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1. Kurtzman  CP, Robnett  CJ,     ( 2003 )

Phylogenetic relationships among yeasts of the 'Saccharomyces complex' determined from multigene sequence analyses.

FEMS yeast research 3 (4)
PMID : 12748053  :   DOI  :   10.1016/S1567-1356(03)00012-6    
Abstract >>
Species of Saccharomyces, Arxiozyma, Eremothecium, Hanseniaspora (anamorph Kloeckera), Kazachstania, Kluyveromyces, Pachytichospora, Saccharomycodes, Tetrapisispora, Torulaspora, and Zygosaccharomyces, as well as three related anamorphic species assigned to Candida (C. castellii, C. glabrata, C. humilis), were phylogenetically analyzed from divergence in genes of the rDNA repeat (18S, 26S, ITS), single copy nuclear genes (translation elongation factor 1alpha, actin-1, RNA polymerase II) and mitochondrially encoded genes (small-subunit rDNA, cytochrome oxidase II). Single-gene phylogenies were congruent for well-supported terminal lineages but deeper branches were not well resolved. Analysis of combined gene sequences resolved the 75 species compared into 14 clades, many of which differ from currently circumscribed genera.
KeywordMeSH Terms
2. Shpakovskiĭ  GV, Baranova  GM,     ( 2000 )

[Chromosomal localization of rpb9+ and tfa1+ genes, coding for components of the mRNA synthesis apparatus of Schizosaccharomyces pombe].

Bioorganicheskaia khimiia 26 (8)
PMID : 11041002  :  
Abstract >>
Using DNA hybridization on cosmid filters of high density, we established chromosomal localization of the rpb9+ gene encoding one of the specific subunits of RNA polymerase II of Schizosaccharomyces pombe and thus filled in the last gap in the mapping of the genes encoding components of RNA polymerase II of the fission yeast. The primary structure of three extended regions of the Sz. pombe chromosome I was elucidated and, as a result, genes neighboring on rpb9+ were identified. One of them proved to be the tfa1+ gene, encoding the large (alpha) subunit of the general factor of transcription initiation TFIIE.
KeywordMeSH Terms
Chromosomes, Fungal
Schizosaccharomyces pombe Proteins
Transcription Factors, TFII
3. Okayama  H, Okazaki  K,     ( 2000 )

The polyubiquitin gene is essential for meiosis in fission yeast.

Experimental cell research 254 (1)
PMID : 10623474  :   DOI  :   10.1006/excr.1999.4728    
Abstract >>
We isolated a novel sporulation-deficient mutant of Schizosaccharomyces pombe. The mutant did not have a mitotic growth defect but aborted meiosis at the first or the second division with condensed chromosomes that failed to separate, abnormal spindle(s), and disintegrated spindle pole bodies (SPBs). During the first division, the centromeres were pulled to near the spindle poles but condensed divalent chromosomes remained at the center. The failure to proceed to anaphase was also observed during a time-lapse recording of a SPB protein tagged with green fluorescent protein. The polyubiquitin gene ubi4(+), which encoded eight ubiquitins fused in tandem, complemented this mutant. The mutation, an A to G substitution, was identified within the ubi4(+) gene at the ATG initiation codon. Disruption of the ubi4(+) gene produced the same phenotypes. The ubi4(+) mRNA was strongly induced for meiosis. However, ubiquitin increases only slightly, suggesting that the role of the polyubiquitin gene is to supply ubiquitin that is consumed by unidentified mechanisms. Before the ubi4 mutant cells entered meiosis, ubiquitin was greatly decreased indicating that shortage of ubiquitin caused abortion of meiosis. This work provides insights for the role of polyubiquitin gene and importance of ubiquitination in SPB integrity at the meiotic divisions.
KeywordMeSH Terms
4. Sekine  M, Oguchi  A, Nagai  Y, Yamamoto  S, Yamazaki  J, Haikawa  Y, Jinnno  K, Kushida  N, Tanaka  T, Kunihiro  S, Yamazaki  S, Machida  M,     ( 2000 )

A 38 kb segment containing the cdc2 gene from the left arm of fission yeast chromosome II: sequence analysis and characterization of the genomic DNA and cDNAs encoded on the segment.

Yeast (Chichester, England) 16 (1)
PMID : 10620777  :   DOI  :   10.1002/(SICI)1097-0061(20000115)16:1<71::AID-YEA505>3.0.CO;2-5    
Abstract >>
A genomic 38 kbp segment on the c1750 cosmid clone containing the cdc2 gene, located in the left arm of chromosome II from Schizosaccharomyces pombe, was sequenced. The segment was found to have five previously known genes, pht1, cdc2, his3, act1 and mei4. Among 11 coding sequences (CDSs) predicted by the gene finding software INTRON.PLOT., four CDSs, pi007, pi010, pi014 and pi016, had considerable similarity to 40S ribosomal protein, glycosyltransferase, cdc2-related protein kinase and alpha-1, 2-mannosyltransferase, respectively. Another unusually huge open reading frame (ORF) (pi011), consisting of 2233 amino acids, existed, having significant homology to alpha-amylase, granule-bound glycogen synthase and the Sz. pombe YS 1110 clone product at the N-terminal, middle and C-terminal regions, respectively. All the predicted 11 CDSs were experimentally analysed by RACE PCR. The sequencing of the RACE products revealed that there were two small overlaps at the 3' untranslated regions (UTRs) between pi004 and pi005 (17 bp) and between pi007 and pi008 (2 bp). The distances between 5' end of the 5'UTR and the putative translation initiation codon varied from 10 to 302 nucleotides (nt) among the nine CDSs successfully analysed by 5'-RACE. The expression level of each CDS on this clone was determined. Among the 16 genes on this clone, the previously determined genes, pht1, cdc2, his3 and act1, were found to be most highly expressed. Finally, cDNAs of all the newly identified genes were detected by RACE, proving the actual expression of these genes. The nucleotide sequence has been submitted to the EMBL database under Accession No. AB004534.
KeywordMeSH Terms
Chromosomes, Fungal
5. Kang  MH, Park  EH, Lim  CJ,     ( 2007 )

Protective role and regulation of Rad9 from the fission yeast Schizosaccharomyces pombe.

FEMS microbiology letters 275 (2)
PMID : 17725619  :   DOI  :   10.1111/j.1574-6968.2007.00898.x    
Abstract >>
To assess novel cellular roles and regulation of Rad9 in the fission yeast Schizosaccharomyces pombe, the full-length rad9 gene was cloned into the shuttle vector pRS316, generating pYFRad9. The rad9 mRNA level was significantly increased in the S. pombe cells harboring the plasmid pYFRad9, suggesting that the cloned rad9 gene is functioning. The S. pombe cells harboring pYFRad9 showed higher survival in the minimal media containing nitric oxide (NO)-generating sodium nitroprusside (SNP, 20 muM) and no nitrogen than the vector control cells. SNP and nitrogen starvation notably enhanced the synthesis of beta-galactosidase from the rad9-lacZ fusion gene in the Pap1-positive cells but not in the Pap1-negative cells. The rad9 mRNA level, detected by semi-quantitative reverse transcriptase (RT)-PCR, was elevated in the Pap1-positive cells but not in the Pap1-negative cells by SNP and nitrogen starvation. It was also increased only in the Pap1-positive cells by diethylmaleate, which activates Pap1. Collectively, the results imply that Rad9 plays a protective role against nitrosative and nutritional stress and is positively regulated by NO and nitrogen starvation in a Pap1-dependent manner.
KeywordMeSH Terms
Gene Expression Regulation, Fungal
6. Kurtzman  CP, Robnett  CJ,     ( 2007 )

Multigene phylogenetic analysis of the Trichomonascus, Wickerhamiella and Zygoascus yeast clades, and the proposal of Sugiyamaella gen. nov. and 14 new species combinations.

FEMS yeast research 7 (1)
PMID : 17311592  :   DOI  :   10.1111/j.1567-1364.2006.00157.x    
Abstract >>
Relationships among species assigned to the ascosporic yeast genera Sporopachydermia, Stephanoascus, Trichomonascus, Wickerhamiella and Zygoascus, and to the associated anamorphic genera Arxula, Blastobotrys, Sympodiomyces and Trigonopsis, were determined from phylogenetic analyses of gene sequences from the nearly complete large-subunit rRNA gene, the mitochondrial small-subunit rRNA gene, and cytochrome oxidase II. The genus Stephanoascus is polyphyletic, resulting in reassignment of two species to the older genus Trichomonascus and the third to Sugiyamaella gen. nov. (type species Sugiyamaella smithiae). The genera Sporopachydermia, Wickerhamiella and Zygoascus appear to be monophyletic. The species Pichia ofunaensis and P. tannicola are proposed for transfer to Zygoascus. Arxula, Blastobotrys and Sympodiomyces are members of the Trichomonascus clade, with the genus Blastobotrys having taxonomic priority for anamorphic states. Trigonopsis variabilis and three species of Candida represent a distinct clade. From the foregoing gene sequence analyses, the new ascosporic genus Sugiyamaella is proposed, as are 14 new species combinations and the new family Trichomonascaceae.
KeywordMeSH Terms
Phylogeny
7. Levin  HL, Weaver  DC, Boeke  JD,     ( 1990 )

Two related families of retrotransposons from Schizosaccharomyces pombe.

Molecular and cellular biology 10 (12)
PMID : 2174117  :   DOI  :   10.1128/mcb.10.12.6791     PMC  :   PMC362960    
Abstract >>
Two related families of transposons were isolated from schizosaccharomyces pombe, an organism which has been the object of extensive genetic studies which had previously produced no evidence for the existence of such elements. These two classes of repeated DNAs, dubbed Tf1 (transposon of fission yeast 1) and Tf2 have many properties of retrotransposons. Tf1 and Tf2 both possess long terminal repeats and predicted protein sequences that resemble the protease, reverse transcriptase, and integrase domains of retroviruses. The chromosomal locations and total numbers of Tf1 and Tf2 differ greatly in various isolates of S. pombe. The Tf elements are expressed in the form of 4.5-kb mRNAs. The complete sequence of Tf1 was determined and suggests that a novel mechanism for regulating its gene expression may be used.
KeywordMeSH Terms
DNA Transposable Elements
8. Kurtzman  CP, Robnett  CJ,     ( 2010 )

Systematics of methanol assimilating yeasts and neighboring taxa from multigene sequence analysis and the proposal of Peterozyma gen. nov., a new member of the Saccharomycetales.

FEMS yeast research 10 (3)
PMID : 20522116  :   DOI  :   10.1111/j.1567-1364.2010.00625.x    
Abstract >>
The relatedness among methanol-assimilating yeasts assigned to the genus Ogataea and neighboring taxa (Phylum Ascomycota, Subphylum Saccharomycotina, Class Saccharomycetes, Order Saccharomycetales) was determined from phylogenetic analyses of gene sequences for nuclear large and small subunit (SSU) rRNAs, translation elongation factor-1alpha and mitochondrial SSU rRNA. On the basis of the analyses, Williopsis salicorniae and seven species of Pichia are proposed for transfer to the genus Ogataea, which has been emended, and Pichia angophorae, a nonhyphal species, is proposed for transfer to the mycelium forming genus Ambrosiozyma. Pichia toletana and Pichia xylosa form an independent lineage and are assigned to the genus Peterozyma, which is newly proposed.
KeywordMeSH Terms
9. Park  JS, Steinbach  SK, Desautels  M, Hemmingsen  SM,     ( 2009 )

Essential role for Schizosaccharomyces pombe pik1 in septation.

PloS one 4 (7)
PMID : 19587793  :   DOI  :   10.1371/journal.pone.0006179     PMC  :   PMC2704394    
Abstract >>
Schizosaccharomyces pombe pik1 encodes a phosphatidylinositol 4-kinase, reported to bind Cdc4, but not Cdc4(G107S). Gene deletion revealed that pik1 is essential. In cells with pik1 deleted, ectopic expression of a loss-of-function allele, created by fusion to a temperature-sensitive dihydrofolate reductase, allowed normal cell proliferation at 25 degrees C. At 36 degrees C, cells arrested with abnormally thick, misplaced or supernumerary septa, indicating a defect late in septation. In addition to being Golgi associated, ectopically expressed GFP-tagged Pik1 was observed at the medial cell plane late in cytokinesis. New alleles, created by site-directed mutagenesis, were expressed ectopically. Lipid kinase and Cdc4-binding activity assays were performed. Pik1(D709A) was kinase-dead, but bound Cdc4. Pik1(R838A) did not bind Cdc4, but was an active kinase. Genomic integration of these substitutions in S. pombe and complementation studies in Saccharomyces cerevisiae pik1-101 cells revealed that D709 is essential in both cases while R838 is dispensable. In S. pombe, ectopic expression of pik1 was dominantly lethal; while, pik1(D709A,R838A) was innocuous, pik1(R838A) was almost innocuous, and pik1(D709A) produced partial lethality and septation defects. The pik1 ectopic expression lethal phenotype was suppressed in cdc4(G107S). Thus, D709 is essential for kinase activity and septation. Pik1 kinase activity is required for septation. The Pik1 R838 residue is required for important protein-protein interactions, possibly with Cdc4.
KeywordMeSH Terms
10. Kurtzman  CP, Robnett  CJ, Basehoar-Powers  E,     ( 2008 )

Phylogenetic relationships among species of Pichia, Issatchenkia and Williopsis determined from multigene sequence analysis, and the proposal of Barnettozyma gen. nov., Lindnera gen. nov. and Wickerhamomyces gen. nov.

FEMS yeast research 8 (6)
PMID : 18671746  :   DOI  :   10.1111/j.1567-1364.2008.00419.x    
Abstract >>
Relationships among species assigned to the yeast genera Pichia, Issatchenkia and Williopsis, which are characterized by the ubiquinone CoQ-7 and inability to utilize methanol, were phylogenetically analyzed from nucleotide sequence divergence in the genes coding for large and small subunit rRNAs and for translation elongation factor-1alpha. From this analysis, the species separated into five clades. Species of Issatchenkia are members of the Pichia membranifaciens clade and are proposed for transfer to Pichia. Pichia dryadoides and Pichia quercuum are basal members of the genus Starmera. Williopsis species are dispersed among hat-spored taxa in each of the remaining three clades, which are proposed as the new genera Barnettozyma, Lindnera and Wickerhamomyces. Lineages previously classified as varieties of Pichia kluyveri, 'Issatchenkia'scutulata, Starmera amethionina and 'Williopsis'saturnus are elevated to species rank based on sequence comparisons.
KeywordMeSH Terms
Phylogeny
Pichia
Saccharomycetales
Sequence Analysis, DNA
11. Toda  T, Shimanuki  M, Yanagida  M,     ( 1991 )

Fission yeast genes that confer resistance to staurosporine encode an AP-1-like transcription factor and a protein kinase related to the mammalian ERK1/MAP2 and budding yeast FUS3 and KSS1 kinases.

Genes & development 5 (1)
PMID : 1899230  :   DOI  :   10.1101/gad.5.1.60    
Abstract >>
Staurosporine, a potent inhibitor of protein kinase C, arrests fission yeast cell elongation specifically at a stage immediately after cell division. We isolated two genes, which, when carried on multicopy plasmids, confer drug resistance in fission yeast. One, spk1+, encodes a protein kinase highly similar (54% identity) to those encoded by the mammalian ERK1/MAP2 kinase and the budding yeast KSS1 and FUS3 genes. It is not essential for vegetative growth of Schizosaccharomyces pombe cells but is required for conjugation. The spk1+ gene product is a 45-kD protein enriched in the nucleus, and its level increases 10-fold after addition of staurosporine. The other gene pap1+ encodes an AP-1-like transcription factor that contains a region rich in basic amino acids followed by a "leucine zipper" motif. The pap1+ gene is required for spk1(+)-conferred staurosporine resistance. These two genes appear to function as a part of the fission yeast growth control pathway.
KeywordMeSH Terms
Fungal Proteins
12. Inoue  M, Watanabe  N, Matsuno  K, Sasaki  J, Tanaka  Y, Hatanaka  H, Amachi  T,     ( 1991 )

Expression of a hybrid Cu/Zn-type superoxide dismutase which has high affinity for heparin-like proteoglycans on vascular endothelial cells.

The Journal of biological chemistry 266 (25)
PMID : 1885572  :  
Abstract >>
Since plasma levels of enzymes, such as superoxide dismutase (SOD), that scavenge reactive oxygen species are low, surface membranes of endothelial and parenchymal cells of various tissues are often exposed to oxidative stress. To dismutase superoxide radicals efficiently in and around vascular endothelial cells, we constructed a fusion gene encoding a hybrid SOD (HB-SOD) consisting of human Cu/Zn-SOD and a C-terminal basic peptide that binds to heparin-like proteoglycans. The fusion gene was expressed in yeast, and the resulting HB-SOD was highly purified. Upon sodium dodecyl sulfate-polyacrylamide gel electrophoresis, HB-SOD revealed a protein band with an apparent molecular weight of 20,000. HB-SOD bound to endothelial cells of aortic segments by a mechanism which was inhibited by heparin but not by antithrombin III. When injected intravenously to rats, 125I-labeled HB-SOD rapidly disappeared from the circulation; the rate of disappearance was decreased by heparin. Less than 1% of the injected HB-SOD was found in the urine 20 min after administration at which time more than 70% of SOD was excreted in its intact form. Immunohistochemical studies revealed that HB-SOD predominantly bound to heparin-like proteoglycans on endothelial cells of the artery and other tissues. HB-SOD might permit studies on pathophysiological roles of superoxide radicals in and around vascular endothelial cells in vivo.
KeywordMeSH Terms
13. Herrera-Camacho  I, Rosas-Murrieta  NH, Rojo-Domínguez  A, Millán  L, Reyes-Leyva  J, Santos-López  G, Suárez-Rendueles  P,     ( 2007 )

Biochemical characterization and structural prediction of a novel cytosolic leucyl aminopeptidase of the M17 family from Schizosaccharomyces pombe.

The FEBS journal 274 (23)
PMID : 18028193  :   DOI  :   10.1111/j.1742-4658.2007.06142.x    
Abstract >>
A new leucyl aminopeptidase activity has been identified in the fission yeast Schizosaccharomyces pombe. The enzyme, which has been purified and named leucyl aminopeptidase yspII (LAP yspII), had a molecular mass of 320 and 54 kDa by gel filtration and SDS/PAGE, respectively, suggesting a homohexameric structure. The enzyme cleaved synthetic aminoacyl-4-nitroanilides at an optimum of pH 8.5, and preferred leucine and methionine as N-terminal amino acids. A clear dependence on Mn2+ concentration for activity was found, and an apparent association constant of 0.33 mM was calculated for the metal ion. Bestatin behaved as a competitive inhibitor of LAP yspII (K(i) = 0.14 microM), while chelating agents such as chloroquine, EDTA and 1,10-phenanthroline also reduced enzyme activity. A MALDI-MS analysis, followed by sequencing of two of the resulting peptides, showed that LAP yspII undoubtedly corresponds to the putative aminopeptidase C13A11.05 identified in the S. pombe genome project. The protein exhibited nearly 40% sequence identity to fungal and mammalian aminopeptidases belonging to the M17 family of metallopeptidases. Catalytic residues (Lys292 and Arg366), as well as those involved in coordination with the cocatalytic metal ions (Lys280, Asp285, Asp303, Asp362 and Glu364) and those forming the hydrophobic pocket for substrate binding (Met300, Asn360, Ala363, Thr390, Leu391, Ala483 and Met486), were perfectly conserved among all known aminopeptidases. The S. pombe enzyme is predicted to be formed two clearly distinguished domains with a well conserved C-terminal catalytic domain showing a characteristic topology of eight beta-sheets surrounded by alpha-helical segments in the form of a saddle.
KeywordMeSH Terms
14. Kudla  B, Persuy  MA, Gaillardin  C, Heslot  H,     ( 1988 )

Construction of an expression vector for the fission yeast Schizosaccharomyces pombe.

Nucleic acids research 16 (17)
PMID : 2843820  :   DOI  :   10.1093/nar/16.17.8603     PMC  :   PMC338579    
Abstract >>
We have isolated and characterized a S. pombe promoter using a functional heterologous gene product assay. Random S. pombe genomic fragments were cloned upstream from the promoterless 'lacZ gene and tested in vivo for their efficiency to promote expression of the beta-galactosidase protein in the fission yeast. An efficient S. pombe promoter called 54/1 was isolated and shown to drive up to 5% of total protein synthesis as beta-galactosidase. The structure and nucleotide sequence of this promoter were determined, precise localization of its mRNA transcriptional start points established. Translational fusion of the Pseudomonas putida XylE gene with the 54/1 gene was shown to allow expression of catechol oxidase activity in S. pombe. An expression vector suitable for transcriptional fusions was then constructed from engineered 54/1 promoter sequences and used to drive expression of the E. coli Tn5 ble gene, thus confering resistance to the fission yeast against bleomycin and phleomycin antibiotics.
KeywordMeSH Terms
Genes, Fungal
Genetic Vectors
Promoter Regions, Genetic
15. Kim  Y, Jo  H, Lim  CJ,     ( 2013 )

Deubiquitinating activity of Sdu1, a putative member of the PPPDE peptidase family, in Schizosaccharomyces pombe.

Canadian journal of microbiology 59 (12)
PMID : 24313451  :   DOI  :   10.1139/cjm-2013-0453    
Abstract >>
The Schizosaccharomyces pombe sdu? gene encoding a putative member of the PPPDE (Permuted Papain fold Peptidases of DsRNA viruses and Eukaryotes) superfamily was cloned into an Escherichia coli - yeast shuttle vector pRS316, resulting in the recombinant plasmid pYSTP. The determined nucleotide sequence carries 1207 bp, which would encode a protein of 201 amino acid residues. The S. pombe cells harboring pYSTP contained higher sdu1? mRNA and deubiquitinating activity levels than the vector control cells, indicating that the sdu1? gene is functioning. They exhibited a better growth in normal rich medium than the vector control cells. When shifted into the fresh medium containing hydrogen peroxide, menadione, or sodium nitroprusside, the S. pombe cells harboring pYSTP were able to grow reasonably well, while the growth of the vector control cells was arrested. The reactive oxygen species and total glutathione levels of the S. pombe cells harboring pYSTP were lower and higher than those of the vector control cells under the same stressful conditions, respectively. They exhibited a lower nitric oxide level than the vector control cells when subjected to sodium nitroprusside. Taken together, the sdu1? gene encodes an actual protein having deubiquitinating activity and is involved in the response against oxidative and nitrosative stresses in S. pombe.
KeywordMeSH Terms
16. Leng  XM, Diao  LT, Li  B, Bi  YZ, Chen  CJ, Zhou  H, Qu  LH,     ( 2014 )

The ribosomal protein rpl26 promoter is required for its 3' sense terminus ncRNA transcription in Schizosaccharomyces pombe, implicating a new transcriptional mechanism for ncRNAs.

Biochemical and biophysical research communications 444 (1)
PMID : 24434141  :   DOI  :   10.1016/j.bbrc.2014.01.018    
Abstract >>
Transcriptome studies have revealed that many non-coding RNAs (ncRNAs) are located near the 3' sense terminus of protein-coding genes. However, the transcription and function of these RNAs remain elusive. Here, we identify a 3' sense termini-associated sRNA (TASR) downstream of rpl26 in Schizosaccharomyces pombe (S. pombe). Structure and function assays indicate that the TASR is an H/ACA box snoRNA required for 18S rRNA pseudouridylation at U121 and U305 sites and is therefore a cognate of snR49 from the budding yeast. Transcriptional studies show that pre-snR49 overlaps most of the coding sequence (CDS) of rpl26. Using scanning deletion analysis within promoter region, we show that the rpl26 promoter is required for the 3' TASR transcription. Interestingly, chromosomal synteny of rpl26-snR49 is found in the Schizosaccharomyces groups. Taken together, we have revealed a new transcriptional mechanism for 3' sense TASRs, which are transcribed by the same promoter as their upstream protein genes. These results further suggest that the origin and function of 3' sense ncRNAs are associated with upstream genes in higher eukaryotes.
KeywordMeSH Terms
3′ Sense ncRNA
Fission yeast
Promoter
Transcription
snR49
17. Schoch  CL, Seifert  KA, Huhndorf  S, Robert  V, Spouge  JL, Levesque  CA, Chen  W, N/A  N/A, N/A  N/A,     ( 2012 )

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi.

Proceedings of the National Academy of Sciences of the United States of America 109 (16)
PMID : 22454494  :   DOI  :   10.1073/pnas.1117018109     PMC  :   PMC3341068    
Abstract >>
Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.
KeywordMeSH Terms
18. Massardo  DR,     ( 1990 )

Nucleotide sequence of the genes encoding tRNA(his), tRNA(pro) and tRNA(gln) in the mitochondrial genome of Schizosaccharomyces pombe strain EF1.

Nucleic acids research 18 (21)
PMID : 2243789  :   DOI  :   10.1093/nar/18.21.6429     PMC  :   PMC332540    
Abstract >>
N/A
KeywordMeSH Terms
Genes, Fungal
19. Yu  C, Bonaduce  MJ, Klar  AJ,     ( 2012 )

Going in the right direction: mating-type switching of Schizosaccharomyces pombe is controlled by judicious expression of two different swi2 transcripts.

Genetics 190 (3)
PMID : 22209903  :   DOI  :   10.1534/genetics.111.137109     PMC  :   PMC3296259    
Abstract >>
Schizosaccharomyces pombe, the fission yeast, cells alternate between P- and M-mating type, controlled by the alternate alleles of the mating-type locus (mat1). The mat1 switching occurs by replacing mat1 with a copy derived from a silenced "donor locus," mat2P or mat3M. The mechanism of donor choice ensuring that switching occurs primarily and productively to the opposite type, called directionality, is largely unknown. Here we identified the mat1-Mc gene, a mammalian sex-determination gene (SRY) homolog, as the primary gene that dictates directionality in M cells. A previously unrecognized, shorter swi2 mRNA, a truncated form of the swi2, was identified, and its expression requires the mat1-Mc function. We also found that the abp1 gene (human CENPB homolog) controls directionality through swi2 regulation. In addition, we implicated a cis-acting DNA sequence in mat2 utilization. Overall, we showed that switching directionality is controlled by judicious expression of two swi2 transcripts through a cell-type-regulated dual promoter. In this respect, this regulation mechanism resembles that of the Drosophila sex-determination Slx gene.
KeywordMeSH Terms
Gene Expression Regulation, Fungal
Genes, Mating Type, Fungal
20.     ( 1997 )

A novel HSP70 gene of Schizosaccharomyces pombe that confers K-252a resistance.

Gene 189 (1)
PMID : 9161410  :   DOI  :   10.1016/s0378-1119(96)00831-1    
Abstract >>
A new gene encoding a heat shock protein 70 family protein of Schizosaccharomyces pombe (Sp), named sks2+, was cloned as a weak suppressor for the K-252a-sensitive mutation, ucm1. The nucleotide sequence of sks2+ revealed an open reading frame of a 613-amino-acid (aa) protein. The deduced aa sequence of sks2+ showed significant homology with Saccharomyces cerevisiae (Sc) Ssb1p and Ssb2p responsible for protein synthesis by non-organelle-localized ribosomes, as well as with other proteins of the HSP70 family. The cells lacking the functional sks2+ gene were viable and showed no increased sensitivity to K-252a but grew slowly with an elongated morphology. These results suggest that the sks2+ gene product plays a role in the cell cycle progression and is able to confer drug resistance in a multicopy state.
KeywordMeSH Terms
21.     ( 1993 )

The Schizosaccharomyces pombe mating-type gene mat-Mc encodes a sequence-specific DNA-binding high mobility group box protein.

The Journal of biological chemistry 268 (33)
PMID : 8227043  :  
Abstract >>
The Schizosaccharomyces pombe gene mat-Mc plays a determinative role in the sexual differentiation of the fission yeast. The mat-Mc protein has been suggested to belong to a novel family of so-called high mobility group (HMG) box proteins, characterized by homology to high mobility group-1 and -2 proteins. Several HMG box proteins, including the mammalian sex-determining gene product SRY and the lymphoid transcription factors TCF-1 and LEF-1, have been shown to bind to DNA in a sequence-specific fashion. To analyze possible DNA-binding properties of mat-Mc, we have cloned and expressed its putative HMG box in Escherichia coli. Gel retardation analysis revealed that the mat-Mc HMG box recognizes the AACAAAG heptamer in a sequence-specific fashion. Combined T-->C and A-->I substitutions on both strands of the AACAAAG heptamer, which change the surface of the major groove while leaving the minor groove intact, did not interfere with sequence-specific binding of mat-Mc. Methylation interference analysis confirmed that the mat-Mc HMG box contacts adenine residues in the minor groove. By using a circular permutation assay, the mat-Mc HMG box was observed to bend DNA. These results indicate that mat-Mc is indeed a member of the HMG box family with DNA-binding characteristics assigned earlier to other members of this novel transcription factor family.
KeywordMeSH Terms
Schizosaccharomyces pombe Proteins
22.     ( 1994 )

Transient, meiosis-induced expression of the rec6 and rec12 genes of Schizosaccharomyces pombe.

Genetics 136 (3)
PMID : 8005432  :   PMC  :   PMC1205883    
Abstract >>
Two meiotic recombination genes, rec6 and rec12, from Schizosaccharomyces pombe have been cloned by genetic complementation and their DNA sequences determined. Gene replacements demonstrated that the cloned fragments contained the rec6 and rec12 genes. Further analysis showed that the functional rec6 gene was within a 1.3-kb fragment and rec12 within a 1.7-kb fragment. The nucleotide sequences of these fragments revealed open reading frames (ORFs) predicting 143 amino acids for the rec6 gene product and 139 amino acids for the rec12 gene product. After pat1-114 temperature-induced meiosis, the transcripts of rec6 and rec12 were induced to maximal levels at 2-3 hr, at about the time of premeiotic DNA synthesis, but were present at much lower levels before and after this time. The transient induction of the transcripts and the phenotypes of the mutants suggest that the rec6 and rec12 gene products are involved primarily in the early steps of meiotic recombination in S. pombe. Near the rec6 gene are two additional ORFs potentially encoding proteins with homology to ribosomal protein S7 of Saccharomyces cerevisiae (ORF137) and to the homeodomain of developmental regulatory proteins (ORF201). The roles of these S. pombe ORFs remain to be determined.
KeywordMeSH Terms
Genes, Fungal
23. Matsusaka  T, Hirata  D, Yanagida  M, Toda  T,     ( 1995 )

A novel protein kinase gene ssp1+ is required for alteration of growth polarity and actin localization in fission yeast.

The EMBO journal 14 (14)
PMID : 7628434  :   PMC  :   PMC394400    
Abstract >>
Temperature-sensitive suppressor mutants were isolated from two fission yeast mutants defective in cell shape control: ppe1, encoding a type 2A-like protein phosphatase, and sts5, one of 11 staurosporine-supersensitive mutants. Complementation tests showed that suppression was due to two chromosomal loci, ssp1 and ssp2. Cells of the ssp1 mutant grown at the restrictive temperature arrested uniformly with an elongated cell body and a 2C content of DNA. Interestingly, these mutant cells grew only in a monopolar manner. At a specific point in the G2 phase of the cell cycle, wild-type cells exhibit a drastic alteration in growth polarity, from mono- to bipolar. This change coincides with the distribution of cortical actin from one end of the cell to both ends. In the ssp1 mutant cells, cortical actin was localized only at one end, suggesting that the mutant fails to change growth polarity. Nucleotide sequence determination showed that ssp1+ encodes a novel protein kinase. Ectopic overexpression of ssp1+ resulted in an altered cell morphology and cortical actin was randomly dispersed within the cells. Immunocytological analysis revealed that the protein was primarily localized in the cytoplasm and that half of the protein existed in an insoluble fraction. These results show that the dynamics of actin-based growth polarity during the cell cycle are regulated, at least in part, by a novel set of protein kinases and phosphatases.
KeywordMeSH Terms
HSP70 Heat-Shock Proteins
Schizosaccharomyces pombe Proteins
24. Shimanuki  M, Saka  Y, Yanagida  M, Toda  T,     ( 1995 )

A novel essential fission yeast gene pad1+ positively regulates pap1(+)-dependent transcription and is implicated in the maintenance of chromosome structure.

Journal of cell science 108 (Pt 2) (N/A)
PMID : 7769002  :  
Abstract >>
Fission yeast pap1+ gene encodes an AP-1-like transcription factor, whose overexpression can confer resistance to staurosporine, a protein kinase inhibitor. We have previously identified a target gene (p25) for pap1+, and shown that, crm1+, which is required for maintenance of higher order chromosome structure, negatively regulates pap1-dependent transcription. In this study, we have characterized a novel gene, pad1+, which was isolated as a multicopy plasmid capable of conferring staurosporine-resistance. We showed that high copy pad1+ induces transcriptional activation of the p25 gene and that the induction by pad1+ is dependent on the pap1+ gene. Furthermore, a cis-element analysis of the 5'-region of the p25 gene showed that two elements (an AP-1 site and a 14 bp palindrome sequence) where pap1 binds in vitro is essential for the induction by pad1+. These results indicate that pad1 can positively regulate pap1-dependent transcription. Through an electromobility shift assay we showed that overexpression of pad1+ is not capable of enhancing the DNA-binding activity of pap1 directly. The pad1+ gene encodes a 35 kDa protein that has significant identity (68%) to Caenorhabditis elegans F37A4.5, and is also similar to mouse Mov34 and human C6.1A. Gene disruption experiments have demonstrated that pad1+ is essential for viability. A disruption mutant of pad1+ obtained after spore germination exhibited an elongated cell body with abberantly folded chromosomes. A mitotic plasmid loss experiment also produced similar cells having an abnormal chromosome structure. These suggest that pad1+ may play an important role in higher order chromosome structure. Taken concurrently with our previous results, two essential genes pad1+ and crm1+ regulate pap1-dependent transcription; pad1+ and crm1+ are positive and negative regulators, respectively.
KeywordMeSH Terms
Chromosomes, Fungal
Genes, Fungal
Karyopherins
Receptors, Cytoplasmic and Nuclear
Schizosaccharomyces pombe Proteins
25. Xie  G, Vo  TV, Thillainadesan  G, Holla  S, Zhang  B, Jiang  Y, Lv  M, Xu  Z, Wang  C, Balachandran  V, Shi  Y, Li  F, Grewal  SIS,     ( 2019 )

A conserved dimer interface connects ERH and YTH family proteins to promote gene silencing.

Nature communications 10 (1)
PMID : 30651569  :   DOI  :   10.1038/s41467-018-08273-9     PMC  :   PMC6335422    
Abstract >>
Gene regulatory mechanisms rely on a complex network of RNA processing factors to prevent untimely gene expression. In fission yeast, the highly conserved ortholog of human ERH, called Erh1, interacts with the YTH family RNA binding protein Mmi1 to form the Erh1-Mmi1 complex (EMC) implicated in gametogenic gene silencing. However, the structural basis of EMC assembly and its functions are poorly understood. Here, we present the co-crystal structure of the EMC that consists of Erh1 homodimers interacting with Mmi1 in a 2:2 stoichiometry via a conserved molecular interface. Structure-guided mutation of the Mmi1Trp112 residue, which is required for Erh1 binding, causes defects in facultative heterochromatin assembly and gene silencing while leaving Mmi1-mediated transcription termination intact. Indeed, EMC targets masked in mmi1? due to termination defects are revealed in mmi1W112A. Our study delineates EMC requirements in gene silencing and identifies an ERH interface required for interaction with an RNA binding protein.
KeywordMeSH Terms
Gene Silencing
26. Trinkl  H, Lang  BF, Wolf  K,     ( 1985 )

The mitochondrial genome of the fission yeast Schizosaccharomyces pombe. 7. Continuous gene for apocytochrome b in strain EF1 (CBS 356) and sequence variation in the region of intron insertion in strain ade 7-50h.

Molecular & general genetics : MGG 198 (2)
PMID : 3856727  :   DOI  :   10.1007/bf00383021    
Abstract >>
The third BamHI fragment, containing most of gene for apocytochrome b, has been cloned and sequenced in the Schizosaccharomyces pombe strain EF1 (CBS 356). In contrast to strain ade 7-50h- (50) from the Leupold collection, in which the gene is interrupted by an intron of group II (Lang et al. 1984), the homologous gene in strain EF1 is continuous. This demonstrates that the intron in the gene for apocytochrome b is optional. Aligning the EF1 sequence with the homologous regions in strain 50, 2 base pair changes were found in the leader and 14 in the coding region. These changes led to 12 altered triplets, but 9 of them specify the same amino acid. Seven base changes were clustered within a stretch of 30 base pairs in the region in which the intron is inserted in strain 50. Five out of the resulting six triplet changes were also silent. These sequence variations around the highly conserved splice point region may be linked to the insertion or excision of the intron.
KeywordMeSH Terms
27. Kelly  M, Burke  J, Smith  M, Klar  A, Beach  D,     ( 1988 )

Four mating-type genes control sexual differentiation in the fission yeast.

The EMBO journal 7 (5)
PMID : 2900761  :   PMC  :   PMC458406    
Abstract >>
The mating-type region of fission yeast consists of three components, mat1, mat2-P and mat3-M, each separated by 15 kb. Cell-type is determined by the alternate allele present at mat1, either P in an h+ or M in an h- cell. mat2-P and mat3-M serve as donors of information that is transposed to mat1 during a switch of mating type. We have determined the nucleotide sequence of each component of mat. The P and M specific regions are 1104 and 1128 bp, respectively, and bounded by sequences common to each mating-type cassette (H1; 59 bp and H2; 135 bp). A third sequence is present at mat2-P and mat3-M but absent at mat1 (H3; 57 bp), and may be involved in transcriptional repression of these cassettes. mat1-P and mat1-M each encode two genes (Pc; 118 amino acids, Pi; 159 amino acids, Mc; 181 amino acids and Mi; 42 amino acids). Introduction of opal or frame-shift mutations into the open-reading-frame of each gene revealed that Pc and Mc are necessary and sufficient for mating and confer an h+ or h- mating type respectively. All four genes are required for meiotic competence in an h+/h- diploid. The transcription of each mat gene is strongly influenced by nutritional conditions and full induction was observed only in nitrogen-free medium. The predicted product of the Pi gene contains a region of homology with the homeobox sequence, suggesting that this gene encodes a DNA binding protein that directly regulates the expression of other genes.
KeywordMeSH Terms
Genes, Fungal
Genes, Mating Type, Fungal
28. Barel  I, Bignell  G, Simpson  A, MacDonald  D,     ( 1988 )

Isolation of a DNA fragment which complements glutamine synthetase deficient strains of S. pombe.

Current genetics 13 (6)
PMID : 2900077  :  
Abstract >>
From a gene bank of S. pombe DNA, a 5.6 kb clone was isolated which complemented mutants defective in glutamine synthetase (GS) activity. Sub-cloning fragments of this 5.6 kb clone showed that the complementing activity was localised in a 1.6 kb HindIII-AvaI fragment and a partial DNA sequence revealed an open reading frame preceded by TATA sequences and a TGACTA sequence. Plasmid constructs carrying up to 3.4 kb of DNA used to transform gln- strains gave transformants which showed a wide range of GS activity, in some cases 100 times the wild-type level. These constructs identify DNA sequences lying downstream from the putative coding sequence which have effects on the total amount of enzyme activity, but do not affect the control imposed by the nitrogen source on which the cells are grown.
KeywordMeSH Terms
DNA, Fungal
29.     ( 2014 )

Protective roles of methionine-R-sulfoxide reductase against stresses in Schizosaccharomyces pombe.

Journal of basic microbiology 54 (1)
PMID : 23456650  :   DOI  :   10.1002/jobm.201200397    
Abstract >>
The Schizosaccharomyces pombe msrB(+) gene encoding methionine-R-sulfoxide reductase (MsrB) was cloned into the shuttle vector pRS316 to generate the recombinant plasmid pFMetSO. The msrB(+) mRNA level was significantly increased in the S. pombe cells harboring pFMetSO, indicating that the cloned msrB(+) gene is functioning. In the presence of 0.1 mM L-methionine-(R,S)-sulfoxide, the S. pombe cells harboring pFMetSO could grow normally but the growth of the vector control cells was almost arrested. The S. pombe cells harboring pFMetSO exhibited the enhanced growth on the minimal medium plates with stress-inducing agents, such as hydrogen peroxide, superoxide radical-generating menadione (MD), nitric oxide (NO)-generating sodium nitroprusside (SNP), and cadmium (Cd), when compared with the vector control cells. They also gave rise to the enhanced growth at the high incubation temperature of 37 �XC than the vector control cells. The S. pombe cells harboring pFMetSO contained lower reactive oxygen species (ROS) and higher total glutathione (GSH) levels than the vector control cells. In brief, the S. pombe MsrB plays a protective role against oxidative, nitrosative, and thermal stresses, and is involved in diminishing intracellular ROS level.
KeywordMeSH Terms
High temperature
Methionine-R-sulfoxide reductase
Nitric oxide
Oxidative stress
Schizosaccharomyces pombe
30.     ( 2013 )

Relationships among genera of the Saccharomycotina (Ascomycota) from multigene phylogenetic analysis of type species.

FEMS yeast research 13 (1)
PMID : 22978764  :   DOI  :   10.1111/1567-1364.12006    
Abstract >>
Relationships among ascomycetous yeast genera (subphylum Saccharomycotina, phylum Ascomycota) have been uncertain. In the present study, type species of 70 currently recognized genera are compared from divergence in the nearly entire nuclear gene sequences for large subunit rRNA, small subunit (SSU) rRNA, translation elongation factor-1�\, and RNA polymerase II, subunits 1 (RPB1) and 2 (RPB2). The analysis substantiates earlier proposals that all known ascomycetous yeast genera now assigned to the Saccharomycotina represent a single clade. Maximum likelihood analysis resolved the taxa into eight large multigenus clades and four-one- and two-genus clades. Maximum parsimony and neighbor-joining analyses gave similar results. Genera of the family Saccharomycetaceae remain as one large clade as previously demonstrated, to which the genus Cyniclomyces is now assigned. Pichia, Saturnispora, Kregervanrija, Dekkera, Ogataea and Ambrosiozyma are members of a single large clade, which is separate from the clade that includes Barnettozyma, Cyberlindnera, Phaffomyces, Starmera and Wickerhamomyces. Other clades include Kodamaea, Metschnikowia, Debaryomyces, Cephaloascus and related genera, which are separate from the clade that includes Zygoascus, Trichomonascus, Yarrowia and others. This study once again demonstrates that there is limited congruence between a system of classification based on phenotype and a system determined from DNA sequences.
KeywordMeSH Terms
Multigene Family
31.     ( 2012 )

Identification and functional analysis of the erh1(+) gene encoding enhancer of rudimentary homolog from the fission yeast Schizosaccharomyces pombe.

PloS one 7 (11)
PMID : 23145069  :   DOI  :   10.1371/journal.pone.0049059     PMC  :   PMC3492181    
Abstract >>
The ERH gene encodes a highly conserved small nuclear protein with a unique amino acid sequence and three-dimensional structure but unknown function. The gene is present in animals, plants, and protists but to date has only been found in few fungi. Here we report that ERH homologs are also present in all four species from the genus Schizosaccharomyces, S. pombe, S. octosporus, S. cryophilus, and S. japonicus, which, however, are an exception in this respect among Ascomycota and Basidiomycota. The ERH protein sequence is moderately conserved within the genus (58% identity between S. pombe and S.japonicus), but the intron-rich genes have almost identical intron-exon organizations in all four species. In S. pombe, erh1(+) is expressed at a roughly constant level during vegetative growth and adaptation to unfavorable conditions such as nutrient limitation and hyperosmotic stress caused by sorbitol. Erh1p localizes preferentially to the nucleus with the exception of the nucleolus, but is also present in the cytoplasm. Cells lacking erh1(+) have an aberrant cell morphology and a comma-like shape when cultured to the stationary phase, and exhibit a delayed recovery from this phase followed by slower growth. Loss of erh1(+) in an auxotrophic background results in enhanced arrest in the G1 phase following nutritional stress, and also leads to hypersensitivity to agents inducing hyperosmotic stress (sorbitol), inhibiting DNA replication (hydroxyurea), and destabilizing the plasma membrane (SDS); this hypersensitivity can be abolished by expression of S. pombe erh1(+) and, to a lesser extent, S. japonicus erh1(+) or human ERH. Erh1p fails to interact with the human Ciz1 and PDIP46/SKAR proteins, known molecular partners of human ERH. Our data suggest that in Schizosaccharomyces sp. erh1(+) is non-essential for normal growth and Erh1p could play a role in response to adverse environmental conditions and in cell cycle regulation.
KeywordMeSH Terms
32.     ( 1997 )

Damage and replication checkpoint control in fission yeast is ensured by interactions of Crb2, a protein with BRCT motif, with Cut5 and Chk1.

Genes & development 11 (24)
PMID : 9407031  :   DOI  :   10.1101/gad.11.24.3387     PMC  :   PMC316798    
Abstract >>
Fission yeast Cut5/Rad4 plays a unique role in the genome maintenance as it is required for replication, replication checkpoint, and normal UV sensitivity. It is unknown, however, how Cut5 protein is linked to other checkpoint proteins, and what part it plays in replication and UV sensitivity. Here we report that Cut5 interacts with a novel checkpoint protein Crb2 and that this interaction is needed for normal genome maintenance. The carboxyl terminus of Crb2 resembles yeast Rad9 and human 53BP1 and BRCA1. Crb2 is required for checkpoint arrests induced by irradiation and polymerase mutations, but not for those induced by inhibited nucleotide supply. Upon UV damage, Crb2 is transiently modified, probably phosphorylated, with a similar timing of phosphorylation in Chk1 kinase, which is reported to restrain Cdc2 activation. Crb2 modification requires other damage-sensing checkpoint proteins but not Chk1, suggesting that Crb2 acts at the upstream of Chk1. The modified Crb2 exists as a slowly sedimenting form, whereas Crb2 in undamaged cells is in a rapidly sedimenting structure. Cut5 and Crb2 interact with Chk1 in a two-hybrid system. Moreover, moderate overexpression of Chk1 suppresses the phenotypes of cut5 and crb2 mutants. Cut5, Crb2, and Chk1 thus may form a checkpoint sensor-transmitter pathway to arrest the cell cycle.
KeywordMeSH Terms
DNA-Binding Proteins
Schizosaccharomyces pombe Proteins
Transglutaminases
33.     ( 1997 )

Identification of open reading frames in Schizosaccharomyces pombe cDNAs.

DNA research : an international journal for rapid publication of reports on genes and genomes 4 (6)
PMID : 9501991  :   DOI  :   10.1093/dnares/4.6.363    
Abstract >>
A total of 214 non-overlapping cDNA clones from Schizosaccharomyces pombe were selected and completely sequenced. The clones not previously reported were divided into the following three groups: 1) homologous to Saccharomyces cerevisiae genes (139 clones); 2) homologous to genes from other organisms but not to those from Sac. cerevisiae (4 clones); and 3) no similar sequences (40 clones). Among the 31 sequences identical to those in the public databases, 4 genes have regions corresponding to introns. Protein sequences which had homologs both in budding yeast and mammals were compared with those from Sac. cerevisiae and mammals. The search revealed that the evolutionary distances among these species are similar at least with genes of this category.
KeywordMeSH Terms
DNA, Fungal
Open Reading Frames

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