An improved method for yeast 2 microns plasmid curing

Curing Saccharomyces cerevisiae of the 2 micron plasmid by targeted DNA damage

Powerful mutagenic screens of yeast Saccharomyces cerevisiae have recently been developed which require strains that lack the endogenous 2 micron plasmid (Burns et al., 1994). Here, we describe a simple and reliable method for curing yeast of the highly stable genetic element. The approach employs heterologous expression of a 'step-arrest' mutant of the Flp recombinase. The mutant, Flp H305L (Parsons et al., 1988), forms long-lived covalent protein-DNA complexes exclusively at 2 micron-borne recombinase target sites. In vivo, the complexes serve as sites of targeted DNA damage. Using Southern hybridization and a colony color assay for plasmid loss, we show that expression of the mutant enzyme results in the effective elimination of the 2 micron from cells.

Molecular engineering with the FRT sequence of the yeast 2 microm plasmid: [cir0] segregant enrichment by counterselection for 2 microm site-specific recombination

Site-specific recombination systems from bacteriophage and yeasts are becoming precious tools for manipulating DNA both in vitro and in living organisms. In this work we describe the isolation of yeast Saccharomyces cerevisiae segregants which have lost the highly stable 2 microm DNA plasmid, exploiting the site-specific recombination system of 2 microm itself. We efficiently isolated [cir0] segregants from two haploid yeast strains and also a diploid. Moreover, the effect of mutations in the core region of the FRT (Flp Recognition Target) sequence was investigated in vivo, studying the result of the recombination event between several mutated and wild-type FRT sequences. From our result it seems that the identity between the core regions of two FRT sites is necessary but not sufficient, indicating that the core sequence itself has a relevant function in the recombination mechanism in vivo.

Identification of a yeast peroxisomal member of the family of AMP-binding proteins

We established a reverse-genetic approach to identify peroxisomal proteins involved in peroxisomal fatty acid metabolism of Saccharomyces cerevisiae. Putative peroxisomal peripheral membrane proteins were isolated by successive extraction of purified peroxisomes and purified by HPLC and SDS/PAGE. Six proteins were identified by peptide sequence analysis, including acyl-CoA oxidase and a trifunctional enzyme of the peroxisomal beta-oxidation system as well as peroxisomal malate dehydrogenase 3 and carnitine acetyltransferase. In addition two previously unknown putative peroxisomal proteins were identified, an unknown 40-kDa protein and a protein which we named Pcs60p, both major constituent of the isolated protein fraction. Pcs60p is encoded by ORF Z36091 of chromosome II from S. cerevisiae and consists of 543 amino acids with a molecular mass of 60.5 kDa. Biochemical, immunofluorescence microscopy and immunocytochemical data confirmed that Pcs60p is a peroxisomal peripheral membrane protein but the protein is also localized in the peroxisomal matrix. Consistent with the intraperoxisomal localization, the consensus sequence for a peroxisomal-targeting signal 1 (PTS1) is present at the extreme C-terminus of Pcs60p. Deletion studies revealed that the peroxisomal localization of the protein depends on the presence of this signal sequence. Expression of Pcs60p is highly inducible by oleic acid, however, the protein is dispensable for growth on oleic acid as single carbon source. Pcs60p belongs to the family of proteins which act via an ATP-dependent covalent binding of AMP to their substrates and shows the highest degree of similarity to the Escherichia coli long chain acyl-CoA synthetase.

Polymorphism within the nuclear and 2 micron genomes of Saccharomyces cerevisiae

Seven strains of bakers' yeast were obtained as a representative sample of the Spanish baking industry. The nuclear genome was monitored for polymorphism by transverse alternating field electrophoresis (TAFE) and restriction maps of 2 micron DNA were produced. All seven strains were uniquely different when evaluated by their total chromosomal lengths whereas only two 2 micron variants were defined. There was no apparent correlation between chromosomal and plasmid polymorphism. The extensive chromosomal polymorphism within one 2 micron DNA type indicates the rapid and relatively recent evolution of the nuclear genome. The hybrid origin (S. cerevisiae-S. monacensis) of lager yeast was critically evaluated by TAFE analysis of S. cerevisiae and S. carlsbergensis chromosomes. The absence of corresponding S. cerevisiae chromosomes III and XIII in S. carlsbergensis argued against the hybrid origin of lager strains. We discuss limitations of the hybrid origin hypothesis of industrial yeasts and propose that the molecular coevolution observed in 2 micron DNA serves as a useful additional mechanism for rationalization of some of the structural polymorphism of the nuclear genome.

DNA sequence divergence and functional conservation at the STB locus of yeast 2 microns circle variants

2 microns DNA isolated from industrial Saccharomyces cerevisiae yeasts exhibited extensive restriction fragment length polymorphisms. At least five 2 microns species were identified from eleven [cir+] strains. Southern hybridization mapped restriction fragment length polymorphisms at STB, a cis-acting locus essential for plasmid partitioning. Some 2 microns variants (e.g., 4110-2 microns and 4108-2 microns) had an altered number of 125-bp consensus repeats at STB. However, the corresponding region of 7754-2 microns has only approximately 70% nucleotide sequence homology with the 125-bp STB consensus repeat. YRp plasmids containing 7754-2 microns STB behave as YEp plasmids in laboratory yeasts, thereby indicating STB sequence divergence coupled to conservation of function.