# refs

id: PMID:27678009
data:
  {"abstract":"The cAMP cascade plays an important role in several biological processes. Thus, study of its molecular details can contribute to a better understanding of these processes, treatment of diseases, or even finding antifungal drug targets. To gain further information about the PKA pathway, and its evolutionarily conserved and species-specific features, the central regulator pka1 gene, which encodes the cAMP-dependent protein kinase catalytic subunit, was studied in the less known haplontic, dimorphic fission yeast Schizosaccharomyces japonicus. Namely, this species belongs to a highly divergent phylogenetic branch of fungi. Furthermore, S. japonicus had only a single copy pka1 gene in contrast to the budding yeasts. Therefore, the pka1 deleted mutant was created, whose RNA sequencing and phenotypic studies revealed that the Pka1 regulated at least 373 genes, among them further kinases, phosphatases and transcriptional regulators. It regulated elongation of hyphae, cell size, aging and stress response. Furthermore, half of the pka1 target genes seemed to be conserved in Schizosaccharomyces pombe and S. japonicus. However, there were oppositely regulated genes in the two closely related species. The target genes suggest that this single gene must be able to fulfill all the functions of TPK1-3 of Saccharomyces cerevisiae. Thus, our results shed light on certain similarities and differences of the PKA pathway of S. japonicus compared to the budding yeasts and confirmed the multifunctionality of the pka1 gene, but further experiments are needed to prove its involvement in the metabolic processes and transport.","alleles_by_uniquename":{"SJAG_04312:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04312","name":"pka1delta","uniquename":"SJAG_04312:allele-1"}},"annotation_curators":[{"annotation_count":6,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-07-07","authors":"Papp L, Sipiczki M, Miklós I","authors_abbrev":"Papp L et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-07-07 12:57:27","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-07-07 12:57:27","canto_session_key":"9dc3302039d46818","canto_session_submitted_date":"2021-07-07 12:56:39","canto_triage_status":"Curatable","citation":"Curr Genet 2017 Jun;63(3):487-497","cv_annotations":{"single_locus_phenotype":[{"annotations":[114566],"is_not":false,"summary":null,"term":"FYPO:0007773"},{"annotations":[114565],"is_not":false,"summary":null,"term":"FYPO:0001122"},{"annotations":[114567],"is_not":false,"summary":null,"term":"FYPO:0000245"},{"annotations":[114569],"is_not":false,"summary":null,"term":"FYPO:0000097"},{"annotations":[114568],"is_not":false,"summary":null,"term":"FYPO:0000087"},{"annotations":[114570],"is_not":false,"summary":null,"term":"FYPO:0001214"}]},"doi":"10.1007/s00294-016-0651-x","gene_count":1,"genes_by_uniquename":{"SJAG_04312":null},"genotypes_by_uniquename":{"pka1delta":{"display_name":"pka1delta","display_uniquename":"pka1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04312:allele-1","expression":"Null"}]}]}},"ltp_gene_count":1,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2017","pubmed_entrez_date":"2016-09-29","pubmed_publication_date":"Jun 2017","terms_by_termid":{"FYECO:0000004":null,"FYECO:0000005":null,"FYECO:0000102":null,"FYECO:0000137":null,"FYPO:0000087":null,"FYPO:0000097":null,"FYPO:0000245":null,"FYPO:0001122":null,"FYPO:0001214":null,"FYPO:0007773":null,"FYPO_EXT:0000002":null,"FYPO_EXT:0000003":null},"title":"Expression pattern and phenotypic characterization of the mutant strain reveals target genes and processes regulated by pka1 in the dimorphic fission yeast Schizosaccharomyces japonicus.","uniquename":"PMID:27678009"}


id: PMID:19473263
data:
  {"abstract":"Schizosaccharomyces cells divide by medial septation, followed by enzymatic degradation of parts of the septum (septum cleavage) to allow the sister cells to separate from each other. In a previous study we found that the cell separation mutant sep9-307 was defective in a gene that encodes a protein highly similar in sequence to the Saccharomyces cerevisiae protein Spt8, a subunit of the SAGA complex. Here, we show that the sep9-307 mutation causes a frameshift in translation. The deletion of sep9(+) is not lethal but abolishes normal septum cleavage by reducing the activity of ace2(+), a gene coding for a transcription factor of numerous genes producing proteins for septum cleavage. Indirect evidence indicates that Sep9 might also act directly in the transcription of certain target genes (e.g. eng1(+)) of this regulator. sep9-307 is synthetically lethal with mutations in the cell separation genes sep11/med18(+) and sep15/med8(+), which encode subunits of the general transcription factor mediator. Heterologous expression of SPT8 and the putative Schizosaccharomyces japonicus sep9(+) orthologue cannot substitute for sep9(+). Both Spt8 and the fission yeast proteins have highly acidic (74-76 amino-acid long) N-terminal regions with no sequence conservation.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Batta G, Szilagyi Z, Laczik M, Sipiczki M","authors_abbrev":"Batta G et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Sequence feature or region","citation":"FEMS Yeast Res 2009 Aug;9(5):757-67","cv_annotations":{},"doi":"10.1111/j.1567-1364.2009.00522.x","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2009","pubmed_entrez_date":"2009-05-29","pubmed_publication_date":"Aug 2009","terms_by_termid":{},"title":"The involvement of the Schizosaccharomyces pombe sep9/spt8 gene in the regulation of septum cleavage.","uniquename":"PMID:19473263"}


id: PMID:26896847
data:
  {"abstract":"Evolution provides the unifying framework with which to understand biology. The coherent investigation of genic and genomic data often requires comparative genomics analyses based on whole-genome alignments, sets of homologous genes and other relevant datasets in order to evaluate and answer evolutionary-related questions. However, the complexity and computational requirements of producing such data are substantial: this has led to only a small number of reference resources that are used for most comparative analyses. The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained elements are obtained. Gene alignments are used to define Ensembl Protein Families, GeneTrees and homologies for both protein-coding and non-coding RNA genes. These resources are updated frequently and have a consistent informatics infrastructure and data presentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views. The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here is relevant to these projects. The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. We use robust software and pipelines to produce reference comparative data and make it freely available. Database URL: http://www.ensembl.org.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Herrero J, Muffato M, Beal K, Fitzgerald S, Gordon L, Pignatelli M, Vilella AJ, Searle SM, Amode R, Brent S, Spooner W, Kulesha E, Yates A, Flicek P","authors_abbrev":"Herrero J et al.","canto_curator_role":"JaponicusDB","citation":"Database (Oxford) 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6425","ortholog_taxonid":4896,"ortholog_uniquename":"SPAC167.09","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_06440","ortholog_taxonid":4896,"ortholog_uniquename":"SPBC119.18","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_06449","ortholog_taxonid":4896,"ortholog_uniquename":"SPBC947.03c","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_06468","ortholog_taxonid":4896,"ortholog_uniquename":"SPAC1F7.14c","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_06514","ortholog_taxonid":4896,"ortholog_uniquename":"SPCC757.10","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_06534","ortholog_taxonid":4896,"ortholog_uniquename":"SPAC222.17","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_06576","ortholog_taxonid":4896,"ortholog_uniquename":"SPAC3H8.08c","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_06586","ortholog_taxonid":4896,"ortholog_uniquename":"SPCC1322.01","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_06588","ortholog_taxonid":4896,"ortholog_uniquename":"SPBC23E6.08","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_06592","ortholog_taxonid":4896,"ortholog_uniquename":"SPBC725.02","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_06597","ortholog_taxonid":4896,"ortholog_uniquename":"SPAC212.06c","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_06597","ortholog_taxonid":4896,"ortholog_uniquename":"SPAC212.11","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_06597","ortholog_taxonid":4896,"ortholog_uniquename":"SPBCPT2R1.08c","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_06598","ortholog_taxonid":4896,"ortholog_uniquename":"SPAC1039.01","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_06598","ortholog_taxonid":4896,"ortholog_uniquename":"SPCC74.04","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_06599","ortholog_taxonid":4896,"ortholog_uniquename":"SPAC3H8.08c","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_06603","ortholog_taxonid":4896,"ortholog_uniquename":"SPAC56F8.04c","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_06611","ortholog_taxonid":4896,"ortholog_uniquename":"SPBP8B7.05c","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_06612","ortholog_taxonid":4896,"ortholog_uniquename":"SPBC1711.06","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_06612","ortholog_taxonid":4896,"ortholog_uniquename":"SPBP8B7.03c","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_06613","ortholog_taxonid":4896,"ortholog_uniquename":"SPBP8B7.01c","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_06621","ortholog_taxonid":4896,"ortholog_uniquename":"SPBC32F12.11","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_06621","ortholog_taxonid":4896,"ortholog_uniquename":"SPBC354.12","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_06622","ortholog_taxonid":4896,"ortholog_uniquename":"SPBC32F12.11","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_06622","ortholog_taxonid":4896,"ortholog_uniquename":"SPBC354.12","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_06634","ortholog_taxonid":4896,"ortholog_uniquename":"SPAC23C11.13c","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_06635","ortholog_taxonid":4896,"ortholog_uniquename":"SPBC14C8.04","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_06636","ortholog_taxonid":4896,"ortholog_uniquename":"SPBC14C8.03","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_06642","ortholog_taxonid":4896,"ortholog_uniquename":"SPAC212.06c","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_06642","ortholog_taxonid":4896,"ortholog_uniquename":"SPAC212.11","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_06642","ortholog_taxonid":4896,"ortholog_uniquename":"SPBCPT2R1.08c","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_16453","ortholog_taxonid":4896,"ortholog_uniquename":"SPBC13E7.01","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_16454","ortholog_taxonid":4896,"ortholog_uniquename":"SPAC17A5.07c","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_16455","ortholog_taxonid":4896,"ortholog_uniquename":"SPAC6F12.16c","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_16456","ortholog_taxonid":4896,"ortholog_uniquename":"SPAC27E2.06c","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_16457","ortholog_taxonid":4896,"ortholog_uniquename":"SPBP35G2.14","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_16459","ortholog_taxonid":4896,"ortholog_uniquename":"SPBC16C6.02c","reference_uniquename":"PMID:26896847"},{"gene_uniquename":"SJAG_MIT03","ortholog_taxonid":4896,"ortholog_uniquename":"SPMIT.05","reference_uniquename":"PMID:26896847"},{"gene_uniq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comparative genomics resources.","uniquename":"PMID:26896847"}


id: PMID:27734801
data:
  {"abstract":"Many eukaryotes assemble a ring-shaped actomyosin network that contracts to drive cytokinesis. Unlike actomyosin in sarcomeres, which cycles through contraction and relaxation, the cytokinetic ring disassembles during contraction through an unknown mechanism. Here we find in  Schizosaccharomyces japonicus  and  Schizosaccharomyces pombe  that, during actomyosin ring contraction, actin filaments associated with actomyosin rings are expelled as micron-scale bundles containing multiple actomyosin ring proteins. Using functional isolated actomyosin rings we show that expulsion of actin bundles does not require continuous presence of cytoplasm. Strikingly, mechanical compression of actomyosin rings results in expulsion of bundles predominantly at regions of high curvature. Our work unprecedentedly reveals that the increased curvature of the ring itself promotes its disassembly. It is likely that such a curvature-induced mechanism may operate in disassembly of other contractile networks.","alleles_by_uniquename":{},"annotation_curators":[{"annotation_count":2,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-07-09","authors":"Huang J, Chew TG, Gu Y, Palani S, Kamnev A, Martin DS, Carter NJ, Cross RA, Oliferenko S, Balasubramanian MK","authors_abbrev":"Huang J et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-07-09 15:10:46","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-07-09 15:10:46","canto_session_key":"f47401f00ac444e0","canto_session_submitted_date":"2021-07-09 15:10:39","canto_triage_status":"Curatable","citation":"Elife 2016 10 13;5","cv_annotations":{"cellular_component":[{"annotations":[114266],"is_not":false,"summary":null,"term":"GO:0032432"},{"annotations":[114265],"is_not":false,"summary":null,"term":"GO:0005826"}]},"doi":"10.7554/eLife.21383","gene_count":1,"genes_by_uniquename":{"SJAG_04887":null},"genotypes_by_uniquename":{},"ltp_gene_count":1,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2016","pubmed_entrez_date":"2016-10-14","pubmed_publication_date":"13 10 2016","terms_by_termid":{"GO:0005826":null,"GO:0032432":null},"title":"Curvature-induced expulsion of actomyosin bundles during cytokinetic ring contraction.","uniquename":"PMID:27734801"}


id: PMID:33837814
data:
  {"abstract":"The capability of RNA isolation with good efficiency and high quality is essential for a downstream application such as RNA sequencing. It requires successful cell culturing and an effective RNA isolation method. Although effective methods are available, production of the homogenous mycelia and extraction of good-quality mycelial RNA from true invasive hyphae, which penetrated into the agar plates, are difficult. To overcome these problems, the aim of this study was to develop technical modifications which allow production of homogenous mycelial biomass without extra stimuli agents and improve quality of the RNA extracted from the fungal hyphae. Our alternative culture medium was suitable for production both yeast-phase cells and hyphae of the Schizosaccharomyces japonicus and other dimorphic species, such as the Candida albicans, Saccharomyces cerevisiae, and Jaminaea angkorensis. To improve quality of the mycelial RNA, we developed an isolation procedure of the hyphal tip, which eliminated the unnecessary vacuoles-containing parts of the hyphae. To increase RNA quantity, we used glass beads in the RNA extraction protocol to achieve stronger breaking of the mycelial walls. All these modifications can also be useful for researchers working with other dimorphic fungi and can contribute to the higher comparability of the transcriptional data coming from yeast-phase cells and hyphae or even from different species.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Papp LA, Ács-Szabó L, Póliska S, Miklós I","authors_abbrev":"Papp LA et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Method or reagent","citation":"Curr Genet 2021 Oct;67(5):823-830","cv_annotations":{},"doi":"10.1007/s00294-021-01181-4","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2021","pubmed_entrez_date":"2021-04-10","pubmed_publication_date":"Oct 2021","terms_by_termid":{},"title":"A modified culture medium and hyphae isolation method can increase quality of the RNA extracted from mycelia of a dimorphic fungal species.","uniquename":"PMID:33837814"}


id: PMID:26774782
data:
  {"abstract":"Eukaryotes remodel the nucleus during mitosis using a variety of mechanisms that differ in the timing and the extent of nuclear envelope (NE) breakdown. Here, we probe the principles enabling this functional diversity by exploiting the natural divergence in NE management strategies between the related fission yeasts Schizosaccharomyces pombe and Schizosaccharomyces japonicus [1-3]. We show that inactivation of Ned1, the phosphatidic acid phosphatase of the lipin family, by CDK phosphorylation is both necessary and sufficient to promote NE expansion required for \"closed\" mitosis in S. pombe. In contrast, Ned1 is not regulated during division in S. japonicus, thus limiting membrane availability and necessitating NE breakage. Interspecies gene swaps result in phenotypically normal divisions with the S. japonicus lipin acquiring an S. pombe-like mitotic phosphorylation pattern. Our results provide experimental evidence for the mitotic regulation of phosphatidic acid flux and suggest that the regulatory networks governing lipin activity diverged in evolution to give rise to strikingly dissimilar mitotic programs. ","alleles_by_uniquename":{"SJAG_01906:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01906","name":"nem1delta","uniquename":"SJAG_01906:allele-1"},"SJAG_02763:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02763","name":"ned1delta","uniquename":"SJAG_02763:allele-1"},"SJAG_02763:allele-2":{"allele_type":"amino_acid_mutation","description":"D422E,D424E","gene_uniquename":"SJAG_02763","name":"ned1cat","synonyms":[{"name":"Catalytic mutant","reference":"PMID:26774782","type":"exact"}],"uniquename":"SJAG_02763:allele-2"},"SJAG_02763:allele-3":{"allele_type":"amino_acid_mutation","description":"S235A; S651","gene_uniquename":"SJAG_02763","name":"ned1S235A/S651","synonyms":[{"name":"refractory to phosphorylation","reference":"PMID:26774782","type":"exact"}],"uniquename":"SJAG_02763:allele-3"},"SJAG_02763:allele-4":{"allele_type":"amino_acid_mutation","description":"S235E; S651E","gene_uniquename":"SJAG_02763","name":"ned1S235E/S651E","synonyms":[{"name":"phosphomimetic","reference":"PMID:26774782","type":"exact"}],"uniquename":"SJAG_02763:allele-4"},"SJAG_02763:allele-5":{"allele_type":"amino_acid_mutation","description":"S499E; S538E; T620E; T638E; S651E","gene_uniquename":"SJAG_02763","name":"ned1-5E","uniquename":"SJAG_02763:allele-5"},"SJAG_02763:allele-6":{"allele_type":"amino_acid_mutation","description":"S499A; S538A; T620A; T638A; S651A","gene_uniquename":"SJAG_02763","name":"ned1-5A","synonyms":[{"name":"refractory to potential proline-directed kinase phosphorylation","reference":"PMID:26774782","type":"exact"}],"uniquename":"SJAG_02763:allele-6"},"SJAG_03940:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03940","name":"nem2delta","uniquename":"SJAG_03940:allele-1"}},"annotation_curators":[{"annotation_count":21,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"},{"annotation_count":3,"community_curator":false,"file_name":null,"file_type":null,"name":"Val Wood","orcid":"0000-0001-6330-7526"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-07-07","authors":"Makarova M, Gu Y, Chen JS, Beckley JR, Gould KL, Oliferenko S","authors_abbrev":"Makarova M et al.","canto_added_date":"2021-05-10 02:37:43","canto_annotation_status":"APPROVED","canto_approved_date":"2021-09-01 07:39:35","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-07-07 15:21:04","canto_session_key":"aa811803aa1555a2","canto_session_submitted_date":"2021-07-09 07:42:46","canto_triage_status":"Curatable","citation":"Curr Biol 2016 Jan 25;26(2):237-243","cv_annotations":{"PSI-MOD":[{"annotations":[114184,114185],"is_not":false,"summary":null,"term":"MOD:00046"}],"biological_process":[{"annotations":[114196],"is_not":false,"summary":null,"term":"GO:0090158"},{"annotations":[114198],"is_not":false,"summary":null,"term":"GO:0019915"},{"annotations":[114197],"is_not":false,"summary":null,"term":"GO:0071763"}],"cellular_component":[{"annotations":[114181],"is_not":false,"summary":null,"term":"GO:0005654"}],"single_locus_phenotype":[{"annotations":[114190,114193],"is_not":false,"summary":null,"term":"FYPO:0006054"},{"annotations":[114195],"is_not":false,"summary":null,"term":"FYPO:0005957"},{"annotations":[114177,114178,114180,114189,114192],"is_not":false,"summary":null,"term":"FYPO:0001784"},{"annotations":[114175,114176,114179,114183,114188,114191],"is_not":false,"summary":null,"term":"FYPO:0001556"},{"annotations":[114187,114194],"is_not":false,"summary":null,"term":"FYPO:0006945"},{"annotations":[114186],"is_not":false,"summary":null,"term":"FYPO:0003751"},{"annotations":[114182],"is_not":false,"summary":null,"term":"FYPO:0001234"}]},"doi":"10.1016/j.cub.2015.11.061","gene_count":4,"genes_by_uniquename":{"SJAG_00088":null,"SJAG_01906":null,"SJAG_02763":null,"SJAG_03940":null},"genotypes_by_uniquename":{"ned1-5A-S499A__S538A__T620A__T638A__S651A-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"ned1-5A(S499A; S538A; T620A; T638A; S651A aa)","display_uniquename":"ned1-5A-S499A__S538A__T620A__T638A__S651A-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02763:allele-6","expression":"Not assayed or wild type"}]}]},"ned1-5E-S499E__S538E__T620E__T638E__S651E-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"ned1-5E(S499E; S538E; T620E; T638E; S651E aa)","display_uniquename":"ned1-5E-S499E__S538E__T620E__T638E__S651E-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02763:allele-5","expression":"Not assayed or wild type"}]}]},"ned1S235A_S651-S235A__S651-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"ned1S235A/S651(S235A; S651 aa)","display_uniquename":"ned1S235A_S651-S235A__S651-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02763:allele-3","expression":"Not assayed or wild type"}]}]},"ned1S235E_S651E-S235E__S651E-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"ned1S235E/S651E(S235E; S651E aa)","display_uniquename":"ned1S235E_S651E-S235E__S651E-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02763:allele-4","expression":"Not assayed or wild type"}]}]},"ned1cat-D422E,D424E-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"ned1cat(D422E,D424E aa)","display_uniquename":"ned1cat-D422E,D424E-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02763:allele-2","expression":"Not assayed or wild type"}]}]},"ned1delta":{"display_name":"ned1delta","display_uniquename":"ned1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02763:allele-1","expression":"Null"}]}]},"nem1delta":{"display_name":"nem1delta","display_uniquename":"nem1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01906:allele-1","expression":"Null"}]}]},"nem2delta":{"display_name":"nem2delta","display_uniquename":"nem2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03940:allele-1","expression":"Null"}]}]}},"ltp_gene_count":4,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2016","pubmed_entrez_date":"2016-01-18","pubmed_publication_date":"25 Jan 2016","references_by_uniquename":{"PMID:26774782":null},"terms_by_termid":{"FYECO:0000005":null,"FYECO:0000162":null,"FYPO:0001234":null,"FYPO:0001556":null,"FYPO:0001784":null,"FYPO:0003751":null,"FYPO:0005957":null,"FYPO:0006054":null,"FYPO:0006945":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null,"GO:0005654":null,"GO:0019915":null,"GO:0071763":null,"GO:0090158":null,"MOD:00046":null},"title":"Temporal Regulation of Lipin Activity Diverged to Account for Differences in Mitotic Programs.","uniquename":"PMID:26774782"}


id: PMID:25942548
data:
  {"abstract":"New work shows the anillin-related protein Mid1 does not position the cytokinetic ring in the fission yeast Schizosaccharomyces japonicus, unlike its role in S. pombe. Further analysis suggests the conserved function of Mid1-like anillin proteins may be in scaffolding, not positioning, the cytokinetic ring. ","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Moseley JB","authors_abbrev":"Moseley JB","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Review or comment","citation":"Curr Biol 2015 May 04;25(9):R364-6","cv_annotations":{},"doi":"10.1016/j.cub.2015.03.017","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2015","pubmed_entrez_date":"2015-05-06","pubmed_publication_date":"04 May 2015","terms_by_termid":{},"title":"Cytokinesis: does Mid1 have an identity crisis?","uniquename":"PMID:25942548"}


id: PMID:1093
data:
  {"abstract":"(11 Cell extracts and extracellular culture fluids of species of the yeast genus Schizosaccharomyces exhibited exo-beta-(1 leads to 3)- and exo-beta-(1 leads to 6)-glucanase (EC 3.2.1.-) activities. (2) Using a combination of Sephadex G-100 and DEAE-cellulose chromatography, the exo-beta-(1 leads to 3)-glucanases from the cell extracts and culture fluid of Schizosaccharomyces japonicus var. versatilis were purified extensively. The enzymes from either location exhibited similar purification and other properties. (3) The purified enzymes hydrolysed the beta-(1 leads to 6)-glucosidic linkage in addition to the beta-(1 leads to 3) linkage. Heat denaturation, inhibition and electrophoretic studies indicated that both hydrolytic activities were properties of a single protein. Laminarin and pustulan hydrolysis followed Michaelis-Menten kinetics. The Km and V for laminarin hydrolysis were 6.25 mg/ml and 350 mumol of glucose released/min/mg protein, and for pustulan they were 166 mg/ml and 52 mumol of glucose released/min/mg protein. (4) The exo-beta-glucanase was assigned a molecular weight of 43 000. (5) the purified enzyme failed to hydrolyse isolated cell walls from either baker's yeast or Schizosaccharomyces pombe or to induce protoplast formation from intact cells of S. japonicus var. versatilis or Saccharomyces cerevisiae.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Fleet GH, Phaff HJ","authors_abbrev":"Fleet GH et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"Biochim Biophys Acta 1975 Dec 18;410(2):318-32","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1975","pubmed_entrez_date":"1975-12-18","pubmed_publication_date":"18 Dec 1975","terms_by_termid":{},"title":"Glucanases in Schizosaccharomyces. Isolation and properties of an exo-beta-glucanase from the cell extracts and culture fluid of Schizosaccharomyces japonicus var. versatilis.","uniquename":"PMID:1093"}


id: GO_REF:0000041
data:
  {"alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"canto_curator_role":"JaponicusDB","cv_annotations":{"biological_process":[{"annotations":[66140],"is_not":false,"summary":null,"term":"GO:0006021"},{"annotations":[67700],"is_not":false,"summary":null,"term":"GO:0006782"}]},"gene_count":2,"genes_by_uniquename":{"SJAG_00097":null,"SJAG_03739":null},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{"GO:0006021":null,"GO:0006782":null},"uniquename":"GO_REF:0000041"}


id: PMID:34353908
data:
  {"abstract":"Biosynthesis of sterols, which are key constituents of canonical eukaryotic membranes, requires molecular oxygen. Anaerobic protists and deep-branching anaerobic fungi are the only eukaryotes in which a mechanism for sterol-independent growth has been elucidated. In these organisms, tetrahymanol, formed through oxygen-independent cyclization of squalene by a squalene-tetrahymanol cyclase, acts as a sterol surrogate. This study confirms an early report [C. J. E. A. Bulder,  Antonie Van Leeuwenhoek , 37, 353-358 (1971)] that  Schizosaccharomyces japonicus  is exceptional among yeasts in growing anaerobically on synthetic media lacking sterols and unsaturated fatty acids. Mass spectrometry of lipid fractions of anaerobically grown  Sch. japonicus  showed the presence of hopanoids, a class of cyclic triterpenoids not previously detected in yeasts, including hop-22(29)-ene, hop-17(21)-ene, hop-21(22)-ene, and hopan-22-ol. A putative gene in  Sch. japonicus  showed high similarity to bacterial squalene-hopene cyclase (SHC) genes and in particular to those of  Acetobacter  species. No orthologs of the putative  Sch. japonicus  SHC were found in other yeast species. Expression of the  Sch. japonicus  SHC gene ( Sjshc1 ) in  Saccharomyces cerevisiae  enabled hopanoid synthesis and stimulated anaerobic growth in sterol-free media, thus indicating that one or more of the hopanoids produced by SjShc1 could at least partially replace sterols. Use of hopanoids as sterol surrogates represents a previously unknown adaptation of eukaryotic cells to anaerobic growth. The fast anaerobic growth of  Sch. japonicus  in sterol-free media is an interesting trait for developing robust fungal cell factories for application in anaerobic industrial processes.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Bouwknegt J, Wiersma SJ, Ortiz-Merino RA, Doornenbal ESR, Buitenhuis P, Giera M, Müller C, Pronk JT","authors_abbrev":"Bouwknegt J et al.","canto_added_date":"2023-05-04 00:40:04","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"Proc Natl Acad Sci U S A 2021 Aug 10;118(32)","cv_annotations":{},"doi":"10.1073/pnas.2105225118","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2021","pubmed_entrez_date":"2021-08-06","pubmed_publication_date":"10 Aug 2021","terms_by_termid":{},"title":"A squalene-hopene cyclase in  Schizosaccharomyces japonicus  represents a eukaryotic adaptation to sterol-limited anaerobic environments.","uniquename":"PMID:34353908"}


id: PMID:24375690
data:
  {"abstract":"The clade of Schizosaccharomyces includes 4 species: S. pombe, S. octosporus, S. cryophilus, and S. japonicus. Although all 4 species exhibit unicellular growth with a binary fission mode of cell division, S. japonicus alone is dimorphic yeast, which can transit from unicellular yeast to long filamentous hyphae. Recently it was found that the hyphal cells response to light and then synchronously activate cytokinesis of hyphae. In addition to hyphal growth, S. japonicas has many properties that aren't shared with other fission yeast. Mitosis of S. japonicas is referred to as semi-open mitosis because dynamics of nuclear membrane is an intermediate mode between open mitosis and closed mitosis. Novel genetic tools and the whole genomic sequencing of S. japonicas now provide us with an opportunity for revealing unique characters of the dimorphic yeast.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Niki H","authors_abbrev":"Niki H","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Review or comment","citation":"Yeast 2014 Mar;31(3):83-90","cv_annotations":{},"doi":"10.1002/yea.2996","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2014","pubmed_entrez_date":"2013-12-31","pubmed_publication_date":"Mar 2014","terms_by_termid":{},"title":"Schizosaccharomyces japonicus: the fission yeast is a fusion of yeast and hyphae.","uniquename":"PMID:24375690"}


id: PMID:9884240
data:
  {"abstract":"Fission yeast cells grow by extension at the ends (poles) and divide by transverse fission. It has previously been reported that Schizosaccharomyces japonicus var. japonicus can switch to unipolar, filamentous growth. Here it is shown that the yeast-to-mycelium transition is a gradual process involving a changeover to unipolar growth associated with asymmetric divisions, the development of large polarly located vacuoles, the modifications of the actin and microtubular cytoskeleton and the repression of cell separation after division. High concentrations of glucose in the medium or supplementation of the medium with caffeine or cAMP support the bipolar yeast phase, inhibit the transition to the mycelial phase and induce the conversion of hyphae to yeasts. These effects suggest that cAMP may be involved in the regulation of dimorphism. Temperatures below 18 degrees C or over 35 degrees C are restrictive for the mycelial phase and provoke a return to yeast phase.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-10-07","authors":"Sipiczki M, Takeo K, Grallert A","authors_abbrev":"Sipiczki M et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-10-07 12:31:51","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-10-07 12:31:51","canto_session_key":"5ac54d09f220d215","canto_session_submitted_date":"2021-09-30 09:01:47","canto_triage_status":"Curatable","citation":"Microbiology (Reading) 1998 Dec;144 ( Pt 12):3475-3485","cv_annotations":{},"doi":"10.1099/00221287-144-12-3475","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1998","pubmed_entrez_date":"1999-01-12","pubmed_publication_date":"Dec 1998","terms_by_termid":{},"title":"Growth polarity transitions in a dimorphic fission yeast.","uniquename":"PMID:9884240"}


id: PMID:35693892
data:
  {"abstract":"The S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 catalyzes biosynthesis of 4-demethylwyosine (imG-14), the precursor for wyosine, the hypermodified guanine-derived nucleotide present at position 37 of phenylalanine tRNAs of archaea and eukarya. Eukaryotic TYW1 enzymes contain N-terminal flavodoxin-like and C-terminal radical-SAM domains. We determined co-crystal structures of the flavodoxin-like domain of the putative Tyw1 from  Schizosaccharomyces japonicus  in complex with flavin mononucleotide (FMN), exploiting an unexpected anomalous scatterer present in the recombinant protein. Our results show how eukaryotic TYW1 enzymes bind the coenzyme FMN and will help further elucidation of the structural enzymology of 4-demethylwyosine synthesis.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Sjekloća L, Ferré-D'Amaré AR","authors_abbrev":"Sjekloća L et al.","canto_added_date":"2023-05-04 00:40:03","canto_curator_role":"JaponicusDB","canto_triage_status":"Structure","citation":"MicroPubl Biol 2022;2022","cv_annotations":{},"doi":"10.17912/micropub.biology.000570","gene_count":1,"genes_by_uniquename":{"SJAG_04265":null},"genotypes_by_uniquename":{},"ltp_gene_count":1,"ortholog_annotations":[],"paralog_annotations":[],"pdb_entries":[{"entry_authors":"Sjekloca L,Ferre-D'Amare AR","entry_authors_abbrev":"Sjekloca L et al.","experimental_method":"X-ray","gene_chains":[{"chain":"A","gene_uniquename":"SJAG_04265","position":"30-251"}],"pdb_id":"6puq","reference_uniquename":"PMID:35693892","resolution":"1.56","title":"1.56 A crystal structure of flavodoxin-like domain of Schizosaccharomyces japonicus putative tRNAPhe 4-demethylwyosine synthase Tyw1 in complex with FMN"},{"entry_authors":"Sjekloca L,Ferre D'Amare AR","entry_authors_abbrev":"Sjekloca L et al.","experimental_method":"X-ray","gene_chains":[{"chain":"A","gene_uniquename":"SJAG_04265","position":"76-251"}],"pdb_id":"6pup","reference_uniquename":"PMID:35693892","resolution":"1.89","title":"1.9 A crystal structure of flavodoxin-like domain of Schizosaccharomyces japonicus putative tRNAPhe 4-demethylwyosine synthase Tyw1 in complex with FMN"}],"physical_interactions":[],"publication_year":"2022","pubmed_entrez_date":"2022-06-13","pubmed_publication_date":"2022","terms_by_termid":{},"title":"Biochemical and structural characterization of the flavodoxin-like domain of the  Schizosaccharomyces japonicus  putative tRNA  Phe  4-demethylwyosine synthase Tyw1 in complex with FMN.","uniquename":"PMID:35693892"}


id: PMID:34656184
data:
  {"abstract":"In most fungi, quinone-dependent Class-II dihydroorotate dehydrogenases (DHODs) are essential for pyrimidine biosynthesis. Coupling of these Class-II DHODHs to mitochondrial respiration makes their in vivo activity dependent on oxygen availability. Saccharomyces cerevisiae and closely related yeast species harbor a cytosolic Class-I DHOD (Ura1) that uses fumarate as electron acceptor and thereby enables anaerobic pyrimidine synthesis. Here, we investigate DHODs from three fungi (the Neocallimastigomycete Anaeromyces robustus and the yeasts Schizosaccharomyces japonicus and Dekkera bruxellensis) that can grow anaerobically but, based on genome analysis, only harbor a Class-II DHOD.\nHeterologous expression of putative Class-II DHOD-encoding genes from fungi capable of anaerobic, pyrimidine-prototrophic growth (Arura9, SjURA9, DbURA9) in an S. cerevisiae ura1Δ strain supported aerobic as well as anaerobic pyrimidine prototrophy. A strain expressing DbURA9 showed delayed anaerobic growth without pyrimidine supplementation. Adapted faster growing DbURA9-expressing strains showed mutations in FUM1, which encodes fumarase. GFP-tagged SjUra9 and DbUra9 were localized to S. cerevisiae mitochondria, while ArUra9, whose sequence lacked a mitochondrial targeting sequence, was localized to the yeast cytosol. Experiments with cell extracts showed that ArUra9 used free FAD and FMN as electron acceptors. Expression of SjURA9 in S. cerevisiae reproducibly led to loss of respiratory competence and mitochondrial DNA. A cysteine residue (C265 in SjUra9) in the active sites of all three anaerobically active Ura9 orthologs was shown to be essential for anaerobic activity of SjUra9 but not of ArUra9.\nActivity of fungal Class-II DHODs was long thought to be dependent on an active respiratory chain, which in most fungi requires the presence of oxygen. By heterologous expression experiments in S. cerevisiae, this study shows that phylogenetically distant fungi independently evolved Class-II dihydroorotate dehydrogenases that enable anaerobic pyrimidine biosynthesis. Further structure-function studies are required to understand the mechanistic basis for the anaerobic activity of Class-II DHODs and an observed loss of respiratory competence in S. cerevisiae strains expressing an anaerobically active DHOD from Sch. japonicus.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Bouwknegt J, Koster CC, Vos AM, Ortiz-Merino RA, Wassink M, Luttik MAH, van den Broek M, Hagedoorn PL, Pronk JT","authors_abbrev":"Bouwknegt J et al.","canto_added_date":"2023-05-04 00:40:04","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"Fungal Biol Biotechnol 2021 Oct 16;8(1):10","cv_annotations":{},"doi":"10.1186/s40694-021-00117-4","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2021","pubmed_entrez_date":"2021-10-17","pubmed_publication_date":"16 Oct 2021","terms_by_termid":{},"title":"Class-II dihydroorotate dehydrogenases from three phylogenetically distant fungi support anaerobic pyrimidine biosynthesis.","uniquename":"PMID:34656184"}


id: PMID:12795405
data:
  {"abstract":"Spectrin, a component of the membrane skeleton in erythrocytes and other animal cells, has also been identified in plant and fungal cells. However, its postulated role, i.e., the maintenance of shape and elasticity of the plasma membrane, is probably not exerted in walled cells. To study spectrin in these cells, we chose yeasts because of a high morphological variability of their life cycle. The localization of spectrin in the cells and protoplasts of Saccharomyces cerevisiae and Schizosaccharomyces japonicus var. versatilis was detected by immunoblotting, indirect immunofluorescence, and immunogold electron microscopy techniques with the use of anti-chicken and anti-human erythrocyte spectrin antibodies. A protein band of 220-240 kDa and some bands of lower relative mass were detected in cell and protoplast extracts of both yeast strains. Spectrin-like proteins were revealed by fluorescence microscopy at cell surfaces and in vacuolar membranes. Immunogold-labelling showed spectrin-like proteins in the plasma membrane, endoplasmic reticulum, vacuoles, nuclei, vesicles, mitochondria, and cell walls. The topology of spectrin was not affected by actin depolymerization with Latrunculin B nor was it changed in either act1-1 or cdc42 mutants, under restrictive conditions. Under osmotic stress, both spectrin and actin were delocalized and appeared in the form of large clusters in the cytoplasm. It is concluded that a protein cross-reacting with spectrin antibodies is present in fission and budding yeasts. Generally, it is located in the proximity of the plasma membrane and other intracellular membranes, probably as a part of the membrane skeleton. No evidence of its relationship to either actin or growth zones of the cell can be provided.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Slaninová I, Holubárová A, Svoboda A","authors_abbrev":"Slaninová I et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Method or reagent","citation":"Can J Microbiol 2003 Mar;49(3):189-96","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2003","pubmed_entrez_date":"2003-06-11","pubmed_publication_date":"Mar 2003","terms_by_termid":{},"title":"Immunodetection of spectrin-like proteins in yeasts.","uniquename":"PMID:12795405"}


id: PMID:24309281
data:
  {"abstract":"How do nuclear components, apart from chromosomes, partition equally to daughter nuclei during mitosis? In Schizosaccharomyces japonicus, the conserved LEM-domain nuclear envelope protein Man1 ensures the formation of identical daughter nuclei by coupling nuclear pore complexes to the segregating chromosomes. ","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Walters AD, Cohen-Fix O","authors_abbrev":"Walters AD et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Review or comment","citation":"Curr Biol 2013 Dec 02;23(23):R1045-7","cv_annotations":{},"doi":"10.1016/j.cub.2013.10.041","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2013","pubmed_entrez_date":"2013-12-07","pubmed_publication_date":"02 Dec 2013","terms_by_termid":{},"title":"Nuclear division: giving daughters their fair share.","uniquename":"PMID:24309281"}


id: PMID:11921097
data:
  {"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).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Bozsik A, Szilagyi Z, Benko Z, Sipiczki M","authors_abbrev":"Bozsik A et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Method or reagent","citation":"Yeast 2002 Apr;19(6):485-98","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2002","pubmed_entrez_date":"2002-03-29","pubmed_publication_date":"Apr 2002","terms_by_termid":{},"title":"Marker construction and cloning of a cut1-like sequence with ARS activity in the fission yeast Schizosaccharomyces japonicus.","uniquename":"PMID:11921097"}


id: PMID:35940784
data:
  {"abstract":"Schizosaccharomyces japonicus have been found as dominant yeast species coexisting with Saccharomyces cerevisiae during late stages of spontaneous fermentation of local grapes in Guizhou, China. Therefore, this study further investigated the impacts of the two indigenous yeast species on typicality of crystal grape (Niagara) wine. Five indigenous and one commercial S. cerevisiae strains were firstly selected based on their genotypes and fermentation traits in synthetic medium. All the six S. cerevisiae exhibited high tolerance to glucose, temperature, and SO 2 . The two killer active strains FBKL2.996 and FBKL2.9126 showed relative higher tolerance capacity of ethanol, pH and osmotic pressure than the other four S. cerevisiae strains. Further pure fermentation of six strains using crystal grape must exhibited different contents of volatile compounds, with commercial strain CECA producing the highest levels of acetate esters (phenethyl acetate), ethyl esters (ethyl caprylate, ethyl hexanoate), n-caprylic acid isobutyl ester, and terpenes (linalool) whereas being ranked the last in the sensory analysis. The co-inoculation of indigenous S. japonicus with each of the six S. cerevisiae strains increased the acetate esters (mainly isoamyl acetate) by 2-3 times in crystal grape wine. The indigenous S. cerevisiae FBKL2.9128 showed the most obvious variation of volatile compounds between pure and mixed fermentation, exhibiting the significant increase of isoamyl acetate, ethyl decanoate, ethyl caprylate, ethyl hexanoate, methyl decanoate, and dodecanal when co-inoculated with S. japonicus. Sugar addition in immature crystal grape juice increased the ethanol, glycerol, and some volatile compounds such as ethyl butyrate, but decreased the volatile compounds with floral and animal odors. The aroma sensory analysis confirmed the decrease of varietal aroma in wines with sugar addition when comparing with wines made from immature crystal grape. The results of this study provide basic information on the impact of indigenous S. cerevisaie and S. japonicus, and sugar addition on typicality of crystal grape wine, which would help to improve the wine flavor made from crystal grape in southwest China.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Wang C, Liang S, Yang J, Wu C, Qiu S","authors_abbrev":"Wang C et al.","canto_added_date":"2023-05-04 00:40:03","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"Food Res Int 2022 Sep;159:111580","cv_annotations":{},"doi":"10.1016/j.foodres.2022.111580","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2022","pubmed_entrez_date":"2022-08-08","pubmed_publication_date":"Sep 2022","terms_by_termid":{},"title":"The impact of indigenous Saccharomyces cerevisiae and Schizosaccharomyces japonicus on typicality of crystal grape (Niagara) wine.","uniquename":"PMID:35940784"}


id: PMID:37457408
data:
  {"abstract":"The online version contains supplementary material available at 10.1007/s10068-023-01265-6.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Choi J, Park SY, Park MK, Kim YS, Ahn C, Kim YJ, Park CS","authors_abbrev":"Choi J et al.","canto_added_date":"2023-07-18 00:40:02","canto_curator_role":"JaponicusDB","canto_triage_status":"Biotech","citation":"Food Sci Biotechnol 2023 Sep;32(10):1383-1393","cv_annotations":{},"doi":"10.1007/s10068-023-01265-6","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2023","pubmed_entrez_date":"2023-07-17","pubmed_publication_date":"Sep 2023","terms_by_termid":{},"title":"Application of  Schizosaccharomyces japonicus  in  makgeolli  fermentation and its brewing characteristics.","uniquename":"PMID:37457408"}


id: PMID:32140970
data:
  {"abstract":"In eukaryotes, chromosome ends (telomeres) are tethered to the inner nuclear membrane. During the early stages of meiosis, telomeres move along the nuclear membrane and gather near the spindle-pole body, resulting in a bouquet-like arrangement of chromosomes. This chromosomal configuration appears to be widely conserved among eukaryotes, and is assumed to play an important role in the normal progression of meiosis, by mediating the proper pairing of homologous chromosomes. In fission yeast, the Bqt1-Bqt2 protein complex plays a key role in tethering the telomere to the inner nuclear membrane. However, the structural details of the complex required to clarify how telomeres are gathered near the spindle-pole body remain enigmatic. Previously, we devised a preparation procedure for the Schizosaccharomyces japonicus Bqt1-Bqt2 complex, in which a SUMO tag was fused to the N-terminus of the Bqt1 protein. This allowed us to purify the Bqt1-Bqt2 complex from the soluble fraction. In the present study, we found that a maltose-binding protein homolog, Athe_0614, served as a better fusion partner than the SUMO protein, resulting in the marked increase in the solubility of the Bqt1-Bqt2 complex. The Athe_0614 fusion partner may open up new avenues for X-ray crystallographic analyses of the structure of the Bqt1-Bqt2 complex.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Yuzurihara H, Aizawa Y, Saotome M, Ichikawa Y, Yokoyama H, Chikashige Y, Haraguchi T, Hiraoka Y, Kurumizaka H, Kagawa W","authors_abbrev":"Yuzurihara H et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Method or reagent","citation":"Protein J 2020 04;39(2):174-181","cv_annotations":{},"doi":"10.1007/s10930-020-09887-z","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2020","pubmed_entrez_date":"2020-03-07","pubmed_publication_date":"04 2020","terms_by_termid":{},"title":"Improved Methods for Preparing the Telomere Tethering Complex Bqt1-Bqt2 for Structural Studies.","uniquename":"PMID:32140970"}


id: PMID:19330769
data:
  {"abstract":"The fission yeast Schizosaccharomyces japonicus var. japonicus belong to the genus Schizosaccharomyces, together with Schizosaccharomyces pombe, which has been well studied as a model organism. In contrast, Sz. japonicus is poorly characterized and genetic tools were yet to be developed. We here report the isolation of the heterothallic haploids NIG2017, NIG2025 and NIG2028, which were derivatives of a Sz. japonicus homothallic strain (NIG2008). Based on the genomic sequence of Sz. japonicus, released by the Broad Institute, we found that Sz. japonicus also possesses orthologues of the mating-type genes of Sz. pombe; two mat-M (-) and two mat-P (+) genes. As expected, heterothallic strains were defective in one of the Sz. japonicus mat genes (mat(sj)). We confirmed that NIG2017 and NIG2025 strains only expressed mRNA from the mat(sj)-P genes, while homothallic strains expressed both mat(sj)-M and mat(sj)-P. Although the NIG2028 strain expressed both gene products, mat(sj)-P was found mutated, which may have conferred the heterothallic phenotype of the mutant. Thus, we concluded that these were stable heterothallic strains. We designated NIG2017 and NIG2025 as h(+) and NIG 2028 as h(-), respectively. We also found additional h(-) strains (NIG5872 and NIG5873) that arose from the cross between NIG2017 and NIG2028 derivatives. In addition to that, we have constructed a ura4(sj)-deleted strain and an ade6(sj)-mutated strain. We used these heterothallic strains and the auxotroph strains to perform spore dissection analysis to determine the genetic distances between several loci, and found that the mating type loci and ade6(sj) locus were linked to centromeres.","alleles_by_uniquename":{"SJAG_01081:allele-1":{"allele_type":"nonsense_mutation","description":"S427>stop","gene_uniquename":"SJAG_01081","name":"ade6-domE","uniquename":"SJAG_01081:allele-1"},"SJAG_03164:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03164","name":"ura4delta","uniquename":"SJAG_03164:allele-1"}},"annotation_curators":[{"annotation_count":2,"community_curator":true,"file_name":null,"file_type":null,"name":"Sho Okamoto","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2022-11-23","authors":"Furuya K, Niki H","authors_abbrev":"Furuya K et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2022-11-23 13:08:27","canto_curator_name":"Sho Okamoto","canto_curator_role":"community","canto_first_approved_date":"2022-11-23 13:08:26","canto_session_key":"386d294cfcac2a63","canto_session_submitted_date":"2022-11-23 13:07:46","canto_triage_status":"Curatable","citation":"Yeast 2009 Apr;26(4):221-33","cv_annotations":{"single_locus_phenotype":[{"annotations":[114210],"is_not":false,"summary":null,"term":"FYPO:0000747"},{"annotations":[114211],"is_not":false,"summary":null,"term":"FYPO:0001012"}]},"doi":"10.1002/yea.1662","gene_count":2,"genes_by_uniquename":{"SJAG_01081":null,"SJAG_03164":null},"genotypes_by_uniquename":{"ade6-domE-S427>stop-nonsense_mutation-expression-not_assayed_or_wild_type":{"display_name":"ade6-domE(S427>stop)","display_uniquename":"ade6-domE-S427>stop-nonsense_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01081:allele-1","expression":"Not assayed or wild type"}]}]},"ura4delta":{"display_name":"ura4delta","display_uniquename":"ura4delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03164:allele-1","expression":"Null"}]}]}},"ltp_gene_count":2,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2009","pubmed_entrez_date":"2009-03-31","pubmed_publication_date":"Apr 2009","terms_by_termid":{"FYPO:0000747":null,"FYPO:0001012":null},"title":"Isolation of heterothallic haploid and auxotrophic mutants of Schizosaccharomyces japonicus.","uniquename":"PMID:19330769"}


id: GO_REF:0000044
data:
  {"alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"canto_curator_role":"JaponicusDB","cv_annotations":{"cellular_component":[{"annotations":[66358],"is_not":false,"summary":null,"term":"GO:0001725"},{"annotations":[67603],"is_not":false,"summary":null,"term":"GO:0031982"}]},"gene_count":2,"genes_by_uniquename":{"SJAG_01739":null,"SJAG_03357":null},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{"GO:0001725":null,"GO:0031982":null},"uniquename":"GO_REF:0000044"}


id: PMID:29566183
data:
  {"abstract":"Dimorphic yeasts transform into filamentous cells or hyphae in response to environmental cues. The mechanisms for the hyphal transition of dimorphic yeasts have mainly been studied in Candida albicans, an opportunistic human fungal pathogen. The Ras1-MAPK pathway is a major signal transduction pathway for hyphal transition in C. albicans. Recently, the non-pathogenic dimorphic yeast Schizosaccharomyces japonicus has also been used for genetic analyses of hyphal induction. We confirmed that Ras1-MAPK and other MAPK pathways exist in Sz. japonicus. To examine how hyphal transition is induced by environmental stress-triggered signal transduction, we studied the hyphal transition of deletion mutants of MAPK pathways in Sz. japonicus. We found that the MAPK pathways are not involved in hyphal induction, although the mating response is dependent on these pathways. However, only Ras1 deletion caused a severe defect in hyphal development via both DNA damage and environmental stressors. In fact, genes on the Cdc42 branch of the Ras1 (Ras1-Cdc42) pathway, efc25Sj, scd1Sj and scd2Sj, are required for hyphal development. Cell morphology analysis indicated that the apical growth of hyphal cells was inhibited in Ras1-Cdc42-pathway deletion mutants. Thus, the control of cell polarity by the Ras1-Cdc42 pathway is crucial for hyphal development.","alleles_by_uniquename":{"SJAG_00514:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00514","name":"scd1delta","uniquename":"SJAG_00514:allele-1"},"SJAG_00993:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00993","name":"byr1delta","uniquename":"SJAG_00993:allele-1"},"SJAG_01181:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01181","name":"pek1delta","uniquename":"SJAG_01181:allele-1"},"SJAG_01718:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01718","name":"byr2delta","uniquename":"SJAG_01718:allele-1"},"SJAG_01794:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01794","name":"scd2delta","uniquename":"SJAG_01794:allele-1"},"SJAG_02342:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02342","name":"wis1delta","uniquename":"SJAG_02342:allele-1"},"SJAG_02379:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02379","name":"gap1delta","uniquename":"SJAG_02379:allele-1"},"SJAG_02486:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02486","name":"ste6delta","uniquename":"SJAG_02486:allele-1"},"SJAG_02592:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02592","name":"sty1delta","uniquename":"SJAG_02592:allele-1"},"SJAG_02819:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02819","name":"efc25delta","uniquename":"SJAG_02819:allele-1"},"SJAG_02923:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02923","name":"spk1delta","uniquename":"SJAG_02923:allele-1"},"SJAG_03384:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03384","name":"wis4delta","uniquename":"SJAG_03384:allele-1"},"SJAG_03453:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03453","name":"ras1delta","uniquename":"SJAG_03453:allele-1"},"SJAG_03753:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03753","name":"mkh1delta","uniquename":"SJAG_03753:allele-1"},"SJAG_04009:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04009","name":"ste11delta","uniquename":"SJAG_04009:allele-1"},"SJAG_04551:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04551","name":"pmk1delta","uniquename":"SJAG_04551:allele-1"},"SJAG_04777:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04777","name":"win1delta","uniquename":"SJAG_04777:allele-1"}},"annotation_curators":[{"annotation_count":38,"community_curator":true,"file_name":null,"file_type":null,"name":"Sho Okamoto","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2022-11-18","authors":"Nozaki S, Furuya K, Niki H","authors_abbrev":"Nozaki S et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2022-11-18 13:44:52","canto_curator_name":"Sho Okamoto","canto_curator_role":"community","canto_first_approved_date":"2022-11-18 13:44:52","canto_session_key":"18862c3d67da0cb0","canto_session_submitted_date":"2022-11-18 13:44:26","canto_triage_status":"Curatable","citation":"FEMS Yeast Res 2018 06 01;18(4)","cv_annotations":{"single_locus_phenotype":[{"annotations":[114139],"is_not":false,"summary":null,"term":"FYPO:0007773"},{"annotations":[114122,114123,114132,114154,114155],"is_not":false,"summary":null,"term":"FYPO:0007789"},{"annotations":[114151],"is_not":false,"summary":null,"term":"FYPO:0000584"},{"annotations":[114121,114125,114129],"is_not":false,"summary":null,"term":"FYPO:0001355"},{"annotations":[114153],"is_not":false,"summary":null,"term":"FYPO:0007790"},{"annotations":[114120,114126,114127,114131,114134,114136,114137,114150,114152],"is_not":false,"summary":null,"term":"FYPO:0000280"},{"annotations":[114128,114133,114135,114138,114140,114141,114142,114143,114144,114145,114146,114147,114148,114149],"is_not":false,"summary":null,"term":"FYPO:0000124"},{"annotations":[114119,114124,114130,114156],"is_not":false,"summary":null,"term":"FYPO:0002380"}]},"doi":"10.1093/femsyr/foy031","gene_count":17,"genes_by_uniquename":{"SJAG_00514":null,"SJAG_00993":null,"SJAG_01181":null,"SJAG_01718":null,"SJAG_01794":null,"SJAG_02342":null,"SJAG_02379":null,"SJAG_02486":null,"SJAG_02592":null,"SJAG_02819":null,"SJAG_02923":null,"SJAG_03384":null,"SJAG_03453":null,"SJAG_03753":null,"SJAG_04009":null,"SJAG_04551":null,"SJAG_04777":null},"genotypes_by_uniquename":{"byr1delta":{"display_name":"byr1delta","display_uniquename":"byr1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00993:allele-1","expression":"Null"}]}]},"byr2delta":{"display_name":"byr2delta","display_uniquename":"byr2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01718:allele-1","expression":"Null"}]}]},"efc25delta":{"display_name":"efc25delta","display_uniquename":"efc25delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02819:allele-1","expression":"Null"}]}]},"gap1delta":{"display_name":"gap1delta","display_uniquename":"gap1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02379:allele-1","expression":"Null"}]}]},"mkh1delta":{"display_name":"mkh1delta","display_uniquename":"mkh1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03753:allele-1","expression":"Null"}]}]},"pek1delta":{"display_name":"pek1delta","display_uniquename":"pek1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01181:allele-1","expression":"Null"}]}]},"pmk1delta":{"display_name":"pmk1delta","display_uniquename":"pmk1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04551:allele-1","expression":"Null"}]}]},"ras1delta":{"display_name":"ras1delta","display_uniquename":"ras1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03453:allele-1","expression":"Null"}]}]},"scd1delta":{"display_name":"scd1delta","display_uniquename":"scd1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00514:allele-1","expression":"Null"}]}]},"scd2delta":{"display_name":"scd2delta","display_uniquename":"scd2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01794:allele-1","expression":"Null"}]}]},"spk1delta":{"display_name":"spk1delta","display_uniquename":"spk1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02923:allele-1","expression":"Null"}]}]},"ste11delta":{"display_name":"ste11delta","display_uniquename":"ste11delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04009:allele-1","expression":"Null"}]}]},"ste6delta":{"display_name":"ste6delta","display_uniquename":"ste6delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02486:allele-1","expression":"Null"}]}]},"sty1delta":{"display_name":"sty1delta","display_uniquename":"sty1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02592:allele-1","expression":"Null"}]}]},"win1delta":{"display_name":"win1delta","display_uniquename":"win1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04777:allele-1","expression":"Null"}]}]},"wis1delta":{"display_name":"wis1delta","display_uniquename":"wis1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02342:allele-1","expression":"Null"}]}]},"wis4delta":{"display_name":"wis4delta","display_uniquename":"wis4delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03384:allele-1","expression":"Null"}]}]}},"ltp_gene_count":17,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2018","pubmed_entrez_date":"2018-03-23","pubmed_publication_date":"01 06 2018","terms_by_termid":{"FYECO:0000137":null,"FYPO:0000124":null,"FYPO:0000280":null,"FYPO:0000584":null,"FYPO:0001355":null,"FYPO:0002380":null,"FYPO:0007773":null,"FYPO:0007789":null,"FYPO:0007790":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null},"title":"The Ras1-Cdc42 pathway is involved in hyphal development of Schizosaccharomyces japonicus.","uniquename":"PMID:29566183"}


id: PMID:20737410
data:
  {"abstract":"Schizosaccharomyces japonicus is a fission yeast for which new genetic tools have recently been developed. Here, we report novel plasmid vectors with high transformation efficiency and an electroporation method for Sz. japonicus. We isolated 44 replicating segments from 12 166 transformants of Sz. japonicus genomic fragments and found a chromosomal fragment, RS1, as a new replicating sequence that conferred high transformation activity to Sz. japonicus cells. This sequence was cloned into a pUC19 vector with ura4(+) of Sz. pombe (pSJU11) or the kan gene on the kanMX6 module (pSJK11) as selection markers. These plasmids transformed Sz. japonicus cells in the early-log phase by electroporation at a frequency of 123 cfu/µg for pSJK11 and 301 cfu/µg for pSJU11, which were higher than previously reported autonomously replicating sequences. Although a portion of plasmids remained in host cells by integration into the chromosome via RS1 segment, the plasmids could be recovered from transformants. The plasmid copy number was estimated to be 1.88 copies per cell by Southern blot analysis using a Sz. pombe ura4(+) probe. The plasmid containing ade6(+) suppressed the auxotrophic growth of the ade6-domE mutant, indicating that the plasmid would be useful for suppressor screening and complementation assays in Sz. japonicus. Furthermore, pSJU11 transformed Sz. pombe cells with the same frequency as the pREP2 plasmid. This study is a report to demonstrate practical use of episomal plasmid vectors for genetic research in Sz. japonicus.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Aoki K, Nakajima R, Furuya K, Niki H","authors_abbrev":"Aoki K et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Method or reagent","citation":"Yeast 2010 Dec;27(12):1049-60","cv_annotations":{},"doi":"10.1002/yea.1815","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2010","pubmed_entrez_date":"2010-08-26","pubmed_publication_date":"Dec 2010","terms_by_termid":{},"title":"Novel episomal vectors and a highly efficient transformation procedure for the fission yeast Schizosaccharomyces japonicus.","uniquename":"PMID:20737410"}


id: PMID:20368354
data:
  {"abstract":"Dimorphic yeasts change between unicellular growth and filamentous growth. Many dimorphic yeasts species are pathogenic for humans and plants, being infectious as invasive hypha. We have studied the determinants of the dimorphic switch in the nonpathogenic fission yeast Schizosaccharomyces japonicus, which is evolutionarily close to the well-characterized fission yeast S. pombe. We report that camptothecin, an inhibitor of topoisomerase I, reversibly induced the unicellular to hyphal transition in S. japonicus at low concentrations of camptothecin that did not induce checkpoint arrest and the transition required the DNA checkpoint kinase Chk1. Furthermore, a mutation of chk1 induced hyphal transition without camptothecin. Thus, we identify a second function for Chk1 distinct from its role in checkpoint arrest. Activation of the switch from single cell bipolar growth to monopolar filamentous growth may assist cells to evade the source of DNA damage.","alleles_by_uniquename":{"SJAG_01410:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01410","name":"rad51delta","uniquename":"SJAG_01410:allele-1"},"SJAG_01605:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01605","name":"rad9delta","uniquename":"SJAG_01605:allele-1"},"SJAG_01680:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01680","name":"chk1delta","uniquename":"SJAG_01680:allele-1"},"SJAG_01680:allele-2":{"allele_type":"amino_acid_mutation","description":"P470L","gene_uniquename":"SJAG_01680","name":"chk1-P470L","synonyms":[{"name":"chk1- hyperactive (chk1-hyp)","reference":"PMID:23090706","type":"exact"},{"name":"chk1-hyperactive (chk1-hyp)","reference":"PMID:20368354","type":"exact"}],"uniquename":"SJAG_01680:allele-2"}},"annotation_curators":[{"annotation_count":6,"community_curator":true,"file_name":null,"file_type":null,"name":"Sho Okamoto","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2022-11-21","authors":"Furuya K, Niki H","authors_abbrev":"Furuya K et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2022-11-21 16:35:04","canto_curator_name":"Sho Okamoto","canto_curator_role":"community","canto_first_approved_date":"2022-11-21 16:35:04","canto_session_key":"f81a194894ea8808","canto_session_submitted_date":"2022-11-21 16:34:55","canto_triage_status":"Curatable","citation":"Mol Cell Biol 2010 Jun;30(12):2909-17","cv_annotations":{"single_locus_phenotype":[{"annotations":[114335,114339],"is_not":false,"summary":null,"term":"FYPO:0007782"},{"annotations":[114334],"is_not":false,"summary":null,"term":"FYPO:0007774"},{"annotations":[114336,114337,114338],"is_not":false,"summary":null,"term":"FYPO:0000085"}]},"doi":"10.1128/MCB.00049-10","gene_count":3,"genes_by_uniquename":{"SJAG_01410":null,"SJAG_01605":null,"SJAG_01680":null},"genotypes_by_uniquename":{"chk1-P470L-P470L-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"chk1-P470L(aa)","display_uniquename":"chk1-P470L-P470L-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01680:allele-2","expression":"Not assayed or wild type"}]}]},"chk1delta":{"display_name":"chk1delta","display_uniquename":"chk1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01680:allele-1","expression":"Null"}]}]},"rad51delta":{"display_name":"rad51delta","display_uniquename":"rad51delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01410:allele-1","expression":"Null"}]}]},"rad9delta":{"display_name":"rad9delta","display_uniquename":"rad9delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01605:allele-1","expression":"Null"}]}]}},"ltp_gene_count":3,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2010","pubmed_entrez_date":"2010-04-07","pubmed_publication_date":"Jun 2010","references_by_uniquename":{"PMID:20368354":null,"PMID:23090706":null},"terms_by_termid":{"FYECO:0000005":null,"FYECO:0000137":null,"FYECO:0000314":null,"FYPO:0000085":null,"FYPO:0007774":null,"FYPO:0007782":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null},"title":"The DNA damage checkpoint regulates a transition between yeast and hyphal growth in Schizosaccharomyces japonicus.","uniquename":"PMID:20368354"}


id: PMID:34200466
data:
  {"abstract":"The Rho family of GTPases represents highly conserved molecular switches involved in a plethora of physiological processes. Fission yeast  Schizosaccharomyces pombe  has become a fundamental model organism to study the functions of Rho GTPases over the past few decades. In recent years, another fission yeast species,  Schizosaccharomyces japonicus , has come into focus offering insight into evolutionary changes within the genus. Both fission yeasts contain only six Rho-type GTPases that are spatiotemporally controlled by multiple guanine-nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs), and whose intricate regulation in response to external cues is starting to be uncovered. In the present review, we will outline and discuss the current knowledge and recent advances on how the fission yeasts Rho family GTPases regulate essential physiological processes such as morphogenesis and polarity, cellular integrity, cytokinesis and cellular differentiation.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Vicente-Soler J, Soto T, Franco A, Cansado J, Madrid M","authors_abbrev":"Vicente-Soler J et al.","canto_added_date":"2023-05-04 00:40:04","canto_curator_role":"JaponicusDB","canto_triage_status":"Review or comment","citation":"Cells 2021 Jun 07;10(6)","cv_annotations":{},"doi":"10.3390/cells10061422","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2021","pubmed_entrez_date":"2021-07-02","pubmed_publication_date":"07 Jun 2021","terms_by_termid":{},"title":"The Multiple Functions of Rho GTPases in Fission Yeasts.","uniquename":"PMID:34200466"}


id: PMID:7166567
data:
  {"abstract":"The fine structure of ascospore formation in the fission yeasts Schizosaccharomyces pombe and Schizosaccharomyces japonicus var. japonicus was studied by serial thin-sectioning and electron microscopy. The morphogenetic events were almost the same in both species. Ascospore development was initiated by the formation of the forespore membrane on the cytoplasmic side of the differentiated nucleus-associated organelle (NAO) in the interval between meiosis I and II in S. pombe, or during the post-meiotic nuclear division in S. japonicus, and the process proceeded almost synchronously through the two or four nuclei in the ascus. The forespore membrane developed by fusion of the cytoplasmic vesicles and this was clearly demonstrated in S. japonicus where the behaviour of vesicles involved in the forespore membrane development could be traced as they were marked by the presence of electron-dense granules. The staining technique, by phosphotungustic acid--chromic acid (PTA-CA) after treatment with periodic acid, was used to attempt to elucidate the origin and the nature of the forespore membrane. The method specific to plasmalemma-type membranes stained both ascus and ascospore plasmalemmas; the forespore membrane was not stained at first but developed the same affinity for stain as the plasma membrane in the course of ascospore development. The results suggest that the forespore membrane did not come directly from the ascus plasma membrane, but from another membrane system such as the endoplasmic reticulum. Spore wall material was deposited in the space between the inner and outer leaflets of the forespore membrane.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Tanaka K, Hirata A","authors_abbrev":"Tanaka K et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"J Cell Sci 1982 Aug;56:263-79","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1982","pubmed_entrez_date":"1982-08-01","pubmed_publication_date":"Aug 1982","terms_by_termid":{},"title":"Ascospore development in the fission yeasts Schizosaccharomyces pombe and S. japonicus.","uniquename":"PMID:7166567"}


id: PMID:28733412
data:
  {"abstract":"Genomic sequencing data and morphological properties demonstrate evolutionary relationships among groups of the fission yeast,  Schizosaccharomyces  Phylogenetically,  S. japonicus  is the furthest removed from other species of fission yeast. The basic characteristics of cell proliferation are shared among all fission yeast, including the process of binary fission during vegetative growth, conjugation and karyogamy with horsetail movement, mating-type switching, and sporulation. However,  S. japonicus  also exhibits characteristics that are unique to filamentous fungi.  S. japonicus  is a nonpathogenic yeast that exhibits dimorphism. Depending on the environmental conditions,  S. japonicus  transforms from yeast cells into filamentous cells (hyphae), and blue light triggers synchronous septation of hyphal cells. A rough version of the whole-genome sequence is now available, facilitating genetic manipulation of  S. japonicus.  Furthermore, the extensive genetic knowledge available for  S. pombe  is aiding the development of genetic tools for analyzing  S. japonicus. S. japonicus  will help shed light on the evolutionary relationships among the fission yeast.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Aoki K, Furuya K, Niki H","authors_abbrev":"Aoki K et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Review or comment","citation":"Cold Spring Harb Protoc 2017 Dec 01;2017(12):pdb.top082651","cv_annotations":{},"doi":"10.1101/pdb.top082651","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2017","pubmed_entrez_date":"2017-07-23","pubmed_publication_date":"01 Dec 2017","terms_by_termid":{},"title":" Schizosaccharomyces japonicus : A Distinct Dimorphic Yeast among the Fission Yeasts.","uniquename":"PMID:28733412"}


id: GO_REF:0000107
data:
  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