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.     

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.     

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.     

Polymorphic karyotypes in related Acremonium strains

Summary A restriction fragment length polymorphism (RFLP) analysis was performed on six related Acremonium strains. With respect to the restriction fragment pattern, all strains of A. chrysogenum were indistinguishable from each other but showed distinctive differences from those of A. strictum, A. flavum and Cephalosporium polyvaleurum. Using pulsed-field gel electrophoresis, we obtained different chromosome patterns from most of the Acremonium strains. Remarkably, the pattern varies in three related A. chrysogenum strains which also differ in their rate of cephalosporin C biosynthesis. The electrophoretic karyotyping was confirmed by the location of rDNA genes on separate chromosomes. Our data indicate that chromosome translocations in industrial strains may be responsible for increased -lactam synthesis.     

Localization of yeast glucoamylase genes by PFGE and OFAGE

Summary Chromosomes of two closely related yeast strains, the amylolytic Saccharomyces diastaticus and the non-amylolytic Saccharomyces cerevisiae, were resolved by pulsed field gel electrophoresis (PFGE) and orthological field alteration gel electrophoresis (OFAGE). Electrophoretic karyotypes of these two strains are identical. Sixteen cloned Saccharomyces genes of known chromosomal location were used to identify individual chromosomes by Southern hybridization analyses. The Southern blots were reprobed with a cloned fragment of the STA2 glucoamylase gene of S. diastaticus. STA2 exhibits homology to STA1 and STA3 as well as the sporulation-specific glucoamylase (SGA) gene from both Saccharomyces strains. The three unlinked, homologous genes, STA1 (DEX2, MAL5), STA2 (DEX1) and STA3 (DEX3) encoding the extracellular glucoamylase isozymes GAI, GAII and GAIII in S. diastaticus were then assigned to chromosomes IV, II and XIV, respectively. The SGA gene, encoding an intracellular glucoamylase in both S. diastaticus and S. cerevisiae, was assigned to chromosome IX. Electrophoretic mapping of the STA and SGA genes is at present the only way to localize these genes, since glucoamylase repressor gene(s) (STA10, INH1 and/or IST2) are present in most laboratory strains of S. cerevisiae and the SGA phenotype is only detectable during sporulation.     

Cloning the Yarrowia lipolytica homologue of the Saccharomyces cerevisiae SEC62 gene

Yarrowia lipolytica SEC62 cDNA was cloned by functional complementation of a thermo-sensitive sec62 Saccharomyces cerevisiae mutant strain. The Y. lipolytica SEC62 promoter region was amplified by the inverse polymerase chain reaction (PCR). The cDNA codes for a 396 amino-acid protein with two potential trans-membrane domains. Y. lipolytica Sec62p behaves as an integral membrane protein as shown by Western blotting. Y. lipolytica SEC62 cDNA is able to complement a S. cerevisiae sec62 null mutant strain confirming functional conservation, although only 53.6% amino-acid similarity is observed between Y. lipolytica and S. cerevisiae Sec62. Received: 21 August / 17 September 1996     

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.     

Genomic comparisons among parental and fusant strains of Candida shehatae and Pichia stipitis

DNA-DNA binding experiments on selected fusants of Candida shehatae and Pichia stipitis showed that the nucleus of these strains was composed predominantly of Pichia DNA. Electrophoretic karyotyping revealed that the fusants contained four chromosomes, similar to those found in the Pichia parental strain. In addition, the fusants showed only marginal increases in cell DNA content when compared with the parents. Karyogamy was confirmed, however, by the isolation of recombinant phenotypic segregants, induced by meiotic and mitotic segregation. The results suggest that the fusion led to integration of Candida genes, rather than whole chromosomes, with the entire genome of P. stipitis.     

Identification of mutations preventing n-hexadecane uptake among 26 n-alkane non-utilizing mutants of Yarrowia (Saccharomycopsis) lipolytica

Summary Genetic analyses of n-alkane non-utilizing mutants of the yeast Yarrowia (Saccharomycopsis) lipolytica were continued. By analyses of inter-mutant complementation and recombination a total of 26 genetic loci have been identified. Mutations representing these loci have phenotypes characteristic of defects in substrate uptake or in one or more of the enzymatic activities making up the hydroxylase complex. Tests of ¹⁴C n-hexadecane uptake by a set of alkane-negative mutants representing the 26 loci show that 16 of the mutations cause a significant reduction in n-alkane uptake. N-alkane uptake by Y. lipolytica is shown to be inducible and to be inhibited by the metabolic poisons 2–4 dinitrophenol and KCN. The latter observation indicates that n-alkane uptake of Y. lipolytica is due to active transport.     

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.     

Inheritance of chromosome-length polymorphisms in Ophiostoma ulmi (sensu lato)

We have investigated the mitotic and meiotic transmission of chromosome-length polymorphisms in Ophiostoma ulmi s.l., the causal agent of Dutch elm disease. The North-American aggressive (NAN) strain CESS16K has an atypical electrophoretic karyotype, carrying two chromosome-sized DNAs (chDNAs) that have not been observed in other members of the NAN biotype. Independent CESS16K chDNA preparations, even after repeated inoculation and recovery from the elm host, and analysis of 16 progeny strains after a cross between the NAN strains FG245B^r-O and CESS16K, demonstrated that these unique chDNAs are integral components of the CESS16K genome. Analysis of the progeny, by electrophoretic karyotyping and hybridizations with probes specific to individual chDNAs, presented evidence that genome rearrangements can occur as a consequence of meiosis. Even though novel electrophoretic karyotypes and a novel-sized chromosome were observed in the karyotypes of the progeny strains, the low level of reassortment between the chromosomes carrying length polymorphisms presented evidence that there are constraints to genome plasticity for this fungus.     

Complementary mating types of Mucor circinelloides show electrophoretic karyotype heterogeneity

Electrophoretic karyotypes of ten strains of Mucor circinelloides f. lusitanicus were generated by contour-clamped homogeneous electric field (CHEF) gel-electrophoresis. Most of the strains analyzed showed polymorphisms, but a different main karyotype pattern could be correlated with each mating type. Genome structure was further analyzed by gene assignment to the chromosome-sized DNAs. Nonradioactive hybridization techniques identified the chromosomal localization of seven cloned genes. The hybridization patterns confirmed the similarity between the mating-type (−) strains and showed some heterogeneity among the mating-type (+) strains. Linkage was found between genes pyrF and chs3 in all the strains, between the gene leuA and the rDNA in all mating-type (−) strains and ATCC 1216b (+), and between chs2 and the rDNA in CBS 969.68 (+). This is the first time that gene linkage in M. circinelloides has been reported, but in some cases the linkage relationships obtained are strain-dependent. Received: 7 June / 2 September 1999     

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.)     

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.     

Nucleotide sequences and characterization of haemolysin genes from Aeromonas hydrophila and Aeromonas sobria

Extracellular haemolysin is thought to be one of the important virulence factors in Aeromonas infection. Two extracellular haemolysin genes (AHH3 and AHH4) from Aeromonas hydrophila strain 28SA, one (AHH5) from A. hydrophila strain AH-1 and one (ASA1) from Aeromonas sobria strain 33 were cloned into cosmid and plasmid vector DNA in Escherichia coli. The nucleotide sequences of the open reading frames of AHH3 and AHH4 are both 1476 basepairs (bp), whereas AHH5 and ASA1 are 1455 and 1467 bp in length, respectively. The deduced amino acid sequences of AHH3, AHH4, AHH5 and the previously reported aerolysin from A. hydrophila showed a significant degree of sequence homology of over 90% each. The amino acid identity of the ASA1 haemolysin and those from A. hydrophila and Aeromonas trota aerolysins ranged from 58–68%. From DNA hybridization analysis using our cloned haemolysin genes as probes, we found that the AHH5 and ASA1 DNA probes hybridized with about 31 and 75% strains of motile Aeromonas species, respectively. The activity of haemolysins of cloned genes were different in medium agar containing various erythrocytes.     

Genomic and phenotypic evaluation of Salmonella typhimurium and Salmonella enteritidis in Iran

Genomic and phenotypic evaluation of Salmonella typhimurium and Salmonella enteritidis by two simple, fast, and applicable methods of random amplified polymorphic DNA (RAPD) polymerase chain reaction (PCR) and antibiotic susceptibility for employment in epidemiologic surveillance screening systems in Iran was the objective in this study. We selected 60 (30 S. typhimurium and 30 S. enteritidis) isolates from different animal sources and different times and places among 1975–2006 in Iran. Serotyping with traditional method and reliable antisera was done and then confirmed with multiplex PCR (with four and three pair of primers, respectively). All of S. typhimurium and S. enteritidis isolates have virulence genes of invA and spv, respectively. Then, from nine primers, two primers that have enough discriminatory power were selected for RAPD analysis. We set up the quality and quantity of DNA template, primers, MgCl₂, Taq DNA polymerase, and deoxyribonucleotide triphosphates concentration for RAPD analysis. We also examined the strains with disk diffusion standard antibiotic susceptibility test. With the application of primer P1254; we saw four and seven and primer 23L, six and three profiles in RAPD analysis and 13 and six profiles of R-type in susceptibility test of S. typhimurium and S. enteritidis, respectively. Combination of two methods differentiated these 30 strains to 20 and 16 different profiles, respectively. The finding of this study indicated that clonality of S. enteritidis is more than S. typhimurium in Iran and RAPD-PCR in combination with antibiotic susceptibility test were fast, easy, relatively reliable, and discriminatory molecular and phenotypic methods in the differentiation of S. typhimurium and S. enteritidis for epidemiologic purposes in Iran.     

Molecular and immunological characterization of the p83/100 protein of various Borrelia burgdorferi sensu lato strains

The complete coding regions of the chromosomally encoded p83/100 protein of four Borrelia garinii strains and one Borrelia burgdorferi sensu stricto strain have been amplified by the polymerase chain reaction (PCR), cloned and sequenced. From alignment studies with the deduced amino acid sequences presented here, and five other published p83/100 sequences, the most heterologous region of the p83/100 molecule was identified to be located between amino acid position 390–540. To study the structure of this heterogeneous region, and internal fragment of the p83/100 genes from 11 additional B. burgdorferi sensu lato strains was amplified by PCR. The PCR products were analyzed by DNA sequencing and restriction enzyme analysis. These internal p83/100 fragments varied in size and sequence. Cluster analysis of internal p83/100 fragments, as well as restriction enzyme analysis, revealed three major groups in accordance with grouping into the three species causing Lyme disease. Strains within the same species (six B. burgdorferi sensu stricto and six B. afzelii strains) showed similar p83/100 partial structures. Nevertheless, nine B. garinii strains showed more sequence variations and could be further divided into two major subgroups. One group is represented by OspA serotype 4 strains, the other more heterogeneous group is represented by OspA serotypes 3, 5, 6 and 7 strains. Phenotypic analysis with four p83/100-specific monoclonal antibodies revealed four distinct reactivity patterns. Antibody L100 1B4 recognized a common epitope of B. burgdorferi sensu stricto and B. afzelii. Antibodies L100 17D3 and L100 18B4 were reactive with an epitope shared by strains of all three species. The broadest reactivity was shown by L100 18B4 which, in constrast to L100 17D3, additionally recognized the relapsing fever borreliae B. turicatae and B. hermsii. L100 8B8 detected a subgroup of the B. burgdorferi sensu stricto strains. Since comparison of the p83/100 molecule with sequences from protein databases showed similarities with characteristics of eukaryotic cell structures, the p83/100 might mimic these structures and may, therefore, be involved in the immune escape mechanism of the pathogenic agent of Lyme disease.     

DNA translocations contribute to chromosome length polymorphisms in Candida albicans

Summary Rotating-gel electrophoresis and DNA hybridization were used to compare the electrophoretic karyotype of six Candida albicans isolates. The hybridization pattern for 22 cloned sequences, including eight previously unmapped genes, indicates that there are eight pair of homologous chromosomes in each strain. However, since homologous chromosomes can differ in length, it is possible to resolve more than eight bands in some strains. The mapping data demonstrate that linkage groups are generally conserved suggesting that, in spite of gross karyotype differences, there is an underlying similarity in the genome organization of different isolates. The hybridization data also provide direct evidence that DNA translocations and reciprocal translocations contribute to chromosome length polymorphisms in C. albicans.     

Electrophoretic karyotype of the astaxanthin-producing yeast Phaffia rhodozyma

The electrophoretic karyotype of three different strains of Phaffia rhodozyma was determined by contour-clamped homogeneous electric field (CHEF)-gel electrophoresis. Significant differences in electrophoretic karyotyping patterns were found among the three strains studied. Between nine and 17 bands were observed. The size of these bands, based on their migration relative to the chromosomal DNA of Schizosaccharomyces pombe, Hansenula wingei was estimated to be between 0.48 and 3.1 Mb.     

New components of <Emphasis Type="Italic">Yarrowia lipolytica</Emphasis> Golgi multi-protein complexes containing the α-1,6-mannosyltransferases YlMnn9p and YlAnl1p

This paper reports the identification and the characterization of two new components of Yarrowia lipolytica Golgi multi-protein complexes. Blast analysis on the Y. lipolytica complete genome allowed us to find a new α-1,6-mannosyltransferase, YlAnl2p, which displays an overall identity of 59% and shares a Golgi cellular localization with the previously described YlAnl1p. Moreover, YlAnl2p was shown to directly interact with YlMnn9p using the two-hybrid system suggesting that the two proteins form a second Golgi sub-complex. In order to further elucidate the composition of the Y. lipolytica Golgi complexes containing α-1,6-mannosyltransferases, as M-Pol complexes in Saccharomyces cerevisiae, two-hybrid screens were performed using either YlMnn9p or YlAnl1p as bait. A specific partner of YlAnl1p, named YlAni1p was identified. The two proteins were shown to co-localize and co-precipitate in Y. lipolytica. YlAni1p, which displays a coiled-coil domain as Golgin, and YlAnl1p could be involved in the Golgi apparatus maintenance in the yeast Y. lipolytica. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.