Fission Yeast Genome Research Articles

Four chromo-domain proteins of Schizosaccharomyces pombe differentially repress transcription at various chromosomal locations.

Transcription is repressed in regions of the fission yeast genome close to centromeres, telomeres, or the silent mating-type cassettes mat2-P and mat3-M. The repression involves the chromo-domain proteins Swi6 and Clr4. We report that two other chromo-domain proteins, Chp1 and Chp2, are also important for these position effects. Chp1 showed a specificity for centromeric regions. Its essentiality for the transcriptional repression of centromeric markers correlates with its importance for chromosome stability. Chp2 appeared more pleiotropic. Its effects on centromeric silencing were less pronounced than those of Chp1, and it participated in telomeric position effects and transcriptional silencing in the mating-type region. We also found that PolII-transcribed genes were repressed when placed in one of the Schizosaccharomyces pombe rDNA clusters, a situation analogous to that in the budding yeast Saccharomyces cerevisiae. Chp2, Swi6, Clr4, and, to a lesser extent, Chp1 participated in that repression.

Organization of DNA replication origins in the fission yeast genome.

Eukaryotic DNA replication initiates at multiple points along the chromosomes known as replication origins (ORIs). We have developed a strategy to identify ORIs directly from replication intermediates in the fission yeast Schizosaccharomyces pombe. Mapping of a selection of the novel ORIs onto the genome reveals their preferential localization at intergenic regions upstream from genes. These results are supported by the observation that a large proportion of regions overlapping gene promoters contain active ORIs. Mapping of the genomic ars1 replication origin at nucleotide resolution shows that replication initiates at a defined position immediately upstream from the hus5(+) promoter. Deletion analysis indicates that the regulatory elements required to initiate transcription and replication lie in close proximity, suggesting a possible relationship between both processes in vivo.

Structural analyses of DNA fragments integrated by illegitimate recombination in Schizosaccharomyces pombe.

In order to elucidate the mechanisms of illegitimate recombination in eukaryotes, we have studied the structure of DNA fragments integrated by illegitimate recombination into the genome of fission yeast. Nonhomologous recombination was rarely identified when a long region of homology with the chromosomal leu1+ gene was present in the introduced leu1::ura4+ DNA fragment; but a decrease in length of homology leads to an increase in the ratio of non-homologous to homologous recombination events. The introduced DNA fragments were integrated into different sites in the chromosomes by nonhomologous recombination. The results suggested that there are multiple modes of integration; most events simply involve both ends of the fragments, while in other cases, fragments were integrated in a more complicated manner, probably via circularization or multimerization. To analyze the mechanism of the major type of integration, DNA fragments containing the recombination junctions of three recombinants were amplified by inverted polymerase chain reaction (IPCR) and their nucleotide sequences were determined. There was no obvious homology between introduced DNA and chromosomal DNA at these recombination sites. Furthermore it was found that each terminal region of the introduced DNA was deleted, but that there were no or very small deletions in the target sites of chromosomal DNA. Two models are proposed to explain the mechanism of nonhomologous integration.

A 13 kb resolution cosmid map of the 14 Mb fission yeast genome by nonrandom sequence-tagged site mapping

We present the application of a nonrandom sequencetagged site (STS) content detection method in mapping an entire genome, that of fission yeast. The novelty of our strategy is in the use of STS probes made from both ends of cosmid clones, selected on the basis of “sample without replacement” (only library clones that show no previous positive hybridization are selected and made into probes). We developed powerful techniques, based on consistency analysis, for error detection and contig assembly. In addition, we probed our library with genetically mapped markers and Notl or Stil linking clones, thereby anchoring contigs onto chromosomes. Our map contains more than 1000 sites, including genes (most were previously unmapped), occurrences of known repetitive elements, and Notl-Stil restriction sites.

Gene database for the fission yeast Schizosaccharomyces pombe

As an aid to the fission yeast genome project, we describe a database for Schizosaccharomyces pombe consisting of both genetic and physical information. As presented, it is therefore both an updated gene list of all the nuclear genes of the fission yeast, and provides an estimate of the physical distance between two mapped genes. Additionally, a field indicates whether the sequence of the gene is available. Currently, sequence information is available for 135 of the 501 known genes.

Characterization of a novel open reading frame, urf a, in the mitochondrial genome of fission yeast: Correlation of urf a mutations with a mitochondrial mutator phenotype and a possible role of frameshifting in urf a expression

Between the genes for tRNA(gin) and tRNA(ile) an open reading frame of 227 amino acids has been identified which is unique among known mitochondrial genomes and which has been termed urf a (Lang et al. 1983; Kornrumpf et al. 1984). It uses the "mitochondrial" genetic code, i.e., it contains a TGA codon, whereas all other protein-encoding genes, and all but one intronic open reading frame, use the "standard" genetic code (UGG for tryptophan). A previous paper has demonstrated that "mutator" strains show an increased formation of mitochondrial drug-resistant and respiration-deficient mutants (including deletions). In this paper we show that the mutator activity is correlated with mutations in urf a. A detailed analysis of one urf a mutant is presented (anar-6), where the deletion of an A residue leads to a frameshift mutation and consequently to premature termination of the putative protein. The phenotype of colonies originating from a single mutant clone varies from no growth up to full growth on non-fermentable substrate. This phenomenon of phenotypic segregation can be explained by the ability of the cell to perform translational frameshifting. A detailed analysis of the DNA sequence and the putative urf a protein will be presented and a possible function of the protein will be discussed.

The mitochondrial genome of fission yeast: inability of all introns to splice autocatalytically, and construction and characterization of an intronless genome

In this paper we report the inability of four group I introns in the gene encoding subunit I of cytochrome c oxidase (cox1) and the group II intron in the apocytochrome b gene (cob) to splice autocatalytically. Furthermore we present the characterization of the first cox1 intron in the mutator strain anar-14 and the construction and characterization of strains with intronless mitochondrial genomes. We provide evidence that removal of introns at the DNA level (termed DNA splicing) is dependent on an active RNA maturase. Finally we demonstrate that the absence of introns does not abolish homologous mitochondrial recombination.

Construction and characterization of centric circular and acentric linear chromosomes in fission yeast

Gene disruption and gap repair of chromosomal DNA have been frequently employed techniques in yeast genetics. To extend the possibility of using these gene manipulations for larger genomic regions, we have examined the maximal sizes of chromosomal DNA disrupted or repaired in vivo. Here we report a simple, potentially general, method for selectively deleting a 150 kb region, or gap-filling a 100 kb region, in the fission yeast genome. This enables the generation of acentric linear chromosomes by deletion, or the cloning of large functional centromeric DNAs into circular minichromosomes by gap-filling. The fidelity of the resulting gap-filling is high, judging from partial-digestion mapping of gap-repaired DNAs. By analysing a series of such circular minichromosomes, we conclude that only a part of the repetitive centromeric region, including the central domain, is essential for mitotic and meiotic chromosome segregation. Acentric linear chromosomes, although unstable, could be maintained, indicating that it may be possible to construct an acentric vector for large DNA fragments in this organism.

The mitochondrial genome of the fission yeast schizosaccharomyces pombe

1) We have identified by electron microscopy and isolated a circular DNA species of approximately 6 µm contour length from DNase treated mitochondrial fractions of the petite negative yeast Schizosaccharomyces pombe (S. pombe). 2) Another molecular species of about 3 µm length is also present in mitochondrial fractions. These molecules, however, disappear after DNase treatment or extensive washing, indicating their extramitochondrial location. There is evidence (Fournier et al. 1981) that these molecules represent a multicopy plasmid coding for the genes of cytoplasmic ribosomal RNAs. 3) A restriction enzyme cleavage map of the 6 µm species was constructed using twelve enzymes. Physical mapping revealed a genome length of approximately 18.9 kilobase pairs, thus confirming the electron microscopic data. 4) Northern hybridization of mitochondrial RNA with restriction fragments of mitochondrial DNA revealed two major signals which are attributed to the small and large ribosomal RNA. Apparently both rRNA genes map close together. 5) Spontaneous mit(-) deletion mutants were characterized phenotypically and the location of their deletions was determined. 6) In strains carrying a cytoplasmic mutator (Seitz-Mayr and Wolf 1982) or derived from mutator strains four restriction sites have been mapped, which are not present in the mitochondrial DNA of the parental strain. These extra sites are very likely consequences of the action of the mutator. 7) In conclusion we have presented evidence that the 6 µm circular DNA species is the mitochondrial genome of fission yeast. Special features of this genome are discussed in comparison with other mitochondrial genomes.

Extrachromosomal mutator inducing point mutations and deletions in mitochondrial genome of fission yeast.

We report the isolation and characterization of a mutator mutant in the fission yeast Schizosaccharomyces pombe. This mutator is of extrachromosomal, very likely mitochondrial, inheritance and acts exclusively on mitochondrial mtDNA. It greatly enhances the frequency of spontaneous mitochondrial drug-resistance mutants compared to the wild type, but it is not obligatory for their occurrence. In contrast, mitochondrial respiratory deficient mutants can only be isolated from mutator strains. It could be shown that this mutator induces point mutations as well as deletions in the mitochondrial genome which lead to respiratory deficiency. This mutator might prove to have a novel function encoded by the mtDNA.