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Etherington GJ, Gil EG, Haerty W, Oliferenko S, Nieduszynski CA. Schizosaccharomyces versatilis represents a distinct evolutionary lineage of fission yeast. Yeast 2024; 41:95-107. [PMID: 38146786 DOI: 10.1002/yea.3919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 12/27/2023] Open
Abstract
The fission yeast species Schizosaccharomyces japonicus is currently divided into two varieties-S. japonicus var. japonicus and S. japonicus var. versatilis. Here we examine the var. versatilis isolate CBS5679. The CBS5679 genome shows 88% identity to the reference genome of S. japonicus var. japonicus at the coding sequence level, with phylogenetic analyses suggesting that it has split from the S. japonicus lineage 25 million years ago. The CBS5679 genome contains a reciprocal translocation between chromosomes 1 and 2, together with several large inversions. The products of genes linked to the major translocation are associated with 'metabolism' and 'cellular assembly' ontology terms. We further show that CBS5679 does not generate viable progeny with the reference strain of S. japonicus. Although CBS5679 shares closer similarity to the 'type' strain of var. versatilis as compared to S. japonicus, it is not identical to the type strain, suggesting population structure within var. versatilis. We recommend that the taxonomic status of S. japonicus var. versatilis is raised, with it being treated as a separate species, Schizosaccharomyces versatilis.
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Affiliation(s)
| | - Elisa Gomez Gil
- Oliferenko Lab, The Francis Crick Institute, London, UK
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Wilfried Haerty
- Research Faculty, The Earlham Institute, Norwich Research Park, Norwich, UK
| | - Snezhana Oliferenko
- Oliferenko Lab, The Francis Crick Institute, London, UK
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Conrad A Nieduszynski
- Research Faculty, The Earlham Institute, Norwich Research Park, Norwich, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
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Kaino T, Tonoko K, Mochizuki S, Takashima Y, Kawamukai M. Schizosaccharomyces japonicus has low levels of CoQ 10 synthesis, respiration deficiency, and efficient ethanol production. Biosci Biotechnol Biochem 2017; 82:1031-1042. [PMID: 29191091 DOI: 10.1080/09168451.2017.1401914] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Coenzyme Q (CoQ) is essential for mitochondrial respiration and as a cofactor for sulfide quinone reductase. Schizosaccharomyces pombe produces a human-type CoQ10. Here, we analyzed CoQ in other fission yeast species. S. cryophilus and S. octosporus produce CoQ9. S. japonicus produces low levels of CoQ10, although all necessary genes for CoQ synthesis have been identified in its genome. We expressed three genes (dps1, dlp1, and ppt1) for CoQ synthesis from S. japonicus in the corresponding S. pombe mutants, and confirmed that they were functional. S. japonicus had very low levels of oxygen consumption and was essentially respiration defective, probably due to mitochondrial dysfunction. S. japonicus grows well on minimal medium during anaerobic culture, indicating that it acquires sufficient energy by fermentation. S. japonicus produces comparable levels of ethanol under both normal and elevated temperature (42 °C) conditions, at which S. pombe is not able to grow.
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Affiliation(s)
- Tomohiro Kaino
- a Department of Life Science and Biotechnology, Faculty of Life and Environmental Science , Shimane University , Matsue , Japan
| | - Kai Tonoko
- a Department of Life Science and Biotechnology, Faculty of Life and Environmental Science , Shimane University , Matsue , Japan
| | - Shiomi Mochizuki
- a Department of Life Science and Biotechnology, Faculty of Life and Environmental Science , Shimane University , Matsue , Japan
| | - Yuriko Takashima
- a Department of Life Science and Biotechnology, Faculty of Life and Environmental Science , Shimane University , Matsue , Japan
| | - Makoto Kawamukai
- a Department of Life Science and Biotechnology, Faculty of Life and Environmental Science , Shimane University , Matsue , Japan
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Sabouri N, Capra JA, Zakian VA. The essential Schizosaccharomyces pombe Pfh1 DNA helicase promotes fork movement past G-quadruplex motifs to prevent DNA damage. BMC Biol 2014; 12:101. [PMID: 25471935 PMCID: PMC4275981 DOI: 10.1186/s12915-014-0101-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 11/20/2014] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND G-quadruplexes (G4s) are stable non-canonical DNA secondary structures consisting of stacked arrays of four guanines, each held together by Hoogsteen hydrogen bonds. Sequences with the ability to form these structures in vitro, G4 motifs, are found throughout bacterial and eukaryotic genomes. The budding yeast Pif1 DNA helicase, as well as several bacterial Pif1 family helicases, unwind G4 structures robustly in vitro and suppress G4-induced DNA damage in S. cerevisiae in vivo. RESULTS We determined the genomic distribution and evolutionary conservation of G4 motifs in four fission yeast species and investigated the relationship between G4 motifs and Pfh1, the sole S. pombe Pif1 family helicase. Using chromatin immunoprecipitation combined with deep sequencing, we found that many G4 motifs in the S. pombe genome were associated with Pfh1. Cells depleted of Pfh1 had increased fork pausing and DNA damage near G4 motifs, as indicated by high DNA polymerase occupancy and phosphorylated histone H2A, respectively. In general, G4 motifs were underrepresented in genes. However, Pfh1-associated G4 motifs were located on the transcribed strand of highly transcribed genes significantly more often than expected, suggesting that Pfh1 has a function in replication or transcription at these sites. CONCLUSIONS In the absence of functional Pfh1, unresolved G4 structures cause fork pausing and DNA damage of the sort associated with human tumors.
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Affiliation(s)
- Nasim Sabouri
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, 901 87, Sweden.
| | - John A Capra
- Department of Biological Sciences and Biomedical Informatics and Center for Human Genetics Research, Vanderbilt University, Nashville, TN, 37235, USA.
| | - Virginia A Zakian
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
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Helston RM, Box JA, Tang W, Baumann P. Schizosaccharomyces cryophilus sp. nov., a new species of fission yeast. FEMS Yeast Res 2010; 10:779-86. [PMID: 20618870 PMCID: PMC2991054 DOI: 10.1111/j.1567-1364.2010.00657.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The genus Schizosaccharomyces is presently comprised of three species, namely Schizosaccharomyces pombe, Schizosaccharomyces octosporus and Schizosaccharomyces japonicus. Here, we describe a hitherto unknown species, Schizosaccharomyces cryophilus, named for its preference for growth at lower temperatures than the other fission yeast species. Although morphologically similar to S. octosporus, analysis of several rapidly evolving sequences, including the D1/D2 divergent domain of the large subunit (LSU) rRNA gene, the RNA subunit of RNAse P and the internal transcribed spacer elements, revealed significant divergence from any previously characterized Schizosaccharomyces strain. Based on phylogenetic analysis of the D1/D2 domain of the LSU rRNA gene, S. octosporus is the closest known relative of S. cryophilus, with the sequences of the two species differing by 25 nucleotide substitutions (>4%). Sequencing of the S. cryophilus genome and phylogenetic analysis of all 1 : 1 protein orthologs confirmed this observation, and together with morphological and physiological characterization, supports the assignment of S. cryophilus as a new species within the genus Schizosaccharomyces. The type strain of the new species is NRRL Y-48691(T) (=NBRC 106824(T)=CBS 11777(T)).
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MESH Headings
- Cluster Analysis
- Cold Temperature
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Fungal Proteins/genetics
- Genes, rRNA
- Genome, Fungal
- Molecular Sequence Data
- Phylogeny
- RNA, Fungal/genetics
- RNA, Ribosomal/genetics
- Ribonuclease P/genetics
- Schizosaccharomyces/classification
- Schizosaccharomyces/cytology
- Schizosaccharomyces/genetics
- Schizosaccharomyces/physiology
- Sequence Analysis, DNA
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Affiliation(s)
- Rachel M. Helston
- Howard Hughes Medical Institute and Stowers Institute for Medical Research, Kansas City, MO 64110, U.S.A
| | - Jessica A. Box
- Howard Hughes Medical Institute and Stowers Institute for Medical Research, Kansas City, MO 64110, U.S.A
| | - Wen Tang
- Howard Hughes Medical Institute and Stowers Institute for Medical Research, Kansas City, MO 64110, U.S.A
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160, U.S.A
| | - Peter Baumann
- Howard Hughes Medical Institute and Stowers Institute for Medical Research, Kansas City, MO 64110, U.S.A
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160, U.S.A
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Bozsik A, Szilagyi Z, Benko Z, Sipiczki M. Marker construction and cloning of a cut1-like sequence with ARS activity in the fission yeast Schizosaccharomyces japonicus. Yeast 2002; 19:485-98. [PMID: 11921097 DOI: 10.1002/yea.853] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The dimorphic fission yeast Schizosaccharomyces japonicus has proved to be an excellent experimental model for the investigation of the eukaryotic cell. Here we show that it has a haplontic life cycle, in which the diploid phase is confined to the zygote. To make it amenable to genetic and molecular analysis, we generated genetic markers and cloned a genomic sequence which acts as ars when integrated into a plasmid. Diploids suitable for testing complementation and recombination between markers can be formed by protoplast fusion. The complementation tests and the recombination frequencies determined in octads of spores identified 28 non-allelic groups (genes) of mutations of the auxotrophic and mycelium-negative mutants. Two groups of linked markers were also identified. The cloned fragment, which expresses ars activity, encodes a putative amino acid sequence highly similar to a conserved domain of proteins Cut1 (Schizosaccharomyces pombe), BimB (Aspergillus nidulans) and Esp1 (Saccharomyces cerevisiae).
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Affiliation(s)
- Aniko Bozsik
- Department of Genetics, University of Debrecen, Debrecen, Hungary
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Ingavale SS, Sharma KG, Bachhawat AK. Construction of fission yeast vectors with a novel selection strategy that allows their use in wild-type fission yeasts. Yeast 2000; 16:1345-50. [PMID: 11015731 DOI: 10.1002/1097-0061(200010)16:14<1345::aid-yea628>3.0.co;2-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Novel vectors that use the Pichia pastoris INO1 gene as a selectable marker and exploit the natural inositol auxotrophy of the fission yeast are described. These plasmids also contained other features desirable in a plasmid cloning vector. These plasmids were evaluated in other species of Schizosaccharomyces and found to replicate autonomously in another variety of S. pombe, S. pombe var. malidevorans. These plasmids can be used for transformation of any wild-type S. pombe strain without the need for selection by induced auxotrophic mutations, or by selection by drug resistance markers, and should greatly assist genetic and molecular manipulations in these yeasts.
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Affiliation(s)
- S S Ingavale
- Institute of Microbial Technology, Sector 39-A, Chandigarh- 160 036, India
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Chen XJ, Clark-Walker GD. The petite mutation in yeasts: 50 years on. INTERNATIONAL REVIEW OF CYTOLOGY 1999; 194:197-238. [PMID: 10494627 DOI: 10.1016/s0074-7696(08)62397-9] [Citation(s) in RCA: 129] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Fifty years ago it was reported that baker's yeast, Saccharomyces cerevisiae, can form "petite colonie" mutants when treated with the DNA-targeting drug acriflavin. To mark the jubilee of studies on cytoplasmic inheritance, a review of the early work will be presented together with some observations on current developments. The primary emphasis is to address the questions of how loss of mtDNA leads to lethality (rho 0-lethality) in petite-negative yeasts and how S. cerevisiae tolerates elimination of mtDNA. Recent investigation have revealed that rho 0-lethality can be suppressed by specific mutations in the alpha, beta, and gamma subunits of the mitochondrial F1-ATPase of the petite-negative yeast Kluyveromyces lactis and by the nuclear ptp alleles in Schizosaccharomyces pombe. In contrast, inactivation of genes coding for F1-ATPase alpha and beta subunits and disruption of AAC2, PGS1/PEL1, and YME1 genes in S. cerevisiae convert this petite-positive yeast into a petite-negative form. Studies on nuclear genes affecting dependence on mtDNA have provided important insight into the functions provided by the mitochondrial genome and the maintenance of structural and functional integrity of the mitochondrial inner membrane.
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Affiliation(s)
- X J Chen
- Molecular and Cellular Genetics Group, Research School of Biological Sciences, Australian National University, ACT, Australia
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Sjamsuridza W, Tajiri Y, Nishida H, Thuan TB, Kawasaki H, Hirata A, Yokota A, Sugiyama J. Evolutionary relationships of members of the genera Taphrina, Protomyces, Schizosaccharomyces, and related taxa within the archiascomycetes: Integrated analysis of genotypic and phenotypic characters. MYCOSCIENCE 1997. [DOI: 10.1007/bf02464084] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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