular weights 83 kd (VL_y-P1) and 77 kd (VL_y-P2). Denatured Ly-dsRNA was used to program a cell-free rabbit reticulocyte translation system, resulting in the appearance of four major products, viz. Ly-P1 (83 kd); L_y-P2 (77 kd); L_y-P3 (74 kd) and L_y-P4 (68 kd). The in vivo viral-associated protein VL_y-P1 co-migrated on SDS-polyacrylamide gels with the in vitro product L_y-P1 and, similarly, VL_y-P2 co-migrated with L_y-P2. Peptide mapping data confirm the identity of the in vivo products (VL_y-P1 and VL_y-P2) and their in vitro counterparts. The conclusion made is that VL_y-P1 and VL_yP2 are almost identical primary translation products of the L_y genome, derived from a single or multiple species of L_y-dsRNA. RNA blot hybridizations using L_1A M₁ and separately, L_2A M₂ probes prepared from appropriate K1 and K2 Saccharomyces cerevisiae killer strains, failed to show any detectable homology to L_y-dsRNA, substantiating the uniqueness of the Ly genome with respect to the K1 and K2 S. cerevisiae dsRNA killer systems.     

Two genes encode 7SL RNAs in the yeast Yarrowia lipolytica

Summary We have identified an abundant cytoplasmic 7S RNA in crude extracts of the yeast Yarrowia lipolytica. A cDNA probe was prepared from this RNA and used to screen a genomic library. The DNA sequence of a positive clone was determined and the end positions of the 7S RNA gene established by comparison with the sequence of the extremities of 7S RNA. This gene, designated SCR2, encodes a 270-nucleotide RNA that can be folded into a secondary structure similar to that of 7SL RNAs. This RNA is 94.4% homologous to a previously identified 7S RNA from this yeast, but is encoded by a separate gene with highly divergent flanking sequences.     

Complementation of Saccharomyces cerevisiae acid phosphatase mutation by a genomic sequence from the yeast Yarrowia lipolytica identifies a new phosphatase

Summary A Yarrowia lipolytica gene library was constructed in vector YRp7 and transformed into a Saccharomyces cerevisiae strain lacking both major acid phosphatase activities. A 2.18 kb genomic sequence restoring the ability to hydrolyze -naphthyl phosphate was isolated. Its sequencing revealed an ORF encoding 358 amino acids without significant homology with any known phosphatase. A putative signal peptide and several possible sites for N-glycosylation were identified. Phosphate-regulated expression of the cloned gene was observed in Y. lipolytica. Disruption data favoured the hypothesis that it might encode a minor phosphatase species.     

Molecular cloning of Rab-related genes in the yeast Yarrowia lipolytica. Analysis of RYL1, an essential gene encoding a SEC4 homologue

Small GTP-binding proteins of the Rab family are involved in the vesicular traffic inside eukaryotic cells. A gene library from the yeast Yarrowia lipolytica was screened with an oligonucleotide deduced from a highly conserved sequence in the Rab family. Four different genes were isolated. One of them, RYL1, was shown to be essential for cell viability. RYL1p displayed a high similarity with and tight phylogenetic relationships to SEC4p. When placed under the control of the GAL10 promoter, RYL1 was able to specifically relieve the thermosensitivity of a sec4–8 mutant of Saccharomyces cerevisiae. Therefore, it is proposed that RYL1 is a functional homologue of the S. cerevisiae SEC4 gene and is involved in the fusion of secretory vesicles with the plasma membrane in the general protein secretion pathway.     

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

Summary 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.Abbreviations UV ultraviolet - dsRNA double-stranded RNA - VLPs viruslike particles, A and B alleles of the mating type locus - TCA trichloracetic acid     

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

Summary 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.(Abbreviations: A and B, alleles of the mating type locus; deg^R, recessive resistance to 2-deoxygiucose (DEG) when acetate is given as carbon source.)     

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.     

Evidence for the control of a mutation in lysine catabolism by the mating type in Yarrowia lipolytica

Summary Reversions of a mutation lye 1.5 blocking the first step of the lysine catabolic pathway were isolated. These reversions mapped inside the LYC1 locus. They exhibited an alteration of the regulation of the lysine pool after nitrogen and phosphorus starvation. This phenomenon did not appear in sexual diploids homozygous for the reversion. Diploids homozygous for the mating type were constructed by protoplast fusion. They displayed a pattern similar to that of the haploids. We conclude that the expression of this mutation is under the control of the physiological state of the mating type.Preliminary accounts were presented at the We International Congress of Genetics (New Delhi, December 1983)     

Formation of intergeneric hybrids of yeast by protoplast fusion of Yarrowia and Kluyveromyces species

Summary Prototrophic hybrids have been obtained by the fusion of auxotrophic haploid strains of the two yeasts Yarrowia (Saccharomycopsis) lipolytica and Kluyveromyces lactis. The hybrid fusants had a colonial morphology intermediate between that of the two parent strains, were uninucleate, and contained an approximately diploid amount of DNA per cell. The growth rates of all the fusants on a minimal glucose medium were slower than those of the two parents. Two of the fusants studied could utilise a novel range of carbon sources.All of these data suggested that the hybrids contained a diploid nucleus formed by the fusion of the two haploid parental nuclei. However, analytical CsCl density gradient centrifugation demonstrated that the nuclear DNA of the fusants was derived almost entirely from the Y. lipolytica parent. Moreover, an examination of the protein constitution of the fusants by two-dimensional gel electrophoresis showed that their protein patterns were indistinguishable from that of Y. lipolytica. Two possible mechanisms for the formation of a diploid nucleus containing DNA derived almost entirely from one of the haploid parents are discussed.     

Cloning and biochemical characterization of LYS5 gene of Saccharomyces cerevisiae

Summary In Saccharomyces cerevisiae, the functions of two unlinked genes (LYS2 and LYS5) are required for the synthesis of the lysine biosynthetic enzyme, -aminoadipate reductase. The LYS5 gene of S. cerevisiae was cloned by functional complementation of a lys5 mutant, X4004-3A, using a YEp24 plasmid library. The cloned LYS5 gene was contained within a 7.5 kb DNA insert of the recombinant plasmid pSC5. Cloning of LYS5 gene was confirmed by second cycle transformation of a lys5 mutant with the pSC5 plasmid, growth response studies, and plasmid loss experiments with Lys5 ⁺ transformants. Analysis of restriction digests of the pSC5 plasmid revealed 3 EcoRI, 5 PvuII, 1 PstI, 1 BglII and 2 HpaI sites in the 7.5 kb insert. A 3.9 kb internal pSC5 fragment hybridized only to the plasmid pSC5, but no homology was observed with LYS2 DNA or the YEp24 vector. The pSC5 transformed Lys5 ⁺ cells and the wild-type strain exhibited same level of -aminoadipate reductase activity, whereas lys5 mutant and plasmid-cured transformed strain exhibited none. Lys2 ⁺ transformants consistently had five times greater -aminoadipate reductase activity when compared with the wildtype and the Lys5 ⁺ transformant. The -aminoadipate reductase activity was repressed in lysine-grown wildtype and Lys5 ⁺ transformed cells but not in Lys2 ⁺ transformed cells. A Lys2 ⁺ and Lys5 ⁺ double transformant exhibited higher a-aminoadipate reductase activity than lys2 ⁺ or lys5 ⁺ transformant.     

The 3-phosphoglycerate kinase gene of the yeastYarrowia lipolytica de-represses on gluconeogenic substrates

We have isolated the 3-phosphoglycerate kinase (PGK) gene of the yeastYarrowia lipolytica by probing a genomic library with a PCR fragment amplified with primers deduced from two highly conserved regions of various PGKs. It is a unique sequence encoding a polypeptide of 417 residues with extensive homology to other PGKs, especially to that ofAspergillus nidulans (76% identity). The expression of theY. lipolytica PGK1 gene proved to be higher on gluconeogenic substrates than on glycolytic ones. Haploid strains harboring a disrupted allele were able to grow on mixtures of a gluconeogenic carbon source and of a glycolytic one, but required proline supplementation in the presence of glucose, and were inhibited by glycerol.     

Isolation and characterization of mitochondrial DNA from the alkane yeast Saccharomycopsis lipolytica

Summary Mitochondrial (mt) DNA of the alkane yeast, Saccharomycopsis lipolytica, was isolated. Its buoyant density in CsCl was found to be of 1.687 g/cm³, indicating a GC content of 27.5% and its melting point T_m = 79.5 °C, indicating a GC content of 24.9%. The corresponding values for nuclear (n) DNA, are 1.709 g/cm³ (GC: 49.5%) and T_m = 90.5 (GC: 51.7%) respectively. Electron microscopy revealed that mtDNA has a circular structure with a contour length of about 14.5 µm corresponding to 45.5 kb per molecule. The size estimated from restriction analyses performed with 7 endonucleases was 48.35 kb/molecule. A restriction map was constructed, using the cleavage data of 4 endonucleases.     

Genetic regulation of isocitrate lyase in the yeastYarrowia lipolytica

Summary Isocitrate lyase-less (Icl^–) mutants were selected from genetically defined strains ofYarrowia lipolytica to investigate the regulation of synthesis of isocitrate lyase (ICL). Eighteen mutations were localized in the geneICLI, which is most probably the structural gene of ICL in this yeast. Atrans-acting positive element (ICL2) could be identified. This gene is not linked toICL1. One mutation was detected in anotherICL gene (ICL3) which is linked to geneICL1. This mutation lowered the ICL activity incis but not intrans position to geneICLI.     

Cloning by genetic complementation and restriction mapping of the yeast HEM1 gene coding for 5-aminolevulinate synthase

Summary We have cloned the structural gene HEM1 for 5-aminolevulinate (ALA) synthase from Saccharomyces cerevisiae by transformation and complementation of a yeast hem1–5 mutant which was previously shown to lack ALA synthase activity (Urban-Grimal and Labbe Bois 1981) and had no immunodetectable ALA synthase protein when tested with yeast ALA synthase antiserum. The gene was selected from a recombinant cosmid pool which contained wild-type yeast genomic DNA fragments of an average size of 40 kb. The cloned gene was identified by the restauration.of growth on a non fermentable carbon source without addition of exogenous ALA. Sub cloning of partial Sau3A digests and functional analysis by transformation allowed us to isolate three independent plasmids, each carrying a 6 kb yeast DNA fragment inserted in either orientation into the single BamHI site of the vector pHCG3 and able to complement hem1–5 mutation. Analysis of the three plasmids by restriction endonucleases showed that HEM1 is contained within a 2.9 kb fragment. The three corresponding yeast trans formants present a 1, 2.5 and 16 fold increase in ALA synthase activity as compared to the wild-type strain. The gene product immunodetected in the transformant yeast cells has identical size as the wild-type yeast ALA synthase and its amount correlates well with the increase in ALA synthase activity.