# refs

id: PMID:23337086
data:
  {"abstract":"During meiosis, chromosomes adopt a bouquet arrangement, which is widely conserved among eukaryotes. This arrangement is assumed to play an important role in the normal progression of meiosis, by mediating the proper pairing of homologous chromosomes. In Schizosaccharomyces pombe, the complex of Bqt1 and Bqt2 plays a key role in telomere clustering and the subsequent bouquet arrangement of chromosomes during early meiotic prophase. Bqt1 and Bqt2 are part of a multi-protein complex that mediates the attachment of the telomere to the nuclear membrane. However, the structural details of the complex are needed to clarify the mechanism of telomere clustering. To enable biophysical studies of Bqt1 and Bqt2, we established a purification procedure for the Schizosaccharomyces japonicus Bqt1-Bqt2 complex, which is closely related to the S. pombe Bqt1-Bqt2 complex. A co-expression vector, in which one of the expressed subunits is fused to a removable SUMO tag, yielded high amounts of the proteins in the soluble fraction. The solubility of the Bqt1-Bqt2 complex after the removal of the SUMO tag was maintained by including CHAPS, a nondenaturing, zwitterionic detergent, in the purification buffers. These procedures enabled us to rapidly purify the stable Bqt1-Bqt2 complex. The co-purified Bqt1 and Bqt2 proteins formed a stable heterodimer, consistent with results from in vivo studies showing the requirement of both proteins for the bouquet arrangement. The expression and purification procedures established here will facilitate further biophysical studies of the Bqt1-Bqt2 complex.","alleles_by_uniquename":{},"annotation_curators":[{"annotation_count":2,"community_curator":false,"file_name":null,"file_type":null,"name":"Val Wood","orcid":"0000-0001-6330-7526"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-05-12","authors":"Ichikawa Y, Kagawa W, Saito K, Chikashige Y, Haraguchi T, Hiraoka Y, Kurumizaka H","authors_abbrev":"Ichikawa Y et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-05-12 14:11:00","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Val Wood","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-05-12 14:11:00","canto_session_key":"34571f3accd180c4","canto_session_submitted_date":"2021-05-11 18:50:05","canto_triage_status":"Curatable","citation":"Protein Expr Purif 2013 Apr;88(2):207-13","cv_annotations":{"molecular_function":[{"annotations":[115492,115493],"is_not":false,"summary":null,"term":"GO:0005515"}]},"doi":"10.1016/j.pep.2013.01.006","gene_count":2,"genes_by_uniquename":{"SJAG_03287":null,"SJAG_05260":null},"genotypes_by_uniquename":{},"ltp_gene_count":2,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[{"evidence":"Co-purification","gene_uniquename":"SJAG_03287","interactor_uniquename":"SJAG_05260","reference_uniquename":"PMID:23337086","throughput":"low"}],"publication_year":"2013","pubmed_entrez_date":"2013-01-23","pubmed_publication_date":"Apr 2013","terms_by_termid":{"GO:0005515":null},"title":"Purification and characterization of the fission yeast telomere clustering factors, Bqt1 and Bqt2.","uniquename":"PMID:23337086"}


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: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_approver_orcid":"0000-0002-8138-6851","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":[115667,115671],"is_not":false,"summary":null,"term":"FYPO:0007782"},{"annotations":[115666],"is_not":false,"summary":null,"term":"FYPO:0007774"},{"annotations":[115668,115669,115670],"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:12402243
data:
  {"abstract":"The structure and localization of the microtubule organization centres (MTOCs) of the fission yeast Schizosaccharomyces japonicus var. japonicus were examined by fluorescence microscopy and electron microscopy. Spindle pole bodies (SPBs), which are the fungal equivalent of centrosomes, of Sz. japonicus were visualized by immunofluorescent staining using a monoclonal anti-gamma-tubulin antibody. The behaviour of the SPBs during the cell cycle mostly coincided with previous reports on the most widely used fission yeast Schizosaccharomyces pombe. We cloned the gamma-tubulin gene from Sz. japonicus by PCR using redundant sets of primers corresponding to conserved regions of known gamma-tubulins. The predicted amino acid sequence of Sz. japonicus gamma-tubulin was most similar to the Sz. pombe gamma-tubulin. Under the electron microscope, the SPBs of Sz. japonicus were detected as electron-dense multilayered structures located just outside the nuclear envelope. The SPBs of Sz. japonicus were composed of three electron-dense layers and were surrounded by fuzzy material. Each layer showed structural changes according to the progression of the cell cycle. In mitotic cells, the SPBs were located on the fenestrae of the nuclear envelopes through which the mitotic spindle microtubules ran into the nucleoplasm. Our results show that Sz. japonicus is a very potent and attractive organism for the investigation of the microtubule nucleation system and morphogenesis in yeasts. The Accession No. for the nucleotide sequence of the Sz. japonicus gtb1(+) gene is AF159163.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Horio T, Kimura N, Basaki A, Tanaka Y, Noguchi T, Akashi T, Tanaka K","authors_abbrev":"Horio T et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Sequence feature or region","citation":"Yeast 2002 Nov;19(15):1335-50","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":"2002-10-29","pubmed_publication_date":"Nov 2002","terms_by_termid":{},"title":"Molecular and structural characterization of the spindle pole bodies in the fission yeast Schizosaccharomyces japonicus var japonicus.","uniquename":"PMID:12402243"}


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: GO_REF:0000085
data:
  {"abstract":"We have created a standard template for classes describing the apoptotic process for a cell type as a biological process. The underlying equivalence axiom template is \"'apoptotic process' and 'occurs in' some C\", where C is a native cell (CL:0000003).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of cell apoptotic process as biological process in the Gene Ontology","uniquename":"GO_REF:0000085"}


id: GO_REF:0000078
data:
  {"abstract":"We have created a standard template for classes describing the transport or vesicle-mediated transport of a chemical entity (ChEBI) from and/or to a cellular component as a biological process. The underlying equivalence axiom templates are \"GO:0006810 and 'transports or maintains localization of' some X [ and 'has_target_start_location' some F] [ and 'has_target_end_location' some T]\" (transport) and \"GO:0016192 and 'transports or maintains localization of' some X [ and 'has_target_start_location' some F] [ and 'has_target_end_location' some T]\" (vesicle-mediated transport), where F and T are cellular components and X is a chemical entity (CHEBI:24431). The approach to combine GO and ChEBI has been described in the following publication: PMID:23895341.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation for the transport or vesicle-mediated transport of a chemical from and/or to a cell component as biological process in the Gene Ontology","uniquename":"GO_REF:0000078"}


id: GO_REF:0000022
data:
  {"abstract":"GO terms describing processes, functions, and cellular components related to the immune system have existed in the GO from its beginning and been used extensively in the annotation of gene products. However, particularly in the biological process ontology, the initial set of terms relating to immunology failed to cover the breadth of known immunological processes, and in many cases diverged from current usage and understanding in their names, definitions, and ontological placement. As part of a larger effort to improve the representation of immunology in the GO, a GO Content Meeting was held November 15-16, 2005, at The Institute for Genomic Research, to discuss improvements to representation of immunology in the biological process ontology of the GO. As a result of the meeting, a number of high level terms for immunological processes were created, an overall structure for immunologically related terms was established, and certain existing terms were renamed or redefined as well to bring them in line with current usage.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Alison Deckhut Augustine (1), Alan Collmer (2), Judith A. Blake (3, 4), Candace W. Collmer (2, 3), Shane C. Burgess (5), Lindsay Grey Cowell (6), Jennifer I. Clark (3, 7), Bernard de Bono (7), Russell T. Collins (8), Alexander D. Diehl (3, 4), Michelle Gwinn Giglio (3, 9), Jamie A. Lee (10), Linda Hannick (3, 9), Jane Lomax (3, 7), Midori A. Harris (3, 7), Christopher J. Mungall (3, 11), David P. Hill (3, 4), Richard H. Scheuermann (10), Amelia Ireland (3, 7), Alessandro Sette (12) (1. NIAID, 2. Cornell University, 3. The GO Consortium, 4. Mouse Genome Informatics, 5. Mississippi State University, 6. Duke University, 7. EMBL-EBI, 8. University of Cambridge, 9. The Institute for Genomic Research, 10. U.T. Southwestern Medical Center, 11. HHMI, 12. La Jolla Institute for Allergy and Immunology)","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Improving the representation of immunology in the biological process Ontology","uniquename":"GO_REF:0000022"}


id: GO_REF:0000095
data:
  {"abstract":"This article is not referenced in PubMed. Please see contributing data resource for details.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Mouse Genome Informatics scientific curators and FlyBase","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Literature reference not indexed by PubMed","uniquename":"GO_REF:0000095"}


id: GO_REF:0000084
data:
  {"abstract":"We have created a standard template for classes describing the structural organization of a plant structure as a biological process. The underlying equivalence axiom template is \"'anatomical structure arrangement' and 'results in structural organization of' some P\", where P is a plant anatomical entity (PO:0025131).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of plant structural organization as biological process in the Gene Ontology","uniquename":"GO_REF:0000084"}


id: GO_REF:0000076
data:
  {"abstract":"We have created a standard template for classes describing the transport or vesicle-mediated transport from cellular component to cellular component as a biological process. The underlying equivalence axiom templates are \"GO:0006810 and 'has_target_start_location' some F and 'has_target_end_location' some T\" (transport) and \"GO:0016192 and 'has_target_start_location' some F and 'has_target_end_location' some T\" (vesicle-mediated transport), where F and T are a cellular components.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of transport or vesicle-mediated transport from cell component to cell component as biological process in the Gene Ontology","uniquename":"GO_REF:0000076"}


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: GO_REF:0000058
data:
  {"abstract":"We have created a standard template for the definition of classes for the regulation of a biological process. This includes the definitions for positive and negative regulation. The equivalence axiom templates are \"GO:0065007 and 'regulates' some X\" (regulation), \"GO:0065007 and 'negatively_regulates' some X\" (negative regulation), and \"GO:0065007 and 'positively_regulates' some X\" (positive regulation), where X is a biological process.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of regulation in the Gene Ontology (biological process) ","uniquename":"GO_REF:0000058"}


id: GO_REF:0000004
data:
  {"abstract":"Transitive assignments using UniProtKB keywords. The UniProtKB keyword controlled vocabulary has been created and used by the UniProt Knowledgebase (UniProtKB) to supply 10 different categories of information to UniProtKB entries. Further information on the UniProtKB keyword resource can be found at http://www.uniprot.org/docs/keywlist. <br>Further information on the UniProt annotation methods is available at  https://www.uniprot.org/help/manual_curation and https://www.uniprot.org/help/automatic_annotation.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GOA curators","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Comments","uniquename":"GO_REF:0000004"}


id: GO_REF:0000066
data:
  {"abstract":"We have created a standard template for classes describing the transport of a chemical entity (ChEBI) as a molecular function. The underlying equivalence axiom template is \"GO:0005215 and 'transports or maintains localization of' some X\", where X is a chemical entity (CHEBI:24431). The approach to combine GO and ChEBI has been described in the following publication: PMID:23895341.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of transport of a chemical entity as molecular function in the Gene Ontology","uniquename":"GO_REF:0000066"}


id: GO_REF:0000063
data:
  {"abstract":"We have created a standard template for classes describing processes regulated by other regulating processes. The underlying equivalence axiom template is \"R and 'results_in' some P\", where R is a biological process and P is a regulation of biological process subclass.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of processes regulated by other regulating processes in the Gene Ontology","uniquename":"GO_REF:0000063"}


id: PMID:22641476
data:
  {"abstract":"Measuring relative genetic distances is one of the best ways to locate genetic loci. Here we report the construction of a strains set for genetic mapping in Schizosaccharomyces japonicus, which belongs to the genus Schizosaccharomyces together with the well-studied fission yeast Sz. pombe. We constructed 29 strains that bear a positive-negative selection marker at different loci. The marker was inserted every 500 kb in the genome of Sz. japonicus. Each marker thus becomes a 'scale mark' of a chromosome that behaves like a yardstick. By determining the genetic distances from the inserted markers, the relative location of a genomic mutation can be determined. We also constructed a fosmid library that covers an entire genome of Sz. japonicus. These tools together would facilitate identification and cloning of the gene.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Furuya K, Aoki K, Niki H","authors_abbrev":"Furuya K et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Method or reagent","citation":"Yeast 2012 Jun;29(6):241-9","cv_annotations":{},"doi":"10.1002/yea.2907","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2012","pubmed_entrez_date":"2012-05-30","pubmed_publication_date":"Jun 2012","terms_by_termid":{},"title":"Construction of an insertion marker collection of Sz. japonicus (IMACS) for genetic mapping and a fosmid library covering its genome.","uniquename":"PMID:22641476"}


id: PMID:34251689
data:
  {"abstract":"The polymerase chain reaction (PCR)-based gene targeting method, which can delete a specific gene or introduce tags, has been widely utilized to study gene function in fission yeast. One of the critical steps in this method is to design primers for amplifying DNA fragments of deletion or tagging modules and for checking the integration of those DNA fragments at designated loci. Although the primer design tool Pombe PCR Primer Program (PPPP) is available for Schizosaccharomyces pombe, there is no such publicly available application for the other three fission yeast species, S. cryophilus, S. japonicus, and S. octosporus. Likewise, no application enabling DNA/protein sequence retrieval for these three fission yeast species is available either. Therefore, access to such functionality would substantially assist in retrieval of gene sequences of interest and primer design in these fission yeast species. In this report, we describe two applications for fission yeast study: Yesprit and Yeaseq. Yesprit is a primer design tool for strain construction using the PCR-based method, and Yeaseq is a sequence viewer that can acquire the DNA/protein sequences of specific genes. Both tools can be run on the Windows, macOS, and Linux platforms. We believe that the Yesprit and Yeaseq will facilitate research using the four fission yeast species.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Wang X, Xu R, Wang Y, Liu Z, Lou R, Sugiyama T","authors_abbrev":"Wang X et al.","canto_added_date":"2023-05-04 00:40:04","canto_curator_role":"JaponicusDB","canto_triage_status":"Method or reagent","citation":"Yeast 2021 Nov;38(11):583-591","cv_annotations":{},"doi":"10.1002/yea.3660","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":"2021-07-12","pubmed_publication_date":"Nov 2021","terms_by_termid":{},"title":"Yesprit and Yeaseq: Applications for designing primers and browsing sequences for research using the four Schizosaccharomyces species.","uniquename":"PMID:34251689"}


id: PMID:28733403
data:
  {"abstract":"This protocol describes the use of electroporation to transform  Schizosaccharomyces japonicus  with plasmids or linear DNA. Plasmids are helpful for the complementation testing of mutations and for the expression of specific genes. Linear DNA fragments integrated into chromosomal DNA by homologous recombination are useful for gene deletion or to fuse a gene with a tag sequence (e.g., encoding a fluorescent protein). To introduce DNA into  S. japonicus , electroporation methods are recommended because  S. japonicus  is sensitive to lithium acetate (LiOAc).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Aoki 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":"Cold Spring Harb Protoc 2017 Dec 01;2017(12):pdb.prot091850","cv_annotations":{},"doi":"10.1101/pdb.prot091850","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":"Transformation of  Schizosaccharomyces japonicus .","uniquename":"PMID:28733403"}


id: PMID:34427722
data:
  {"abstract":"Fungal pathogens, from phytopathogenic fungus to human pathogens, are able to alternate between the yeast-like form and filamentous forms. This morphological transition (dimorphism) is in close connection with their pathogenic lifestyles and with their responses to changing environmental conditions. The mechanisms governing these morphogenetic conversions are still not fully understood. Therefore, we studied the filamentous growth of the less-known, non-pathogenic dimorphic fission yeast, S. japonicus, which belongs to an ancient and early evolved branch of the Ascomycota. Its RNA sequencing revealed that several hundred genes were up- or down-regulated in the hyphae compared to the yeast-phase cells. These genes belonged to different GO categories, confirming that mycelial growth is a rather complex process. The genes of transport- and metabolic processes appeared especially in high numbers among them. High expression of genes involved in glycolysis and ethanol production was found in the hyphae, while other results pointed to the regulatory role of the protein kinase A (PKA) pathway. The homologues of 49 S. japonicus filament-associated genes were found by sequence alignments also in seven distantly related dimorphic and filamentous species. The comparative genomic analyses between S. japonicus and the closely related but non-dimorphic S. pombe shed some light on the differences in their genomes. All these data can contribute to a better understanding of hyphal growth and those genomic rearrangements that underlie it.","alleles_by_uniquename":{},"annotation_curators":[{"annotation_count":2,"community_curator":true,"file_name":null,"file_type":null,"name":"Ida Miklos","orcid":"0000-0002-7074-4019"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-10-06","authors":"Papp LA, Ács-Szabó L, Batta G, Miklós I","authors_abbrev":"Papp LA et al.","canto_added_date":"2021-09-29 13:11:40","canto_annotation_status":"APPROVED","canto_approved_date":"2021-10-06 13:34:09","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Ida Miklos","canto_curator_role":"community","canto_first_approved_date":"2021-10-06 13:34:09","canto_session_key":"acb5c82405799ef1","canto_session_submitted_date":"2021-09-29 13:38:18","canto_triage_status":"Curatable","citation":"Curr Genet 2021 Dec;67(6):953-968","cv_annotations":{"biological_process":[{"annotations":[115487,115488],"is_not":false,"summary":null,"term":"GO:0030448"}]},"doi":"10.1007/s00294-021-01206-y","gene_count":2,"genes_by_uniquename":{"SJAG_00124":null,"SJAG_04312":null},"genotypes_by_uniquename":{},"ltp_gene_count":2,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2021","pubmed_entrez_date":"2021-08-24","pubmed_publication_date":"Dec 2021","terms_by_termid":{"GO:0030448":null},"title":"Molecular and comparative genomic analyses reveal evolutionarily conserved and unique features of the Schizosaccharomyces japonicus mycelial growth and the underlying genomic changes.","uniquename":"PMID:34427722"}


id: GO_REF:0000051
data:
  {"abstract":"Keywords derived from manually curated primary annotation, e.g. gene product descriptions, are mapped to GO terms. Annotations made by this method have the evidence code Non-traceable Author Statement (NAS), and are filtered from the PomBase annotation files wherever another annotation exists that is equally or more specific, and supported by experimental or manually evaluated comparative evidence (such as ISS and its subtypes). Formerly GOC:pombekw2GO.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"PomBase curators","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"S. pombe keyword mapping","uniquename":"GO_REF:0000051"}


id: PMID:35359202
data:
  {"abstract":"The fission yeast genus Schizosaccharomyces contains important model organisms for biological research. In particular, S. pombe is a widely used model eukaryote. So far little is known about the natural and artificial habitats of species in this genus. Finding out where S. pombe and other fission yeast species occur and how they live in their habitats can promote better understanding of their biology. Here we investigate in which substrates S. pombe, S. octosporus, S. osmophilus and S. japonicus are present. To this end about 2100 samples consisting of soil, tree sap fluxes, fresh fruit, dried fruit, honey, cacao beans, molasses and other substrates were analyzed. Effective isolation methods that allow efficient isolation of the above mentioned species were developed. Based on the frequency of isolating different fission yeast species in various substrates and on extensive literature survey, conclusions are drawn on their ecology. The results suggest that the primary habitat of S. pombe and S. octosporus is honeybee honey. Both species were also frequently detected on certain dried fruit like raisins, mango or pineapple to which they could be brought by the honey bees during ripening or during drying. While S. pombe was regularly isolated from grape mash and from fermented raw cacao beans S. octosporus was never isolated from fresh fruit. The main habitat of S. osmophilus seems to be solitary bee beebread. It was rarely isolated from raisins. S. japonicus was mainly found in forest substrates although it occurs on fruit and in fruit fermentations, too.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Brysch-Herzberg M, Jia GS, Seidel M, Assali I, Du LL","authors_abbrev":"Brysch-Herzberg M et al.","canto_added_date":"2023-05-04 00:40:04","canto_curator_role":"JaponicusDB","canto_triage_status":"Phylogeny and evolutionary studies","citation":"Antonie Van Leeuwenhoek 2022 May;115(5):661-695","cv_annotations":{},"doi":"10.1007/s10482-022-01720-0","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":"2022-04-01","pubmed_publication_date":"May 2022","terms_by_termid":{},"title":"Insights into the ecology of Schizosaccharomyces species in natural and artificial habitats.","uniquename":"PMID:35359202"}


id: PMID:27697163
data:
  {"abstract":"The present work demonstrates that yeasts belonging to the Schizosaccharomyces genus release a high quantity of polysaccharides of cell wall origin starting from the onset of the alcoholic fermentation. By the end of the alcoholic fermentation, all of the Schizosaccharomyces yeast strains released a quantity of polysaccharides approximately 3-7 times higher than that released by a commercial Saccharomyces cerevisiae yeast strain under the same fermentative conditions of synthetic juice. A higher content of polysaccharide was found in media fermented by Schizosaccharomyces japonicus with respect to that of Schizosaccharomyces pombe. Some of the strains evaluated were also able to produce high levels of pyruvic acid, which has been shown to be an important compound for color stability of wine. The presence of strains with different malic acid consumption patterns along with high polysaccharide release would enable production of naturally modified wines with enhanced mouth feel and reduced acidity. The chemical analysis of the released polysaccharides demonstrated divergence between the two yeast species S. pombe and S. japonicus. A different mannose/galactose ratio and a different percentage of proteins was observed on the polysaccharides released by S. pombe as compared to S. japonicus. Analysis of the proteins released in the media revealed the presence of a glycoprotein with a molecular size around 32-33 kDa only for the species S. japonicus. Mass spectrometry analysis of carbohydrate moieties showed similar proportions among the N-glycan chains released in the media by both yeast species but differences between the two species were also observed. These observations suggest a possible role of rapid MALDI-TOF screening of N-glycans compositional fingerprint as a taxonomic tool for this genus. Polysaccharides release in the media, in particular galactomannoproteins in significant amounts, could make these yeasts particularly interesting also for the industrial production of exogenous polysaccharide preparations.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Domizio P, Liu Y, Bisson LF, Barile D","authors_abbrev":"Domizio P et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"Food Microbiol 2017 Feb;61:136-149","cv_annotations":{},"doi":"10.1016/j.fm.2016.08.010","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":"2016-10-05","pubmed_publication_date":"Feb 2017","terms_by_termid":{},"title":"Cell wall polysaccharides released during the alcoholic fermentation by Schizosaccharomyces pombe and S. japonicus: quantification and characterization.","uniquename":"PMID:27697163"}


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_approver_orcid":"0000-0002-8138-6851","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: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:26457121
data:
  {"abstract":"Transposable elements (TEs) are common constituents of centromeres. However, it is not known what causes this relationship. Schizosaccharomyces japonicus contains 10 families of Long Terminal Repeat (LTR)-retrotransposons and these elements cluster in centromeres and telomeres. In the related yeast, Schizosaccharomyces pombe LTR-retrotransposons Tf1 and Tf2 are distributed in the promoter regions of RNA pol II transcribed genes. Sequence analysis of TEs indicates that Tj1 of S. japonicus is related to Tf1 and Tf2, and uses the same mechanism of self-primed reverse transcription. Thus, we wondered why these related retrotransposons localized in different regions of the genome.\nTo characterize the integration behavior of Tj1 we expressed it in S. pombe. We found Tj1 was active and capable of generating de novo integration in the chromosomes of S. pombe. The expression of Tj1 is similar to Type C retroviruses in that a stop codon at the end of Gag must be present for efficient integration. 17 inserts were sequenced, 13 occurred within 12 bp upstream of tRNA genes and 3 occurred at other RNA pol III transcribed genes. The link between Tj1 integration and RNA pol III transcription is reminiscent of Ty3, an LTR-retrotransposon of Saccharomyces cerevisiae that interacts with TFIIIB and integrates upstream of tRNA genes.\nThe integration of Tj1 upstream of tRNA genes and the centromeric clustering of tRNA genes in S. japonicus demonstrate that the clustering of this TE in centromere sequences is due to a unique pattern of integration.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Guo Y, Singh PK, Levin HL","authors_abbrev":"Guo Y et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Sequence feature or region","citation":"Mob DNA 2015;6:19","cv_annotations":{},"doi":"10.1186/s13100-015-0048-2","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":"2015-10-13","pubmed_publication_date":"2015","terms_by_termid":{},"title":"A long terminal repeat retrotransposon of Schizosaccharomyces japonicus integrates upstream of RNA pol III transcribed genes.","uniquename":"PMID:26457121"}


id: PMID:9611807
data:
  {"abstract":"The fission yeast Schizosaccharomyces pombe shows bipolar growth and is a convenient model for studying cell polarity and polar growth. This paper shows that the related Schiz. japonicus var. japonicus can switch to unipolar growth and can exist in both yeast and mycelial phases. On solid media, the yeast phase is unstable and prone to switch to the mycelial form, which shows unipolar growth by tip elongation. The hyphae can colonize the body of the substrate (true mycelium) or just its surface (pseudo-mycelium). The yeast-to-mycelium transition and the growth of the mycelium are regulated by a nutritional gradient and are associated with extensive vacuolation. The mycelium can convert into arthroconidia or return to the yeast phase in response to environmental changes. These environmentally controlled morphological transitions make Schiz. japonicus var. japonicus an attractive model for the investigation of cell polarity and morphogenesis.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-10-07","authors":"Sipiczki M, Takeo K, Yamaguchi M, Yoshida S, Miklos I","authors_abbrev":"Sipiczki M et al.","canto_added_date":"2021-09-30 08:50:02","canto_annotation_status":"APPROVED","canto_approved_date":"2021-10-07 12:30:26","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-10-07 12:30:26","canto_session_key":"fced61f1377cd206","canto_session_submitted_date":"2021-09-30 08:52:46","canto_triage_status":"Curatable","citation":"Microbiology (Reading) 1998 May;144 ( Pt 5):1319-1330","cv_annotations":{},"doi":"10.1099/00221287-144-5-1319","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":"1998-06-05","pubmed_publication_date":"May 1998","terms_by_termid":{},"title":"Environmentally controlled dimorphic cycle in a fission yeast.","uniquename":"PMID:9611807"}


id: PMID:32915139
data:
  {"abstract":"Cytokinesis, which enables the physical separation of daughter cells once mitosis has been completed, is executed in fungal and animal cells by a contractile actin- and myosin-based ring (CAR). In the fission yeast  Schizosaccharomyces pombe,  the formin For3 nucleates actin cables and also co-operates for CAR assembly during cytokinesis. Mitogen-activated protein kinases (MAPKs) regulate essential adaptive responses in eukaryotic organisms to environmental changes. We show that the stress-activated protein kinase pathway (SAPK) and its effector, MAPK Sty1, downregulates CAR assembly in  S. pombe  when its integrity becomes compromised during cytoskeletal damage and stress by reducing For3 levels. Accurate control of For3 levels by the SAPK pathway may thus represent a novel regulatory mechanism of cytokinesis outcome in response to environmental cues. Conversely, SAPK signaling favors CAR assembly and integrity in its close relative  Schizosaccharomyces japonicus,  revealing a remarkable evolutionary divergence of this response within the fission yeast clade.","alleles_by_uniquename":{"SJAG_00266:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00266","name":"atf1delta","uniquename":"SJAG_00266:allele-1"},"SJAG_02592:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02592","name":"sty1delta","uniquename":"SJAG_02592:allele-1"}},"annotation_curators":[{"annotation_count":5,"community_curator":true,"file_name":null,"file_type":null,"name":"Elisa Gómez Gil","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-05-13","authors":"Gómez-Gil E, Martín-García R, Vicente-Soler J, Franco A, Vázquez-Marín B, Prieto-Ruiz F, Soto T, Pérez P, Madrid M, Cansado J","authors_abbrev":"Gómez-Gil E et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2023-06-24 05:18:12","canto_approver_orcid":"0000-0001-6330-7526","canto_curator_name":"Elisa Gómez Gil","canto_curator_role":"community","canto_first_approved_date":"2021-05-13 16:19:42","canto_session_key":"382ba25ae62a1134","canto_session_submitted_date":"2021-05-13 14:28:51","canto_triage_status":"Curatable","citation":"Elife 2020 09 11;9","cv_annotations":{"PSI-MOD":[{"annotations":[115693],"is_not":false,"summary":null,"term":"MOD:00696"}],"biological_process":[{"annotations":[115694],"is_not":false,"summary":null,"term":"GO:1903499"}],"single_locus_phenotype":[{"annotations":[115692],"is_not":false,"summary":null,"term":"FYPO:0002998"},{"annotations":[115690,115691],"is_not":false,"summary":null,"term":"FYPO:0000107"}]},"doi":"10.7554/eLife.57951","gene_count":2,"genes_by_uniquename":{"SJAG_00266":null,"SJAG_02592":null},"genotypes_by_uniquename":{"atf1delta":{"display_name":"atf1delta","display_uniquename":"atf1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00266:allele-1","expression":"Null"}]}]},"sty1delta":{"display_name":"sty1delta","display_uniquename":"sty1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02592:allele-1","expression":"Null"}]}]}},"ltp_gene_count":2,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2020","pubmed_entrez_date":"2020-09-11","pubmed_publication_date":"11 09 2020","terms_by_termid":{"FYECO:0000137":null,"FYECO:0000248":null,"FYPO:0000107":null,"FYPO:0002998":null,"FYPO_EXT:0000001":null,"GO:0120306":null,"GO:1903499":null,"MOD:00696":null},"title":"Stress-activated MAPK signaling controls fission yeast actomyosin ring integrity by modulating formin For3 levels.","uniquename":"PMID:32915139"}


id: GO_REF:0000061
data:
  {"abstract":"We have created a standard template for classes describing molecular function involved in other biological processes. The underlying equivalence axiom template is \"P and 'part_of' some W\", where P is a molecular function and W is a biological processes.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of a molecular function involved in a biological process in the Gene Ontology","uniquename":"GO_REF:0000061"}


id: GO_REF:0000065
data:
  {"abstract":"We have created a standard template for classes describing transport of a chemical entity (ChEBI) as a biological process. The underlying equivalence axiom template is \"GO:0006810 and 'transports or maintains localization of' some X\", where X is a chemical entity (CHEBI:24431). The approach to combine GO and ChEBI has been described in the following publication: PMID:23895341.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of transport of a chemical entity as a biological process in the Gene Ontology","uniquename":"GO_REF:0000065"}


id: GO_REF:0000021
data:
  {"abstract":"Current genetic and molecular studies in many model organisms are aimed at understanding formation and development of the nervous system. Up until this point, the GO has had a very shallow representation of processes pertaining to the nervous system. In June 2006, curators from MGI and ZFIN met with researchers studying central nervous system development to improve the representation of these processes in GO. In particular, emphasis was placed on three areas that are being addressed actively in current research: forebrain development, hindbrain development and neural tube development. This collaboration resulted in the addition of over 500 terms that reflect the development of the forebrain, the hindbrain, and the neural tube from the perspective of biological process and anatomical structure.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Judith Blake (1, 2), William Bug (3), Rex Chisholm (1, 4), Jennifer Clark (1, 5), Erika Feltrin (6), Jacqueline Finger (2), David Hill (1, 2), Midori Harris (1, 5), Terry Hayamizu (2), Doug Howe (9), Maryanne Martone (7), Kathleen Millen (8), Francis Sele (4) (1. The Gene Ontology Consortium, 2. Mouse Genome Informatics, Bar Harbor, ME, 3. Drexel University, Philadelphia, PA, 4. Northwestern University, Chicago, IL, 5. EMBL-EBI, Hinxton, Cambridgeshire, UK, 6. The University of Padua, Padua, Italy, 7. The University of California at San Diego, San Diego, CA, 8. The University of Chicago, Chicago, IL, 9. The Zebrafish Information Network, University of Oregon, Eugene, OR)","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Improving the representation of central nervous system development in the biological process ontology","uniquename":"GO_REF:0000021"}


id: PMID:22531001
data:
  {"abstract":"DNA replication initiates at distinct origins in eukaryotic genomes, but the genomic features that define these sites are not well understood.\nWe have taken a combined experimental and bioinformatic approach to identify and characterize origins of replication in three distantly related fission yeasts: Schizosaccharomyces pombe, Schizosaccharomyces octosporus and Schizosaccharomyces japonicus. Using single-molecule deep sequencing to construct amplification-free high-resolution replication profiles, we located origins and identified sequence motifs that predict origin function. We then mapped nucleosome occupancy by deep sequencing of mononucleosomal DNA from the corresponding species, finding that origins tend to occupy nucleosome-depleted regions.\nThe sequences that specify origins are evolutionarily plastic, with low complexity nucleosome-excluding sequences functioning in S. pombe and S. octosporus, and binding sites for trans-acting nucleosome-excluding proteins functioning in S. japonicus. Furthermore, chromosome-scale variation in replication timing is conserved independently of origin location and via a mechanism distinct from known heterochromatic effects on origin function. These results are consistent with a model in which origins are simply the nucleosome-depleted regions of the genome with the highest affinity for the origin recognition complex. This approach provides a general strategy for understanding the mechanisms that define DNA replication origins in eukaryotes.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Xu J, Yanagisawa Y, Tsankov AM, Hart C, Aoki K, Kommajosyula N, Steinmann KE, Bochicchio J, Russ C, Regev A, Rando OJ, Nusbaum C, Niki H, Milos P, Weng Z, Rhind N","authors_abbrev":"Xu J et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Sequence feature or region","citation":"Genome Biol 2012 Apr 24;13(4):R27","cv_annotations":{},"doi":"10.1186/gb-2012-13-4-r27","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2012","pubmed_entrez_date":"2012-04-26","pubmed_publication_date":"24 Apr 2012","terms_by_termid":{},"title":"Genome-wide identification and characterization of replication origins by deep sequencing.","uniquename":"PMID:22531001"}


id: GO_REF:0000015
data:
  {"abstract":"Direct annotations to any of the three root terms 'molecular function; GO:0003674', 'biological process; GO:0008150' or 'cellular component; GO:0005575' indicate that curators have found no data supporting an annotation to a more specific term, either in the literature and/or by sequence similarity for this gene or protein as of the date of the annotation.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO Curators","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Use of the ND evidence code for Gene Ontology (GO) terms.","uniquename":"GO_REF:0000015"}


id: PMID:1934083
data:
  {"abstract":"By rhodamine-phalloidin fluorescence, distinct continuous F-actin rings were visualized in 18-20% of the protoplasts of Schizosaccharomyces pombe and S. japonicus var. versatilis, in addition to randomly distributed F-actin dots. Whereas the reversion of ring-lacking protoplasts coincided with the polarization of the dotted F-actin pattern, the ring-containing protoplasts became furrowed as the F-actin rings constricted. The furrowing was more conspicuous in S. japonicus var. versatilis than in S. pombe protoplasts and it was blocked when the reversion was inhibited by Novozyme 234 indicating that the cell wall formation is essential for the F-actin ring constriction.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Jochová J, Rupes I, Streiblová E","authors_abbrev":"Jochová J et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"Cell Biol Int Rep 1991 Jul;15(7):607-10","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1991","pubmed_entrez_date":"1991-07-01","pubmed_publication_date":"Jul 1991","terms_by_termid":{},"title":"F-actin contractile rings in protoplasts of the yeast Schizosaccharomyces.","uniquename":"PMID:1934083"}


id: GO_REF:0000072
data:
  {"abstract":"We have created a standard template for classes describing the homeostasis and cellular homeostasis for a chemical entity (ChEBI) as a biological process. The underlying equivalence axiom templates are \"GO:0048878 and 'regulates level of' some X\" (homeostasis) and \"GO:0055082 and 'regulates level of' some X\" (cellular homeostasis), where X is a chemical entity (CHEBI:24431). The approach to combine GO and ChEBI has been described in the following publication: PMID:23895341.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of chemical homeostasis and cellular chemical homeostasisl as biological process in the Gene Ontology","uniquename":"GO_REF:0000072"}


id: PMID:30664646
data:
  {"abstract":"Cells of a specific cell type may divide within a certain size range. Yet, functionally optimal cellular organization is typically maintained across different cell sizes, a phenomenon known as scaling. The mechanisms underlying scaling and its physiological significance remain elusive. Here we approach this problem by interfering with scaling in the rod-shaped fission yeast Schizosaccharomyces japonicus that relies on cellular geometry cues to position the division site. We show that S. japonicus uses the Cdc42 polarity module to adjust its geometry to changes in the cell size. When scaling is prevented resulting in abnormal cellular length-to-width aspect ratio, cells exhibit severe division site placement defects. We further show that despite the generally accepted view, a similar scaling phenomenon can occur in the sister species, Schizosaccharomyces pombe. Our results demonstrate that scaling is required for normal cell function and delineate possible rules for cellular geometry maintenance in populations of proliferating cells.","alleles_by_uniquename":{"SJAG_00028:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00028","name":"rga6delta","uniquename":"SJAG_00028:allele-1"},"SJAG_00514:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00514","name":"scd1delta","uniquename":"SJAG_00514:allele-1"},"SJAG_03048:allele-1":{"allele_type":"amino_acid_mutation","description":"G146D","gene_uniquename":"SJAG_03048","name":"cdc2-1w","uniquename":"SJAG_03048:allele-1"},"SJAG_03581:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03581","name":"gef1delta","uniquename":"SJAG_03581:allele-1"},"SJAG_04280:allele-1":{"allele_type":"amino_acid_mutation","description":"T582G","gene_uniquename":"SJAG_04280","name":"wee1-as8","uniquename":"SJAG_04280:allele-1"},"SJAG_04280:allele-2":{"allele_type":"amino_acid_mutation","description":"G788E","gene_uniquename":"SJAG_04280","name":"wee1-G788E","uniquename":"SJAG_04280:allele-2"},"SJAG_04522:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04522","name":"rga4delta","uniquename":"SJAG_04522:allele-1"}},"annotation_curators":[{"annotation_count":3,"community_curator":false,"file_name":null,"file_type":null,"name":"Val Wood","orcid":"0000-0001-6330-7526"},{"annotation_count":22,"community_curator":true,"file_name":null,"file_type":null,"name":"Ying Gu","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-07-02","authors":"Gu Y, Oliferenko S","authors_abbrev":"Gu Y et al.","canto_added_date":"2021-05-10 02:37:31","canto_annotation_status":"APPROVED","canto_approved_date":"2021-09-01 07:53:28","canto_approver_orcid":"0000-0001-6330-7526","canto_curator_name":"Ying Gu","canto_curator_role":"community","canto_first_approved_date":"2021-07-02 12:32:27","canto_session_key":"0922e2a5229110bd","canto_session_submitted_date":"2021-06-30 22:18:13","canto_triage_status":"Curatable","citation":"Nat Commun 2019 01 21;10(1):268","cv_annotations":{"biological_process":[{"annotations":[115315],"is_not":false,"summary":null,"term":"GO:0061171"},{"annotations":[115316,115317],"is_not":false,"summary":null,"term":"GO:0008360"}],"multi_locus_phenotype":[{"annotations":[115303,115308],"is_not":false,"summary":null,"term":"FYPO:0007783"},{"annotations":[115314],"is_not":false,"summary":null,"term":"FYPO:0004105"},{"annotations":[115305],"is_not":false,"summary":null,"term":"FYPO:0001369"},{"annotations":[115307],"is_not":false,"summary":null,"term":"FYPO:0004293"}],"single_locus_phenotype":[{"annotations":[115309],"is_not":false,"summary":null,"term":"FYPO:0000198"},{"annotations":[115310,115311,115313],"is_not":false,"summary":null,"term":"FYPO:0005503"},{"annotations":[115304],"is_not":false,"summary":null,"term":"FYPO:0007783"},{"annotations":[115298],"is_not":false,"summary":null,"term":"FYPO:0004105"},{"annotations":[115312],"is_not":false,"summary":null,"term":"FYPO:0002870"},{"annotations":[115306],"is_not":false,"summary":null,"term":"FYPO:0001369"},{"annotations":[115299],"is_not":false,"summary":null,"term":"FYPO:0001234"},{"annotations":[115293,115294,115297],"is_not":false,"summary":null,"term":"FYPO:0000648"},{"annotations":[115295,115296,115302],"is_not":false,"summary":null,"term":"FYPO:0001877"},{"annotations":[115300,115301],"is_not":false,"summary":null,"term":"FYPO:0006616"}]},"doi":"10.1038/s41467-018-08218-2","gene_count":8,"genes_by_uniquename":{"SJAG_00028":null,"SJAG_00030":null,"SJAG_00514":null,"SJAG_01794":null,"SJAG_03048":null,"SJAG_03581":null,"SJAG_04280":null,"SJAG_04522":null},"genotypes_by_uniquename":{"cdc2-1w-G146D-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"cdc2-1w(G146D aa)","display_uniquename":"cdc2-1w-G146D-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03048:allele-1","expression":"Not assayed or wild type"}]}]},"gef1delta":{"display_name":"gef1delta","display_uniquename":"gef1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03581:allele-1","expression":"Null"}]}]},"rga4delta":{"display_name":"rga4delta","display_uniquename":"rga4delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04522:allele-1","expression":"Null"}]}]},"rga4delta__rga6delta":{"display_name":"rga4delta rga6delta","display_uniquename":"rga4delta__rga6delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04522:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_00028:allele-1","expression":"Null"}]}]},"rga4delta__wee1-G788E-G788E-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"rga4delta wee1-G788E(aa)","display_uniquename":"rga4delta__wee1-G788E-G788E-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04522:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_04280:allele-2","expression":"Not assayed or wild type"}]}]},"rga4delta__wee1-as8-T582G-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"rga4delta wee1-as8(T582G aa)","display_uniquename":"rga4delta__wee1-as8-T582G-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04522:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_04280:allele-1","expression":"Not assayed or wild type"}]}]},"rga6delta":{"display_name":"rga6delta","display_uniquename":"rga6delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00028:allele-1","expression":"Null"}]}]},"rga6delta__wee1-as8-T582G-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"rga6delta wee1-as8(T582G aa)","display_uniquename":"rga6delta__wee1-as8-T582G-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00028:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_04280:allele-1","expression":"Not assayed or wild type"}]}]},"scd1delta":{"display_name":"scd1delta","display_uniquename":"scd1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00514:allele-1","expression":"Null"}]}]},"wee1-G788E-G788E-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"wee1-G788E(aa)","display_uniquename":"wee1-G788E-G788E-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04280:allele-2","expression":"Not assayed or wild type"}]}]},"wee1-as8-T582G-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"wee1-as8(T582G aa)","display_uniquename":"wee1-as8-T582G-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04280:allele-1","expression":"Not assayed or wild type"}]}]}},"ltp_gene_count":6,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2019","pubmed_entrez_date":"2019-01-22","pubmed_publication_date":"21 01 2019","terms_by_termid":{"FYECO:0000004":null,"FYECO:0000005":null,"FYECO:0000006":null,"FYECO:0000103":null,"FYECO:0000126":null,"FYECO:0000137":null,"FYECO:0000338":null,"FYPO:0000198":null,"FYPO:0000648":null,"FYPO:0001234":null,"FYPO:0001369":null,"FYPO:0001877":null,"FYPO:0002870":null,"FYPO:0004105":null,"FYPO:0004293":null,"FYPO:0005503":null,"FYPO:0006616":null,"FYPO:0007783":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null,"GO:0008360":null,"GO:0061171":null},"title":"Cellular geometry scaling ensures robust division site positioning.","uniquename":"PMID:30664646"}


id: PMID:33791858
data:
  {"abstract":"Mitogen-activated protein kinase (MAPK) signalling pathways regulate multiple cellular functions in eukaryotic organisms in response to environmental cues, including the dynamic remodeling of the actin cytoskeleton. The fission yeast S. pombe is an optimal model to investigate the conserved regulatory mechanisms of cytokinesis, which relies in an actomyosin-based contractile ring (CAR) that prompts the physical separation of daughter cells during cellular division. Our group has recently shown that p38 MAPK ortholog Sty1, the core component of the stress-activated pathway (SAPK), negatively modulates CAR assembly and integrity in S. pombe during actin cytoskeletal damage induced with Latrunculin A and in response to environmental stress. This response involves downregulation of protein levels of the formin For3, which assembles actin filaments for cables and the CAR, likely through an ubiquitin-mediated degradation mechanism. Contrariwise, Sty1 function positively reinforces CAR assembly during stress in the close relative dimorphic fission yeast S. japonicus. The opposite effect of SAPK signaling on CAR integrity may represent an evolutionary refined adaptation to cope with the marked differences in cytokinesis onset in both fission yeast species.","alleles_by_uniquename":{"SJAG_00266:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00266","name":"atf1delta","uniquename":"SJAG_00266:allele-1"},"SJAG_02592:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02592","name":"sty1delta","uniquename":"SJAG_02592:allele-1"}},"annotation_curators":[{"annotation_count":4,"community_curator":true,"file_name":null,"file_type":null,"name":"Elisa Gómez Gil","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-09-14","authors":"Madrid M, Gómez-Gil E, Cansado J","authors_abbrev":"Madrid M et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-09-14 21:24:28","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Elisa Gómez Gil","canto_curator_role":"community","canto_first_approved_date":"2021-09-14 21:24:28","canto_session_key":"84ac20b0ff20a3cd","canto_session_submitted_date":"2021-09-14 16:45:32","canto_triage_status":"Curatable","citation":"Curr Genet 2021 Oct;67(5):715-721","cv_annotations":{"PSI-MOD":[{"annotations":[115335],"is_not":false,"summary":null,"term":"MOD:00696"}],"single_locus_phenotype":[{"annotations":[115334],"is_not":false,"summary":null,"term":"FYPO:0002998"},{"annotations":[115332,115333],"is_not":false,"summary":null,"term":"FYPO:0000107"}]},"doi":"10.1007/s00294-021-01155-6","gene_count":2,"genes_by_uniquename":{"SJAG_00266":null,"SJAG_02592":null},"genotypes_by_uniquename":{"atf1delta":{"display_name":"atf1delta","display_uniquename":"atf1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00266:allele-1","expression":"Null"}]}]},"sty1delta":{"display_name":"sty1delta","display_uniquename":"sty1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02592:allele-1","expression":"Null"}]}]}},"ltp_gene_count":2,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2021","pubmed_entrez_date":"2021-04-01","pubmed_publication_date":"Oct 2021","terms_by_termid":{"FYECO:0000248":null,"FYPO:0000107":null,"FYPO:0002998":null,"FYPO_EXT:0000001":null,"GO:0120306":null,"MOD:00696":null},"title":"Negative control of cytokinesis by stress-activated MAPK signaling.","uniquename":"PMID:33791858"}


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:32243490
data:
  {"abstract":"The nuclear envelope (NE) undergoes dynamic remodeling to maintain NE integrity, a process involving the inner nuclear membrane protein LEM2 recruiting CHMP7/Cmp7 and then ESCRT-III. However, prior work has hinted at CHMP7/ESCRT-independent mechanisms. To identify such mechanisms, we studied NE assembly in Schizosaccharomyces japonicus, a fission yeast that undergoes partial mitotic NE breakdown and reassembly. S. japonicus cells lacking Cmp7 have compromised NE sealing after mitosis but are viable. A genetic screen identified mutations that promote NE integrity in cmp7Δ cells. Unexpectedly, loss of Lem2 or its interacting partner Nur1 suppressed cmp7Δ defects. In the absence of Cmp7, Lem2 formed aggregates that appear to interfere with ESCRT-independent NE sealing. A gain-of-function mutation implicated a membrane and ESCRT-III regulator, Alx1, in this alternate pathway. Additional results suggest a potentially general role for unsaturated fatty acids in NE integrity. These findings establish the existence of mechanisms for NE sealing independent of the canonical ESCRT pathway.","alleles_by_uniquename":{"SJAG_01242:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01242","name":"vps32delta","uniquename":"SJAG_01242:allele-1"},"SJAG_01745:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01745","name":"lem2delta","uniquename":"SJAG_01745:allele-1"},"SJAG_03891:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03891","name":"alx1delta","uniquename":"SJAG_03891:allele-1"},"SJAG_05207:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_05207","name":"cmp7delta","uniquename":"SJAG_05207: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":4,"community_curator":false,"file_name":null,"file_type":null,"name":"Val Wood","orcid":"0000-0001-6330-7526"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-07-09","authors":"Lee IJ, Stokasimov E, Dempsey N, Varberg JM, Jacob E, Jaspersen SL, Pellman D","authors_abbrev":"Lee IJ et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-07-14 11:10:55","canto_approver_orcid":"0000-0001-6330-7526","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-07-09 15:55:25","canto_session_key":"e134ba05c345c3f5","canto_session_submitted_date":"2021-07-09 15:55:19","canto_triage_status":"Curatable","citation":"J Cell Biol 2020 06 01;219(6)","cv_annotations":{"biological_process":[{"annotations":[115544,115545,115546,115547],"is_not":false,"summary":null,"term":"GO:0007084"}],"cellular_component":[{"annotations":[115543],"is_not":false,"summary":null,"term":"GO:0005783"},{"annotations":[115529,115531,115541],"is_not":false,"summary":null,"term":"GO:0044732"},{"annotations":[115530,115532,115540],"is_not":false,"summary":null,"term":"GO:0005635"}],"single_locus_phenotype":[{"annotations":[115533],"is_not":false,"summary":null,"term":"FYPO:0001375"},{"annotations":[115538],"is_not":false,"summary":null,"term":"FYPO:0000080"},{"annotations":[115534,115535,115542],"is_not":false,"summary":null,"term":"FYPO:0007772"},{"annotations":[115539],"is_not":false,"summary":null,"term":"FYPO:0000714"},{"annotations":[115536,115537],"is_not":false,"summary":null,"term":"FYPO:0001234"}]},"doi":"10.1083/jcb.201908232","gene_count":6,"genes_by_uniquename":{"SJAG_01050":null,"SJAG_01242":null,"SJAG_01745":null,"SJAG_03891":null,"SJAG_03943":null,"SJAG_05207":null},"genetic_interactions":[[{"gene_a_uniquename":"SJAG_05207","gene_b_uniquename":"SJAG_01745","interaction_type":"Phenotypic Suppression"},[{"reference_uniquename":"PMID:32243490","throughput":"low"}]],[{"gene_a_uniquename":"SJAG_01745","gene_b_uniquename":"SJAG_01050","interaction_type":"Phenotypic Suppression"},[{"reference_uniquename":"PMID:32243490","throughput":"low"}]],[{"gene_a_uniquename":"SJAG_01242","gene_b_uniquename":"SJAG_01050","interaction_type":"Phenotypic Suppression"},[{"reference_uniquename":"PMID:32243490","throughput":"low"}]],[{"gene_a_uniquename":"SJAG_01242","gene_b_uniquename":"SJAG_01745","interaction_type":"Phenotypic Suppression"},[{"reference_uniquename":"PMID:32243490","throughput":"low"}]],[{"gene_a_uniquename":"SJAG_01242","gene_b_uniquename":"SJAG_03891","interaction_type":"Phenotypic Enhancement"},[{"reference_uniquename":"PMID:32243490","throughput":"low"}]],[{"gene_a_uniquename":"SJAG_05207","gene_b_uniquename":"SJAG_03943","interaction_type":"Dosage Rescue"},[{"reference_uniquename":"PMID:32243490","throughput":"low"}]]],"genotypes_by_uniquename":{"alx1delta":{"display_name":"alx1delta","display_uniquename":"alx1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03891:allele-1","expression":"Null"}]}]},"cmp7delta":{"display_name":"cmp7delta","display_uniquename":"cmp7delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_05207:allele-1","expression":"Null"}]}]},"lem2delta":{"display_name":"lem2delta","display_uniquename":"lem2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01745:allele-1","expression":"Null"}]}]},"vps32delta":{"display_name":"vps32delta","display_uniquename":"vps32delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01242:allele-1","expression":"Null"}]}]}},"ltp_gene_count":6,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2020","pubmed_entrez_date":"2020-04-04","pubmed_publication_date":"01 06 2020","terms_by_termid":{"FYECO:0000006":null,"FYPO:0000080":null,"FYPO:0000714":null,"FYPO:0001234":null,"FYPO:0001375":null,"FYPO:0007772":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000003":null,"GO:0005635":null,"GO:0005783":null,"GO:0007084":null,"GO:0044732":null},"title":"Factors promoting nuclear envelope assembly independent of the canonical ESCRT pathway.","uniquename":"PMID:32243490"}


id: PMID:30726171
data:
  {"abstract":"Many fungal species are dimorphic, exhibiting both unicellular yeast-like and filamentous forms. Schizosaccharomyces japonicus, a member of the fission yeast clade, is one such dimorphic fungus. Here, we first identify fruit extracts as natural, stress-free, starvation-independent inducers of filamentation, which we use to describe the properties of the dimorphic switch. During the yeast-to-hypha transition, the cell evolves from a bipolar to a unipolar system with 10-fold accelerated polarized growth but constant width, vacuoles segregated to the nongrowing half of the cell, and hyper-lengthening of the cell. We demonstrate unusual features of S. japonicus hyphae: these cells lack a Spitzenkörper, a vesicle distribution center at the hyphal tip, but display more rapid cytoskeleton-based transport than the yeast form, with actin cables being essential for the transition. S. japonicus hyphae also remain mononuclear and undergo complete cell divisions, which are highly asymmetric: one daughter cell inherits the vacuole, the other the growing tip. We show that these elongated cells scale their nuclear size, spindle length, and elongation rates, but display altered division size controls. This establishes S. japonicus as a unique system that switches between symmetric and asymmetric modes of growth and division.","alleles_by_uniquename":{"SJAG_02392:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02392","name":"pom1delta","uniquename":"SJAG_02392:allele-1"},"SJAG_02695:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02695","name":"tip1delta","uniquename":"SJAG_02695:allele-1"},"SJAG_04703:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04703","name":"for3delta","uniquename":"SJAG_04703:allele-1"}},"annotation_curators":[{"annotation_count":21,"community_curator":true,"file_name":null,"file_type":null,"name":"Sophie Martin","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-06-16","authors":"Kinnaer C, Dudin O, Martin SG","authors_abbrev":"Kinnaer C et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-06-16 18:49:31","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Sophie Martin","canto_curator_role":"community","canto_first_approved_date":"2021-06-16 18:49:31","canto_session_key":"bf05a60cb09b4cdb","canto_session_submitted_date":"2021-06-04 10:25:08","canto_triage_status":"Curatable","citation":"Mol Biol Cell 2019 04 01;30(8):975-991","cv_annotations":{"cellular_component":[{"annotations":[115228],"is_not":false,"summary":null,"term":"GO:0051286"},{"annotations":[115210,115212,115214,115216,115218,115220],"is_not":false,"summary":null,"term":"GO:0035838"},{"annotations":[115229],"is_not":false,"summary":null,"term":"GO:0085039"},{"annotations":[115211,115213,115215,115217,115219,115221],"is_not":false,"summary":null,"term":"GO:0001411"},{"annotations":[115222],"is_not":false,"summary":null,"term":"GO:0035371"},{"annotations":[115223],"is_not":false,"summary":null,"term":"GO:0030133"}],"single_locus_phenotype":[{"annotations":[115225],"is_not":false,"summary":null,"term":"FYPO:0003315"},{"annotations":[115226],"is_not":false,"summary":null,"term":"FYPO:0001355"},{"annotations":[115230],"is_not":false,"summary":null,"term":"FYPO:0007801"},{"annotations":[115227],"is_not":false,"summary":null,"term":"FYPO:0004293"},{"annotations":[115224],"is_not":false,"summary":null,"term":"FYPO:0001956"}]},"doi":"10.1091/mbc.E18-12-0774","gene_count":9,"genes_by_uniquename":{"SJAG_01196":null,"SJAG_02392":null,"SJAG_02695":null,"SJAG_03011":null,"SJAG_03625":null,"SJAG_03915":null,"SJAG_04624":null,"SJAG_04703":null,"SJAG_04960":null},"genotypes_by_uniquename":{"for3delta":{"display_name":"for3delta","display_uniquename":"for3delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04703:allele-1","expression":"Null"}]}]},"pom1delta":{"display_name":"pom1delta","display_uniquename":"pom1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02392:allele-1","expression":"Null"}]}]},"tip1delta":{"display_name":"tip1delta","display_uniquename":"tip1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02695:allele-1","expression":"Null"}]}]}},"ltp_gene_count":9,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2019","pubmed_entrez_date":"2019-02-07","pubmed_publication_date":"01 04 2019","terms_by_termid":{"FYPO:0001355":null,"FYPO:0001956":null,"FYPO:0003315":null,"FYPO:0004293":null,"FYPO:0007801":null,"GO:0001411":null,"GO:0030133":null,"GO:0035371":null,"GO:0035838":null,"GO:0051286":null,"GO:0085039":null},"title":"Yeast-to-hypha transition of Schizosaccharomyces japonicus in response to environmental stimuli.","uniquename":"PMID:30726171"}


id: PMID:27059155
data:
  {"abstract":"In the fission yeast Schizosaccharomyces pombe (Sp), Mid1/Dmf1 plays an important role in positioning the division site by inducing formation of the contractile ring (CR). Mid1, emanating from the nucleus located in the cell center, forms a dozen of nodes in the middle cell cortex ahead of mitosis, and actin filaments and myosin II accumulated at each node interact and assemble the CR in metaphase. Curiously, in another fission yeast S. japonicus (Sj), CR formation begins after nuclear segregation in late anaphase. Here, we investigated the role of S. japonicus Mid1 during mitosis to compare the molecular mechanisms that determine the cell division site in Schizosaccharomyces. Similar to Sp Mid1, Sj Mid1 often accumulated in the nucleus of interphase cells. Moreover, Sj Mid1 localized to cortical dots with myosin II in the future division site and formed a medial ring in mitotic cells. However, S. japonicus cells without Mid1 function still carried out symmetrical binary division. Therefore, the Mid1 dependency for positional control of the cell division site is possibly different between the two species. Meanwhile, we found that Sj Mid1 enhanced CR formation, in a manner possibly similar to that by Sp Mid1. ","alleles_by_uniquename":{"SJAG_01143:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01143","name":"mid1delta","uniquename":"SJAG_01143:allele-1"}},"annotation_curators":[{"annotation_count":3,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"},{"annotation_count":1,"community_curator":false,"file_name":null,"file_type":null,"name":"Val Wood","orcid":"0000-0001-6330-7526"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-07-28","authors":"Yasuda T, Takaine M, Numata O, Nakano K","authors_abbrev":"Yasuda T et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-09-01 07:07:40","canto_approver_orcid":"0000-0001-6330-7526","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-07-28 11:44:06","canto_session_key":"f86427f99db0ccf7","canto_session_submitted_date":"2021-07-28 11:44:00","canto_triage_status":"Curatable","citation":"Genes Cells 2016 Jun;21(6):594-607","cv_annotations":{"biological_process":[{"annotations":[115446],"is_not":false,"summary":null,"term":"GO:1903475"}],"cellular_component":[{"annotations":[115443],"is_not":false,"summary":null,"term":"GO:0005826"},{"annotations":[115444],"is_not":false,"summary":null,"term":"GO:1990753"}],"single_locus_phenotype":[{"annotations":[115445],"is_not":false,"summary":null,"term":"FYPO:0000729"}]},"doi":"10.1111/gtc.12368","gene_count":1,"genes_by_uniquename":{"SJAG_01143":null},"genotypes_by_uniquename":{"mid1delta":{"display_name":"mid1delta","display_uniquename":"mid1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01143:allele-1","expression":"Null"}]}]}},"ltp_gene_count":1,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2016","pubmed_entrez_date":"2016-04-10","pubmed_publication_date":"Jun 2016","terms_by_termid":{"FYPO:0000729":null,"GO:0005826":null,"GO:0051329":null,"GO:1903475":null,"GO:1990753":null},"title":"Anillin-related protein Mid1 regulates timely formation of the contractile ring in the fission yeast Schizosaccharomyces japonicus.","uniquename":"PMID:27059155"}


id: PMID:23786411
data:
  {"abstract":"Three types of mitosis, which are open, closed or semi-open mitosis, function in eukaryotic cells, respectively. The open mitosis involves breakage of the nuclear envelope before nuclear division, whereas the closed mitosis proceeds with an intact nuclear envelope. To understand the mechanism and significance of three types of mitotic division in eukaryotes, we investigated the process of semi-open mitosis, in which the nuclear envelope is only partially broken, in the fission yeast Schizosaccharomyces japonicus. In anaphase-promoting complex/cyclosome (APC/C) mutants of Sz. japonicus, the nuclear envelope remained relatively intact during anaphase, resulting in impaired semi-open mitosis. As a suppressor of apc2 mutant, a mutation of Oar2, which was a 3-oxoacyl-[acyl carrier protein] reductase, was obtained. The level of the Oar2, which had two destruction-box motifs recognized by APC/C, was increased in APC/C mutants. Furthermore, the defective semi-open mitosis observed in an apc2 mutant was restored by mutated oar2+. Based on these findings, we propose that APC/C regulates the dynamics of the nuclear envelope through degradation of Oar2 dependent on APC/C during the metaphase-to-anaphase transition of semi-open mitosis in Sz. japonicus.","alleles_by_uniquename":{"SJAG_01946:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01946","name":"cem1delta","uniquename":"SJAG_01946:allele-1"},"SJAG_01956:allele-1":{"allele_type":"amino_acid_mutation","description":"E405K ts","gene_uniquename":"SJAG_01956","name":"nuc2-1051","uniquename":"SJAG_01956:allele-1"},"SJAG_03198:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03198","name":"oar2delta","uniquename":"SJAG_03198:allele-1"},"SJAG_03198:allele-2":{"allele_type":"amino_acid_mutation","description":"Y189D cold sensitive","gene_uniquename":"SJAG_03198","name":"oar2-51","uniquename":"SJAG_03198:allele-2"},"SJAG_03198:allele-3":{"allele_type":"amino_acid_mutation","description":"R72A,L75A,R106A,L109A","gene_uniquename":"SJAG_03198","name":"oar2-dm12","synonyms":[{"name":"destruction box mutations","reference":"PMID:23786411","type":"exact"}],"uniquename":"SJAG_03198:allele-3"},"SJAG_03351:allele-1":{"allele_type":"amino_acid_mutation","description":"A186T ts","gene_uniquename":"SJAG_03351","name":"cut23-415","uniquename":"SJAG_03351:allele-1"},"SJAG_03575:allele-1":{"allele_type":"amino_acid_mutation","description":"E548K ts","gene_uniquename":"SJAG_03575","name":"apc2-361","uniquename":"SJAG_03575:allele-1"}},"annotation_curators":[{"annotation_count":22,"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":"Aoki K, Shiwa Y, Takada H, Yoshikawa H, Niki H","authors_abbrev":"Aoki K et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2022-11-21 18:57:14","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Sho Okamoto","canto_curator_role":"community","canto_first_approved_date":"2022-11-21 18:57:14","canto_session_key":"a0c3e1394f326db9","canto_session_submitted_date":"2022-11-21 18:57:00","canto_triage_status":"Curatable","citation":"Genes Cells 2013 Sep;18(9):733-52","cv_annotations":{"cellular_component":[{"annotations":[115699],"is_not":false,"summary":null,"term":"GO:0005730"}],"multi_locus_phenotype":[{"annotations":[115713,115714,115715,115717],"is_not":false,"summary":null,"term":"FYPO:0000674"}],"single_locus_phenotype":[{"annotations":[115700,115701,115702,115716],"is_not":false,"summary":null,"term":"FYPO:0000080"},{"annotations":[115709,115710,115711],"is_not":false,"summary":null,"term":"FYPO:0000618"},{"annotations":[115718,115719,115720],"is_not":false,"summary":null,"term":"FYPO:0001327"},{"annotations":[115706,115707,115708],"is_not":false,"summary":null,"term":"FYPO:0001387"},{"annotations":[115703,115704,115705],"is_not":false,"summary":null,"term":"FYPO:0000324"},{"annotations":[115712],"is_not":false,"summary":null,"term":"FYPO:0004683"}]},"doi":"10.1111/gtc.12072","gene_count":6,"genes_by_uniquename":{"SJAG_00259":null,"SJAG_01946":null,"SJAG_01956":null,"SJAG_03198":null,"SJAG_03351":null,"SJAG_03575":null},"genotypes_by_uniquename":{"apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"apc2-361(E548K ts)","display_uniquename":"apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03575:allele-1","expression":"Not assayed or wild type"}]}]},"apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type__cem1delta":{"display_name":"apc2-361(E548K ts) cem1delta","display_uniquename":"apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type__cem1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03575:allele-1","expression":"Not assayed or wild type"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_01946:allele-1","expression":"Null"}]}]},"apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type__oar2-51-Y189D_cold_sensitive-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"apc2-361(E548K ts) oar2-51(Y189D cold sensitive)","display_uniquename":"apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type__oar2-51-Y189D_cold_sensitive-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03575:allele-1","expression":"Not assayed or wild type"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_03198:allele-2","expression":"Not assayed or wild type"}]}]},"apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type__oar2-dm12-R72A,L75A,R106A,L109A-amino_acid_mutation-expression-overexpression":{"display_name":"apc2-361(E548K ts) oar2-dm12(R72A,L75A,R106A,L109A aa)[Overexpression]","display_uniquename":"apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type__oar2-dm12-R72A,L75A,R106A,L109A-amino_acid_mutation-expression-overexpression","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03575:allele-1","expression":"Not assayed or wild type"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_03198:allele-3","expression":"Overexpression"}]}]},"apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type__oar2delta":{"display_name":"apc2-361(E548K ts) oar2delta","display_uniquename":"apc2-361-E548K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type__oar2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03575:allele-1","expression":"Not assayed or wild type"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_03198:allele-1","expression":"Null"}]}]},"cem1delta":{"display_name":"cem1delta","display_uniquename":"cem1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01946:allele-1","expression":"Null"}]}]},"cut23-415-A186T_ts-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"cut23-415(A186T ts)","display_uniquename":"cut23-415-A186T_ts-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03351:allele-1","expression":"Not assayed or wild type"}]}]},"nuc2-1051-E405K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"nuc2-1051(E405K ts)","display_uniquename":"nuc2-1051-E405K_ts-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01956:allele-1","expression":"Not assayed or wild type"}]}]},"oar2-51-Y189D_cold_sensitive-amino_acid_mutation-expression-overexpression":{"display_name":"oar2-51(Y189D cold sensitive)[Overexpression]","display_uniquename":"oar2-51-Y189D_cold_sensitive-amino_acid_mutation-expression-overexpression","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03198:allele-2","expression":"Overexpression"}]}]},"oar2-dm12-R72A,L75A,R106A,L109A-amino_acid_mutation-expression-overexpression":{"display_name":"oar2-dm12(R72A,L75A,R106A,L109A aa)[Overexpression]","display_uniquename":"oar2-dm12-R72A,L75A,R106A,L109A-amino_acid_mutation-expression-overexpression","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03198:allele-3","expression":"Overexpression"}]}]},"oar2delta":{"display_name":"oar2delta","display_uniquename":"oar2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03198:allele-1","expression":"Null"}]}]}},"ltp_gene_count":6,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2013","pubmed_entrez_date":"2013-06-22","pubmed_publication_date":"Sep 2013","references_by_uniquename":{"PMID:23786411":null},"terms_by_termid":{"FYECO:0000004":null,"FYECO:0000006":null,"FYECO:0000137":null,"FYPO:0000080":null,"FYPO:0000324":null,"FYPO:0000618":null,"FYPO:0000674":null,"FYPO:0001327":null,"FYPO:0001387":null,"FYPO:0004683":null,"FYPO_EXT:0000001":null,"GO:0005730":null},"title":"Regulation of nuclear envelope dynamics via APC/C is necessary for the progression of semi-open mitosis in Schizosaccharomyces japonicus.","uniquename":"PMID:23786411"}


id: PMID:31150379
data:
  {"abstract":"Quorum sensing (QS), a mechanism of microbial communication dependent on cell density, governs developmental decisions in many bacteria and in some pathogenic and non-pathogenic fungi including yeasts. In these simple eukaryotes this response is mediated by the release into the growth medium of quorum-sensing molecules (QSMs) whose concentration increases proportionally to the population density. To date the occurrence of QS is restricted to a few yeast species. We show that a QS mediated by the aromatic alcohols phenylethanol and tryptophol represses the dimorphic yeast to hypha differentiation in the fission yeast S. japonicus in response to an increased population density. In addition, the stress activated MAPK pathway (SAPK), which controls cell cycle progression and adaptation to environmental changes in this organism, constitutively represses yeast to hypha differentiation both at transcriptional and post-translational levels. Moreover, deletion of its main effectors Sty1 MAPK and Atf1 transcription factor partially suppressed the QS-dependent block of hyphal development under inducing conditions. RNAseq analysis showed that the expression of nrg1+, which encodes a putative ortholog of the transcription factor Nrg1 that represses yeast to hypha dimorphism in C. albicans, is downregulated both by QS and the SAPK pathway. Remarkably, Nrg1 may act in S. japonicus as an activator of hyphal differentiation instead of being a repressor. S. japonicus emerges as an attractive and amenable model organism to explore the QS mechanisms that regulate cellular differentiation in fungi.","alleles_by_uniquename":{"SJAG_00124:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00124","name":"SJAG_00124delta","uniquename":"SJAG_00124:allele-1"},"SJAG_00266:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00266","name":"atf1delta","uniquename":"SJAG_00266:allele-1"},"SJAG_02013:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02013","name":"pyp1delta","uniquename":"SJAG_02013:allele-1"},"SJAG_02592:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02592","name":"sty1delta","uniquename":"SJAG_02592:allele-1"}},"annotation_curators":[{"annotation_count":37,"community_curator":true,"file_name":null,"file_type":null,"name":"Elisa Gómez Gil","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-08-04","authors":"Gómez-Gil E, Franco A, Madrid M, Vázquez-Marín B, Gacto M, Fernández-Breis J, Vicente-Soler J, Soto T, Cansado J","authors_abbrev":"Gómez-Gil E et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-08-04 11:11:18","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Elisa Gómez Gil","canto_curator_role":"community","canto_first_approved_date":"2021-08-04 11:11:18","canto_session_key":"0da7a90b15f75d86","canto_session_submitted_date":"2021-08-03 17:26:10","canto_triage_status":"Curatable","citation":"PLoS Genet 2019 05;15(5):e1008192","cv_annotations":{"PSI-MOD":[{"annotations":[115412,115413,115414,115415],"is_not":false,"summary":null,"term":"MOD:00046"}],"multi_locus_phenotype":[{"annotations":[115440],"is_not":false,"summary":null,"term":"FYPO:0007779"}],"single_locus_phenotype":[{"annotations":[115408,115420],"is_not":false,"summary":null,"term":"FYPO:0004481"},{"annotations":[115436],"is_not":false,"summary":null,"term":"FYPO:0007778"},{"annotations":[115435,115438],"is_not":false,"summary":null,"term":"FYPO:0007776"},{"annotations":[115419],"is_not":false,"summary":null,"term":"FYPO:0000708"},{"annotations":[115437,115439],"is_not":false,"summary":null,"term":"FYPO:0007780"},{"annotations":[115441,115442],"is_not":false,"summary":null,"term":"FYPO:0007824"},{"annotations":[115406,115418],"is_not":false,"summary":null,"term":"FYPO:0001122"},{"annotations":[115430,115434],"is_not":false,"summary":null,"term":"FYPO:0007777"},{"annotations":[115429,115433],"is_not":false,"summary":null,"term":"FYPO:0007775"},{"annotations":[115428,115432],"is_not":false,"summary":null,"term":"FYPO:0007774"},{"annotations":[115431],"is_not":false,"summary":null,"term":"FYPO:0007779"},{"annotations":[115411,115423],"is_not":false,"summary":null,"term":"FYPO:0000097"},{"annotations":[115410,115422],"is_not":false,"summary":null,"term":"FYPO:0000726"},{"annotations":[115409,115421],"is_not":false,"summary":null,"term":"FYPO:0000271"},{"annotations":[115424],"is_not":false,"summary":null,"term":"FYPO:0000841"},{"annotations":[115407],"is_not":false,"summary":null,"term":"FYPO:0000280"},{"annotations":[115427],"is_not":false,"summary":null,"term":"FYPO:0000648"}]},"doi":"10.1371/journal.pgen.1008192","gene_count":4,"genes_by_uniquename":{"SJAG_00124":null,"SJAG_00266":null,"SJAG_02013":null,"SJAG_02592":null},"genotypes_by_uniquename":{"SJAG_00124delta":{"display_name":"SJAG_00124delta","display_uniquename":"SJAG_00124delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00124:allele-1","expression":"Null"}]}]},"SJAG_00124delta__sty1delta":{"display_name":"SJAG_00124delta sty1delta","display_uniquename":"SJAG_00124delta__sty1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00124:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_02592:allele-1","expression":"Null"}]}]},"atf1delta":{"display_name":"atf1delta","display_uniquename":"atf1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00266:allele-1","expression":"Null"}]}]},"pyp1delta":{"display_name":"pyp1delta","display_uniquename":"pyp1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02013:allele-1","expression":"Null"}]}]},"sty1delta":{"display_name":"sty1delta","display_uniquename":"sty1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02592:allele-1","expression":"Null"}]}]}},"ltp_gene_count":4,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2019","pubmed_entrez_date":"2019-06-01","pubmed_publication_date":"05 2019","terms_by_termid":{"FYECO:0000004":null,"FYECO:0000078":null,"FYECO:0000137":null,"FYECO:0000207":null,"FYECO:0000272":null,"FYECO:0000314":null,"FYPO:0000097":null,"FYPO:0000271":null,"FYPO:0000280":null,"FYPO:0000648":null,"FYPO:0000708":null,"FYPO:0000726":null,"FYPO:0000841":null,"FYPO:0001122":null,"FYPO:0004481":null,"FYPO:0007774":null,"FYPO:0007775":null,"FYPO:0007776":null,"FYPO:0007777":null,"FYPO:0007778":null,"FYPO:0007779":null,"FYPO:0007780":null,"FYPO:0007824":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null,"FYPO_EXT:0000003":null,"GO:0034599":null,"GO:0034605":null,"GO:0071475":null,"GO:1904547":null,"MOD:00046":null},"title":"Quorum sensing and stress-activated MAPK signaling repress yeast to hypha transition in the fission yeast Schizosaccharomyces japonicus.","uniquename":"PMID:31150379"}


id: PMID:20618870
data:
  {"abstract":"The genus Schizosaccharomyces is presently comprised of three species, namely Schizosaccharomyces pombe, Schizosaccharomyces octosporus and Schizosaccharomyces japonicus. Here, we describe a hitherto unknown species, Schizosaccharomyces cryophilus, named for its preference for growth at lower temperatures than the other fission yeast species. Although morphologically similar to S. octosporus, analysis of several rapidly evolving sequences, including the D1/D2 divergent domain of the large subunit (LSU) rRNA gene, the RNA subunit of RNAse P and the internal transcribed spacer elements, revealed significant divergence from any previously characterized Schizosaccharomyces strain. Based on phylogenetic analysis of the D1/D2 domain of the LSU rRNA gene, S. octosporus is the closest known relative of S. cryophilus, with the sequences of the two species differing by 25 nucleotide substitutions (>4%). Sequencing of the S. cryophilus genome and phylogenetic analysis of all 1 : 1 protein orthologs confirmed this observation, and together with morphological and physiological characterization, supports the assignment of S. cryophilus as a new species within the genus Schizosaccharomyces. The type strain of the new species is NRRL Y-48691(T) (=NBRC 106824(T)=CBS 11777(T)).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Helston RM, Box JA, Tang W, Baumann P","authors_abbrev":"Helston RM et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Phylogeny and evolutionary studies","citation":"FEMS Yeast Res 2010 Sep;10(6):779-86","cv_annotations":{},"doi":"10.1111/j.1567-1364.2010.00657.x","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":"2010-07-13","pubmed_publication_date":"Sep 2010","terms_by_termid":{},"title":"Schizosaccharomyces cryophilus sp. nov., a new species of fission yeast.","uniquename":"PMID:20618870"}


id: GO_REF:0000034
data:
  {"abstract":"Skeletal cell terms and relationships were added and revised at the Skeletal Anatomy Jamboree held by Phenoscape (NSF grant BDI-0641025) and hosted by the National Evolutionary Synthesis Center (NESCent), April 9-10, 2010.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Brian K. Hall (Dalhousie University), Matthew Vickaryous (Ontario Veterinary College, University of Guelph), David Blackburn, University of Kansas; Wasila Dahdul, University of South Dakota and NESCent; Alexander Diehl, Mouse Genome Informatics (MGI); Melissa Haendel, Oregon Health Sciences University; John G. Lundberg, Department of Ichthyology, Academy of Natural Sciences, Philadelphia; Paula Mabee, Department of Biology, University of South Dakota; Martin Ringwald, Mouse Genome Informatics (MGI); Erik Segerdell, Oregon Health Sciences University; Ceri Van Slyke, Zebrafish Information Network (ZFIN); Monte Westerfield, Zebrafish Information Network (ZFIN) and Institute of Neuroscience, University of Oregon.","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Phenoscape Skeletal Anatomy Jamboree","uniquename":"GO_REF:0000034"}


id: GO_REF:0000080
data:
  {"abstract":"We have created a standard template for classes describing the development of a plant structure as a biological process. The underlying equivalence axiom template is \"'anatomical structure development' and 'results in development of' some P\", where P is a plant anatomical entity (PO:0025131).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of plant development as biological process in the Gene Ontology","uniquename":"GO_REF:0000080"}


id: GO_REF:0000092
data:
  {"abstract":"We have created a standard template for classes describing the biosynthesis of a chemical entity from or via an other chemical entity as biological processes. The underlying equivalence axiom templates are \"GO:0009058 and 'has output' some T and 'has input' some F\" (biosynthesis from) and \"GO:0009058 and 'has output' some T and 'has intermediate' some I\" (biosynthesis via), where T,F, and I are chemical entities (CHEBI:24431). The approach to combine GO and ChEBI has been described in the following publication: PMID:23895341.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation for the biosynthesis from or via a chemical as biological process in the Gene Ontology","uniquename":"GO_REF:0000092"}


id: PMID:23150598
data:
  {"abstract":"A key question in developmental biology addresses the mechanism of asymmetric cell division. Asymmetry is crucial for generating cellular diversity required for development in multicellular organisms. As one of the potential mechanisms, chromosomally borne epigenetic difference between sister cells that changes mating/cell type has been demonstrated only in the Schizosaccharomyces pombe fission yeast. For technical reasons, it is nearly impossible to determine the existence of such a mechanism operating during embryonic development of multicellular organisms. Our work addresses whether such an epigenetic mechanism causes asymmetric cell division in the recently sequenced fission yeast, S. japonicus (with 36% GC content), which is highly diverged from the well-studied S. pombe species (with 44% GC content). We find that the genomic location and DNA sequences of the mating-type loci of S. japonicus differ vastly from those of the S. pombe species. Remarkably however, similar to S. pombe, the S. japonicus cells switch cell/mating type after undergoing two consecutive cycles of asymmetric cell divisions: only one among four \"granddaughter\" cells switches. The DNA-strand-specific epigenetic imprint at the mating-type locus1 initiates the recombination event, which is required for cellular differentiation. Therefore the S. pombe and S. japonicus mating systems provide the first two examples in which the intrinsic chirality of double helical structure of DNA forms the primary determinant of asymmetric cell division. Our results show that this unique strand-specific imprinting/segregation epigenetic mechanism for asymmetric cell division is evolutionary conserved. Motivated by these findings, we speculate that DNA-strand-specific epigenetic mechanisms might have evolved to dictate asymmetric cell division in diploid, higher eukaryotes as well.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Yu C, Bonaduce MJ, Klar AJ","authors_abbrev":"Yu C et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"Genetics 2013 Jan;193(1):85-94","cv_annotations":{},"doi":"10.1534/genetics.112.146233","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":"2012-11-15","pubmed_publication_date":"Jan 2013","terms_by_termid":{},"title":"Defining the epigenetic mechanism of asymmetric cell division of Schizosaccharomyces japonicus yeast.","uniquename":"PMID:23150598"}


id: GO_REF:0000115
data:
  {"abstract":"Rfam (http://rfam.org, PMID:29112718) is a database of non-coding RNA families which are manually","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"RNAcentral (1). (1) European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, United Kingdom","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Automatic Gene Ontology annotation of non-coding RNA sequences through association of Rfam records with GO terms","uniquename":"GO_REF:0000115"}


id: GO_REF:0000089
data:
  {"abstract":"We have created a standard template for classes describing the single-organism and multi-organism biological processes. The underlying equivalence axiom templates are \"P and 'bearer_of' some PATO:0002487\" (single-organism) and \"P and 'bearer_of' some PATO:0002486\" (multi-organism), where P is a biological process.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of single-organism and multi-organism biological processes in the Gene Ontology","uniquename":"GO_REF:0000089"}


id: PMID:28655757
data:
  {"abstract":"Cytokinesis in many eukaryotes involves a tension-generating actomyosin-based contractile ring. Many components of actomyosin rings turn over during contraction, although the significance of this turnover has remained enigmatic. Here, using  Schizosaccharomyces japonicus , we investigate the role of turnover of actin and myosin II in its contraction. Actomyosin ring components self-organize into ∼1-µm-spaced clusters instead of undergoing full-ring contraction in the absence of continuous actin polymerization. This effect is reversed when actin filaments are stabilized. We tested the idea that the function of turnover is to ensure actin filament homeostasis in a synthetic system, in which we abolished turnover by fixing rings in cell ghosts with formaldehyde. We found that these rings contracted fully upon exogenous addition of a vertebrate myosin. We conclude that actin turnover is required to maintain actin filament homeostasis during ring contraction and that the requirement for turnover can be bypassed if homeostasis is achieved artificially.","alleles_by_uniquename":{},"annotation_curators":[{"annotation_count":5,"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":"Chew TG, Huang J, Palani S, Sommese R, Kamnev A, Hatano T, Gu Y, Oliferenko S, Sivaramakrishnan S, Balasubramanian MK","authors_abbrev":"Chew TG et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-07-09 13:45:34","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-07-09 13:45:34","canto_session_key":"5ead7a365a97d8ab","canto_session_submitted_date":"2021-07-09 13:45:28","canto_triage_status":"Curatable","citation":"J Cell Biol 2017 09 04;216(9):2657-2667","cv_annotations":{"cellular_component":[{"annotations":[115205,115206,115207,115208,115209],"is_not":false,"summary":null,"term":"GO:0005826"}]},"doi":"10.1083/jcb.201701104","gene_count":5,"genes_by_uniquename":{"SJAG_01665":null,"SJAG_02431":null,"SJAG_03596":null,"SJAG_03703":null,"SJAG_04498":null},"genotypes_by_uniquename":{},"ltp_gene_count":5,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2017","pubmed_entrez_date":"2017-06-29","pubmed_publication_date":"04 09 2017","terms_by_termid":{"GO:0005826":null},"title":"Actin turnover maintains actin filament homeostasis during cytokinetic ring contraction.","uniquename":"PMID:28655757"}


id: PMID:22572960
data:
  {"abstract":"The aim of mitosis is to produce two daughter nuclei, each containing a chromosome complement identical to that of the mother nucleus. This can be accomplished through a variety of strategies, with \"open\" and \"closed\" modes of mitosis positioned at the opposite ends of the spectrum and a range of intermediate patterns in between. In the \"closed\" mitosis, the nuclear envelope remains intact throughout the nuclear division. In the \"open\" division type, the envelope of the original nucleus breaks down early in mitosis and reassembles around the segregated daughter genomes. In any case, the nuclear membrane has to remodel to accommodate the mitotic spindle assembly, chromosome segregation and formation of the daughter nuclei. We have recently shown that within the fission yeast clade, the mitotic control of the nuclear surface area may determine the choice between the nuclear envelope breakdown and a fully \"closed\" division. Here we discuss our data and argue that comparative cell biology studies using two fission yeast species, Schizosaccharomyces pombe and Schizosaccharomyces japonicus, could provide unprecedented insights into physiology and evolution of mitosis.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Gu Y, Yam C, Oliferenko S","authors_abbrev":"Gu Y et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Review or comment","citation":"Nucleus 2012 May;3(3):220-5","cv_annotations":{},"doi":"10.4161/nucl.19514","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2012","pubmed_entrez_date":"2012-05-11","pubmed_publication_date":"May 2012","terms_by_termid":{},"title":"Divergence of mitotic strategies in fission yeasts.","uniquename":"PMID:22572960"}


id: GO_REF:0000090
data:
  {"abstract":"We have created a rule-based approach to create relations between the branches of the Gene Ontology. The approach uses the equivalence axioms and a given pattern to create non-subClassOf relationships between the three different branches of the Gene Ontology (biological process, molecular function, cellular component). Currently, there are the following rules: \"'transporter activity' and 'transports_or_maintains_localization_of' some X' -part_of-> \"transport and 'transports_or_maintains_localization_of' some X\"; \"'transmembrane transporter activity' and 'transports_or_maintains_localization_of' some X -part_of-> 'transmembrane transport' and 'transports_or_maintains_localization_of' some X\"","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Automatic creation of relationships between ontology branches in the Gene Ontology","uniquename":"GO_REF:0000090"}


id: PMID:9396147
data:
  {"abstract":"Both living and fixed cells of Schizosaccharomyces japonicus var. versatilis showed thread-like mitochondria when studied by phase-contrast and fluorescence microscopy. In the interphase cells, mitochondria extended from pole to pole and converged towards the growing tips. The mitochondrial threads did not disrupt but persisted during mitosis and, subsequently, their bundle was split between the two daughter cells by a concentrically growing septum. Mitochondria in the interphase cells were accompanied by cytoplasmic microtubules. These disappeared during mitosis and, instead, spindle microtubules were formed in the nucleus. The cytoplasmic microtubules reappeared after anaphase B, again in coaligment with mitochondria. Protoplasting as well as the action of microtubule inhibitors methyl-1-(butylcarbamoyl)-2-benzimidazolecarbamate (benomyl) and 2-methylbenzimidazole (MBC) resulted in rapid disintegration of microtubules and, suprisingly, also in disruption of mitochondria into small bodies. Removal of the inhibitors or a short regeneration of protoplasts allowed both the cytoplasmic microtubules and the thread-like mitochondria to reaggregate into the original pattern. Cytochalasin D treatment caused a complete disintegration of actin filaments, while the cytoplasmic microtubules and mitochondria remained intact. These findings of a transient close association of mitochondria and microtubules and their relative independence of the arrangement of actin filaments suggest that microtubules, but not actin cables, form supports for positioning or movement of mitochondria along the cylindrical cells. The persistence of mitochondria in the cell centre during mitosis may be accounted for by the fact that disrupted microtubules fail to provide support for mitochondrial movement towards the cell poles.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Svoboda A, Slaninová I","authors_abbrev":"Svoboda A et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"Can J Microbiol 1997 Oct;43(10):945-53","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1997","pubmed_entrez_date":"1997-12-13","pubmed_publication_date":"Oct 1997","terms_by_termid":{},"title":"Colocalization of microtubules and mitochondria in the yeast Schizosaccharomyces japonicus var. versatilis.","uniquename":"PMID:9396147"}


id: GO_REF:0000097
data:
  {"abstract":"FlyBase occasionally makes GO annotations based on information that has been sent to us directly by researchers as a personal communication to FlyBase. In each case, the full details of the communication including any associated data and analyses are recorded in a FlyBase publication (FBrf) available from our website (http://flybase.org).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"FlyBase","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Gene Ontology annotation based on personal communication to FlyBase","uniquename":"GO_REF:0000097"}


id: PMID:33495454
data:
  {"abstract":"The endoplasmic reticulum (ER) network consists of tubules with high membrane curvature in cross-section, generated by the reticulons and REEPs. These proteins have two pairs of trans-membrane (TM) segments, followed by an amphipathic helix (APH), but how they induce curvature is poorly understood. Here, we show that REEPs form homodimers by interaction within the membrane. When overexpressed or reconstituted at high concentrations with phospholipids, REEPs cause extreme curvature through their TMs, generating lipoprotein particles instead of vesicles. The APH facilitates curvature generation, as its mutation prevents ER network formation of reconstituted proteoliposomes, and synthetic L- or D-amino acid peptides abolish ER network formation in Xenopus egg extracts. In Schizosaccharomyces japonicus, the APH is required for reticulon's exclusive ER-tubule localization and restricted mobility. Thus, the TMs and APH cooperate to generate high membrane curvature. We propose that the formation of splayed REEP/reticulon dimers is responsible for ER tubule formation.","alleles_by_uniquename":{"SJAG_01374:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01374","name":"nup132delta","uniquename":"SJAG_01374:allele-1"}},"annotation_curators":[{"annotation_count":8,"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":"Wang N, Clark LD, Gao Y, Kozlov MM, Shemesh T, Rapoport TA","authors_abbrev":"Wang N et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-07-09 16:24:24","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-07-09 16:24:24","canto_session_key":"23c6ae79d435aba5","canto_session_submitted_date":"2021-07-09 16:24:16","canto_triage_status":"Curatable","citation":"Nat Commun 2021 01 25;12(1):568","cv_annotations":{"biological_process":[{"annotations":[115336,115342],"is_not":false,"summary":null,"term":"GO:0097753"}],"cellular_component":[{"annotations":[115337,115338],"is_not":false,"summary":null,"term":"GO:0032541"},{"annotations":[115339,115340],"is_not":false,"summary":null,"term":"GO:0005643"}],"single_locus_phenotype":[{"annotations":[115341],"is_not":false,"summary":null,"term":"FYPO:0003973"}]},"doi":"10.1038/s41467-020-20625-y","gene_count":4,"genes_by_uniquename":{"SJAG_01374":null,"SJAG_01834":null,"SJAG_01848":null,"SJAG_03795":null},"genotypes_by_uniquename":{"nup132delta":{"display_name":"nup132delta","display_uniquename":"nup132delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01374:allele-1","expression":"Null"}]}]}},"ltp_gene_count":4,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[{"evidence":"Reconstituted Complex","gene_uniquename":"SJAG_03795","interactor_uniquename":"SJAG_03795","reference_uniquename":"PMID:33495454","throughput":"low"}],"publication_year":"2021","pubmed_entrez_date":"2021-01-26","pubmed_publication_date":"25 01 2021","terms_by_termid":{"FYPO:0003973":null,"GO:0005643":null,"GO:0032541":null,"GO:0097753":null},"title":"Mechanism of membrane-curvature generation by ER-tubule shaping proteins.","uniquename":"PMID:33495454"}


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_approver_orcid":"0000-0001-6330-7526","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":[115278,115279],"is_not":false,"summary":null,"term":"MOD:00046"}],"biological_process":[{"annotations":[115290],"is_not":false,"summary":null,"term":"GO:0090158"},{"annotations":[115292],"is_not":false,"summary":null,"term":"GO:0019915"},{"annotations":[115291],"is_not":false,"summary":null,"term":"GO:0071763"}],"cellular_component":[{"annotations":[115275],"is_not":false,"summary":null,"term":"GO:0005654"}],"single_locus_phenotype":[{"annotations":[115284,115287],"is_not":false,"summary":null,"term":"FYPO:0006054"},{"annotations":[115289],"is_not":false,"summary":null,"term":"FYPO:0005957"},{"annotations":[115271,115272,115274,115283,115286],"is_not":false,"summary":null,"term":"FYPO:0001784"},{"annotations":[115269,115270,115273,115277,115282,115285],"is_not":false,"summary":null,"term":"FYPO:0001556"},{"annotations":[115281,115288],"is_not":false,"summary":null,"term":"FYPO:0006945"},{"annotations":[115280],"is_not":false,"summary":null,"term":"FYPO:0003751"},{"annotations":[115276],"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:12236685
data:
  {"abstract":"Dimethyl dicarbonate (DMDC) was added to grape must and to synthetic media and results showed that, at 20 degrees C, 150 mg.L(-)(1) DMDC completely inhibited the fermentation of a grape must that was previously inoculated with 10(6) cells.mL(-)(1) Saccharomyces bayanus and Saccharomyces uvarum. Brettanomyces intermedius, Candida guilliermondii, Hansenula jadinii, Hansenula petersonii, Kloeckera apiculata, Pichia membranaefaciens, and Saccharomyces cerevisiae were inhibited by 250 mg.L(-)(1). Candida valida was inhibited in the presence of 350 mg.L(-)(1), whereas Hanseniaspora osmophila, Saccharomycodes ludwigii, Schizosaccharomyces pombe, and Zygosaccharomyces bailii required 400 mg.L(-)(1). Delay of fermentation (but not inhibition) was noted in the presence of 400 mg.L(-)(1) for the following cultures: Brettanomyces anomalus, Hanseniaspora uvarum, Metschnikowia pulcherrima, Schizosaccharomyces japonicus, Torulaspora delbrueckii, and Zygosaccharomyces florentinus. Acetobacter aceti and Lactobacillus sp. were completely inhibited using 1000 and 500 mg.L(-)(1) DMDC, respectively. The fermentation of a grape must inoculated with 10(6) cells.mL(-)(1) of different wine yeasts was delayed for 4 days after the prior addition of 200 mg.L(-)(1) of DMDC; 200 mg.L(-)(1) DMDC did not show any residual inhibitory effect after 12 h, nor did 300 mg.L(-)(1) 24 h after the addition. In cellar experiments, indigenously contaminated grape musts (with and without skins) showed a delay in fermentation of 48 h after the addition of only 50 mg.L(-)(1) DMDC. The possibility of using DMDC (as pure grade as commercially available) in grape must as a disinfectant for the decontamination of musts indigenously contaminated with wild yeast should be considered seriously, despite its apparent low solubility in water.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Delfini C, Gaia P, Schellino R, Strano M, Pagliara A, Ambrò S","authors_abbrev":"Delfini C et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Biotech","citation":"J Agric Food Chem 2002 Sep 25;50(20):5605-11","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":"2002-09-19","pubmed_publication_date":"25 Sep 2002","terms_by_termid":{},"title":"Fermentability of grape must after inhibition with dimethyl dicarbonate (DMDC).","uniquename":"PMID:12236685"}


id: GO_REF:0000111
data:
  {"abstract":"The Gene Ontology Consortium uses the IC (Inferred by Curator; ECO:0000305) evidence code when assignment of a GO term cannot be supported by direct experimental or sequence-based evidence, but can, based on a curator’s biological knowledge, be reasonably inferred from existing GO annotations to the same gene/gene product.  Use of the IC evidence code with GO_REF:0000111 indicates that a curator inferred the GO term based on at least one supporting annotation with an 'Inferred from Sequence Similarity' (ISS; ECO:0000250) evidence code.  Note that additional supporting annotations may be experimentally evidenced. When using GO_REF:0000111, the 'with/from' field must contain all GO identifiers used as supporting annotations.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"TBD","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Gene Ontology annotations Inferred by Curator (IC) using at least one Inferred by Sequence Similarity (ISS) annotation to support the inference","uniquename":"GO_REF:0000111"}


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:25318672
data:
  {"abstract":"Excess fatty acids and sterols are stored as triacylglycerols and sterol esters in specialized cellular organelles, called lipid droplets. Understanding what determines the cellular amount of neutral lipids and their packaging into lipid droplets is of fundamental and applied interest. Using two species of fission yeast, we show that cycling cells deficient in the function of the ER-resident CDP-DG synthase Cds1 exhibit markedly increased triacylglycerol content and assemble large lipid droplets closely associated with the ER membranes. We demonstrate that these unusual structures recruit the triacylglycerol synthesis machinery and grow by expansion rather than by fusion. Our results suggest that interfering with the CDP-DG route of phosphatidic acid utilization rewires cellular metabolism to adopt a triacylglycerol-rich lifestyle reliant on the Kennedy pathway. ","alleles_by_uniquename":{"SJAG_00426:allele-1":{"allele_type":"amino_acid_mutation","description":"P363S","gene_uniquename":"SJAG_00426","name":"bbl1-P363S","uniquename":"SJAG_00426:allele-1"}},"annotation_curators":[{"annotation_count":8,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-05-17","authors":"He Y, Yam C, Pomraning K, Chin JS, Yew JY, Freitag M, Oliferenko S","authors_abbrev":"He Y et al.","canto_added_date":"2021-05-10 02:38:06","canto_annotation_status":"APPROVED","canto_approved_date":"2021-05-17 12:42:41","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-05-17 12:42:41","canto_session_key":"f89ee2d26032c510","canto_session_submitted_date":"2021-05-17 12:42:28","canto_triage_status":"Curatable","citation":"Mol Biol Cell 2014 Dec 15;25(25):4083-95","cv_annotations":{"biological_process":[{"annotations":[115659],"is_not":false,"summary":null,"term":"GO:0016024"}],"cellular_component":[{"annotations":[115660],"is_not":false,"summary":null,"term":"GO:0005783"}],"molecular_function":[{"annotations":[115658],"is_not":false,"summary":null,"term":"GO:0004605"}],"single_locus_phenotype":[{"annotations":[115662],"is_not":false,"summary":null,"term":"FYPO:0000356"},{"annotations":[115661],"is_not":false,"summary":null,"term":"FYPO:0006433"},{"annotations":[115664],"is_not":false,"summary":null,"term":"FYPO:0004695"},{"annotations":[115663],"is_not":false,"summary":null,"term":"FYPO:0002227"},{"annotations":[115665],"is_not":false,"summary":null,"term":"FYPO:0001357"}]},"doi":"10.1091/mbc.E14-03-0832","gene_count":1,"genes_by_uniquename":{"SJAG_00426":null},"genotypes_by_uniquename":{"bbl1-P363S-P363S-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"bbl1-P363S(aa)","display_uniquename":"bbl1-P363S-P363S-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00426:allele-1","expression":"Not assayed or wild type"}]}]}},"ltp_gene_count":1,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2014","pubmed_entrez_date":"2014-10-17","pubmed_publication_date":"15 Dec 2014","terms_by_termid":{"FYECO:0000004":null,"FYECO:0000006":null,"FYECO:0000162":null,"FYPO:0000356":null,"FYPO:0001357":null,"FYPO:0002227":null,"FYPO:0004695":null,"FYPO:0006433":null,"FYPO_EXT:0000001":null,"GO:0004605":null,"GO:0005783":null,"GO:0008654":null,"GO:0016024":null},"title":"Increase in cellular triacylglycerol content and emergence of large ER-associated lipid droplets in the absence of CDP-DG synthase function.","uniquename":"PMID:25318672"}


id: PMID:32109380
data:
  {"abstract":"Eukaryotic genomes are organized within the nucleus through interactions with inner nuclear membrane (INM) proteins. How chromatin tethering to the INM is controlled in interphase and how this process contributes to subsequent mitotic nuclear envelope (NE) remodeling remains unclear. We have probed these fundamental questions using the fission yeast Schizosaccharomyces japonicus, which breaks and reforms the NE during mitosis. We show that attachments between heterochromatin and the transmembrane Lem2-Nur1 complex at the INM are remodeled in interphase by the ESCRT-III/Vps4 machinery. Failure of ESCRT-III/Vps4 to release Lem2-Nur1 from heterochromatin leads to persistent association of chromosomes with the INM throughout mitosis. At mitotic exit, such trapping of Lem2-Nur1 on heterochromatin prevents it from re-establishing nucleocytoplasmic compartmentalization. Our work identifies the Lem2-Nur1 complex as a substrate for the nuclear ESCRT machinery and explains how the dynamic tethering of chromosomes to the INM is linked to the establishment of nuclear compartmentalization.","alleles_by_uniquename":{"SJAG_01050:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01050","name":"nur1delta","uniquename":"SJAG_01050:allele-1"},"SJAG_01242:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01242","name":"vps32delta","uniquename":"SJAG_01242:allele-1"},"SJAG_01330:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01330","name":"mad2delta","uniquename":"SJAG_01330:allele-1"},"SJAG_01745:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01745","name":"lem2delta","uniquename":"SJAG_01745:allele-1"},"SJAG_03250:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03250","name":"sst4delta","uniquename":"SJAG_03250:allele-1"},"SJAG_03783:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03783","name":"vps24delta","uniquename":"SJAG_03783:allele-1"},"SJAG_03892:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03892","name":"vps4delta","uniquename":"SJAG_03892:allele-1"},"SJAG_03892:allele-2":{"allele_type":"amino_acid_mutation","description":"E233Q","gene_uniquename":"SJAG_03892","name":"Vps4-EQ","uniquename":"SJAG_03892:allele-2"},"SJAG_03892:allele-3":{"allele_type":"amino_acid_mutation","description":"I307T 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GH, Sprenger S, Teis D, Oliferenko S","authors_abbrev":"Pieper GH et al.","canto_added_date":"2021-05-10 02:37:07","canto_annotation_status":"APPROVED","canto_approved_date":"2021-06-17 17:46:25","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-06-17 17:46:25","canto_session_key":"89c611dbc0229af1","canto_session_submitted_date":"2021-06-17 17:46:16","canto_triage_status":"Curatable","citation":"Dev Cell 2020 04 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L327S aa)","display_uniquename":"vps4-ts-I307T_L327S-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03892:allele-3","expression":"Not assayed or wild type"}]}]},"vps4delta":{"display_name":"vps4delta","display_uniquename":"vps4delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03892:allele-1","expression":"Null"}]}]}},"ltp_gene_count":15,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[{"evidence":"Reconstituted Complex","gene_uniquename":"SJAG_01242","interactor_uniquename":"SJAG_03892","reference_uniquename":"PMID:32109380","throughput":"low"},{"evidence":"Reconstituted Complex","gene_uniquename":"SJAG_04489","interactor_uniquename":"SJAG_03892","reference_uniquename":"PMID:32109380","throughput":"low"},{"evidence":"Reconstituted Complex","gene_uniquename":"SJAG_05207","interactor_uniquename":"SJAG_01242","reference_uniquename":"PMID:32109380","throughput":"low"},{"evidence":"Reconstituted Complex","gene_uniquename":"SJAG_05207","interactor_uniquename":"SJAG_01745","reference_uniquename":"PMID:32109380","throughput":"low"},{"evidence":"Reconstituted Complex","gene_uniquename":"SJAG_05207","interactor_uniquename":"SJAG_03892","reference_uniquename":"PMID:32109380","throughput":"low"}],"publication_year":"2020","pubmed_entrez_date":"2020-02-29","pubmed_publication_date":"06 04 2020","terms_by_termid":{"FYECO:0000004":null,"FYECO:0000137":null,"FYPO:0001132":null,"FYPO:0001234":null,"FYPO:0001370":null,"FYPO:0001440":null,"FYPO:0003657":null,"FYPO:0003780":null,"FYPO:0004318":null,"FYPO:0004718":null,"FYPO:0007073":null,"FYPO:0007770":null,"FYPO:0007771":null,"FYPO:0007772":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null,"GO:0000093":null,"GO:0000776":null,"GO:0000781":null,"GO:0000792":null,"GO:0000815":null,"GO:0005643":null,"GO:0005771":null,"GO:0005783":null,"GO:0005816":null,"GO:0031965":null,"GO:0032585":null,"GO:0043515":null,"GO:1990343":null},"title":"ESCRT-III/Vps4 Controls Heterochromatin-Nuclear Envelope Attachments.","uniquename":"PMID:32109380"}


id: PMID:35226668
data:
  {"abstract":"RNA interference (RNAi) is a conserved mechanism of small RNA-mediated genome regulation commonly involved in suppression of transposable elements (TEs) through both post-transcriptional silencing, and transcriptional repression via heterochromatin assembly. The fission yeast Schizosaccharomyces pombe has been extensively utilised as a model for studying RNAi pathways. However, this species is somewhat atypical in that TEs are not major targets of RNAi, and instead small RNAs correspond primarily to non-coding pericentromeric repeat sequences, reflecting a specialised role for the pathway in promoting heterochromatin assembly in these regions. In contrast, in the related fission yeast Schizosaccharomyces japonicus, sequenced small RNAs correspond primarily to TEs. This suggests there may be fundamental differences in the operation of RNAi pathways in these two related species. To investigate these differences, we probed RNAi function in S. japonicus. Unexpectedly, and in contrast to S. pombe, we found that RNAi is essential in this species. Moreover, viability of RNAi mutants can be rescued by mutations implicated in enhancing RNAi-independent heterochromatin propagation. These rescued strains retain heterochromatic marks on TE sequences, but exhibit derepression of TEs at the post-transcriptional level. Our findings indicate that S. japonicus retains the ancestral role of RNAi in facilitating suppression of TEs via both post-transcriptional silencing and heterochromatin assembly, with specifically the heterochromatin pathway being essential for viability, likely due to a function in genome maintenance. The specialised role of RNAi in heterochromatin assembly in S. pombe appears to be a derived state that emerged after the divergence of S. japonicus.","alleles_by_uniquename":{"SJAG_02409:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02409","name":"stc1delta","uniquename":"SJAG_02409:allele-1"},"SJAG_02594:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02594","name":"arb1delta","uniquename":"SJAG_02594:allele-1"},"SJAG_02621:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02621","name":"ago1delta","uniquename":"SJAG_02621:allele-1"},"SJAG_02668:allele-1":{"allele_type":"amino_acid_mutation","description":"R77W","gene_uniquename":"SJAG_02668","name":"mpe1-R77W","uniquename":"SJAG_02668:allele-1"},"SJAG_03118:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03118","name":"leo1delta","uniquename":"SJAG_03118:allele-1"},"SJAG_03118:allele-2":{"allele_type":"nonsense_mutation","description":"aa61->stop","gene_uniquename":"SJAG_03118","name":"frameshift","uniquename":"SJAG_03118:allele-2"},"SJAG_03356:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03356","name":"rdp1delta","uniquename":"SJAG_03356:allele-1"},"SJAG_03689:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03689","name":"dcr1delta","uniquename":"SJAG_03689:allele-1"},"SJAG_03916:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03916","name":"chp1delta","uniquename":"SJAG_03916:allele-1"},"SJAG_04061:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04061","name":"arb2delta","uniquename":"SJAG_04061:allele-1"},"SJAG_04574:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04574","name":"clr4delta","uniquename":"SJAG_04574:allele-1"}},"annotation_curators":[{"annotation_count":31,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2022-03-07","authors":"Chapman E, Taglini F, Bayne EH","authors_abbrev":"Chapman E et al.","canto_added_date":"2022-03-07 09:13:19","canto_annotation_status":"APPROVED","canto_approved_date":"2022-03-07 12:35:06","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2022-03-07 12:35:06","canto_session_key":"3d6467bf1cb92446","canto_session_submitted_date":"2022-03-07 12:34:56","canto_triage_status":"Curatable","citation":"PLoS Genet 2022 Feb 28;18(2):e1010100","cv_annotations":{"biological_process":[{"annotations":[115521,115522],"is_not":false,"summary":null,"term":"GO:0031507"},{"annotations":[115519,115520],"is_not":false,"summary":null,"term":"GO:0016441"}],"multi_locus_phenotype":[{"annotations":[115515,115517],"is_not":false,"summary":null,"term":"FYPO:0004982"},{"annotations":[115516,115518],"is_not":false,"summary":null,"term":"FYPO:0004573"},{"annotations":[115512],"is_not":false,"summary":null,"term":"FYPO:0002061"},{"annotations":[115513,115514],"is_not":false,"summary":null,"term":"FYPO:0006989"},{"annotations":[115507,115508,115509,115510],"is_not":false,"summary":null,"term":"FYPO:0002058"}],"single_locus_phenotype":[{"annotations":[115501],"is_not":false,"summary":null,"term":"FYPO:0004205"},{"annotations":[115503],"is_not":false,"summary":null,"term":"FYPO:0004982"},{"annotations":[115505],"is_not":false,"summary":null,"term":"FYPO:0000595"},{"annotations":[115502],"is_not":false,"summary":null,"term":"FYPO:0004574"},{"annotations":[115494,115495,115496,115497,115498,115499,115500,115511],"is_not":false,"summary":null,"term":"FYPO:0002061"},{"annotations":[115506],"is_not":false,"summary":null,"term":"FYPO:0006989"},{"annotations":[115504],"is_not":false,"summary":null,"term":"FYPO:0000596"}]},"doi":"10.1371/journal.pgen.1010100","gene_count":10,"genes_by_uniquename":{"SJAG_02409":null,"SJAG_02594":null,"SJAG_02621":null,"SJAG_02668":null,"SJAG_03118":null,"SJAG_03356":null,"SJAG_03689":null,"SJAG_03916":null,"SJAG_04061":null,"SJAG_04574":null},"genetic_interactions":[[{"gene_a_uniquename":"SJAG_03689","gene_b_uniquename":"SJAG_03118","interaction_type":"Phenotypic 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leo1delta","display_uniquename":"clr4delta__leo1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04574:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_03118:allele-1","expression":"Null"}]}]},"dcr1delta":{"display_name":"dcr1delta","display_uniquename":"dcr1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03689:allele-1","expression":"Null"}]}]},"dcr1delta__frameshift-aa61->stop-nonsense_mutation-expression-not_assayed_or_wild_type":{"display_name":"dcr1delta frameshift(aa61->stop)","display_uniquename":"dcr1delta__frameshift-aa61->stop-nonsense_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03689:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_03118:allele-2","expression":"Not assayed or wild type"}]}]},"dcr1delta__leo1delta":{"display_name":"dcr1delta leo1delta","display_uniquename":"dcr1delta__leo1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03689:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_03118:allele-1","expression":"Null"}]}]},"dcr1delta__mpe1-R77W-R77W-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"dcr1delta mpe1-R77W(aa)","display_uniquename":"dcr1delta__mpe1-R77W-R77W-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03689:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_02668:allele-1","expression":"Not assayed or wild type"}]}]},"rdp1delta":{"display_name":"rdp1delta","display_uniquename":"rdp1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03356:allele-1","expression":"Null"}]}]},"stc1delta":{"display_name":"stc1delta","display_uniquename":"stc1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02409:allele-1","expression":"Null"}]}]}},"ltp_gene_count":10,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2022","pubmed_entrez_date":"2022-02-28","pubmed_publication_date":"28 Feb 2022","terms_by_termid":{"FYECO:0000005":null,"FYECO:0000162":null,"FYPO:0000595":null,"FYPO:0000596":null,"FYPO:0002058":null,"FYPO:0002061":null,"FYPO:0004205":null,"FYPO:0004573":null,"FYPO:0004574":null,"FYPO:0004982":null,"FYPO:0006989":null,"FYPO_EXT:0000001":null,"GO:0016441":null,"GO:0031507":null},"title":"Separable roles for RNAi in regulation of transposable elements and viability in the fission yeast Schizosaccharomyces japonicus.","uniquename":"PMID:35226668"}


id: GO_REF:0000081
data:
  {"abstract":"We have created a standard template for classes describing the formation of a plant structure as a biological process. The underlying equivalence axiom template is \"'anatomical structure formation involved in morphogenesis' and 'results in formation of' some P\", where P is a plant anatomical entity (PO:0025131).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of plant formation as biological process in the Gene Ontology","uniquename":"GO_REF:0000081"}


id: PMID:36058798
data:
  {"abstract":"Schizosaccharomyces japonicus is a dimorphic yeast, transiting between unicellular and hyphal growth. The glycoproteins of fission yeast contain, in addition to mannose (Man), a large number of galactose (Gal) residues. Previously, we reported that the cell-surface O-glycans of S. japonicus comprise mainly tri-saccharides (Gal-Man-Man) as a main component, in contrast to the tetra-saccharides observed in other Schizosaccharomyces species. Here we have investigated the function of cell-surface Gal residues in S. japonicus. Because disruption of gms1 + , encoding the UDP-Gal transporter required for galactomannan synthesis, abolishes cell-surface galactosylation in Schizosaccharomyces pombe, we constructed a deletion mutant of the homologous gene in S. japonicus gms1Δ [gms1 (S.j)] and determined the N- and O-linked oligosaccharide structures present on the cell surface. Disruption of gms1 (S.j) resulted in a complete lack of Gal on the cell surface, indicating that Gms1 plays an essential role in supplying UDP-Gal from the cytoplasm to the Golgi lumen. Analytical microscopy of gms1Δ demonstrated that the lack of cell-surface Gal did not affect cell growth or morphology during vegetative growth. However, hyphal development was blocked in gms1Δ, even in the presence of the topoisomerase I inhibitor camptothecin, which is known to induce hyphal differentiation in wild-type S. japonicus. Collectively, these findings show that Gal-containing oligosaccharides are required for cell wall integrity during filamentous growth in S. japonicus.","alleles_by_uniquename":{"SJAG_04697:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04697","name":"gms1delta","uniquename":"SJAG_04697: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":"2022-12-01","authors":"Fukunaga T, Ohashi T, Tanaka Y, Yoshimatsu T, Higuchi Y, Maekawa H, Takegawa K","authors_abbrev":"Fukunaga T et al.","canto_added_date":"2022-11-25 12:12:27","canto_annotation_status":"APPROVED","canto_approved_date":"2022-12-01 10:35:53","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2022-12-01 10:35:53","canto_session_key":"465355706dc223a3","canto_session_submitted_date":"2022-11-25 12:49:07","canto_triage_status":"Curatable","citation":"J Biosci Bioeng 2022 Nov;134(5):384-392","cv_annotations":{"single_locus_phenotype":[{"annotations":[115481],"is_not":false,"summary":null,"term":"FYPO:0008029"},{"annotations":[115477],"is_not":false,"summary":null,"term":"FYPO:0000082"},{"annotations":[115480],"is_not":false,"summary":null,"term":"FYPO:0007776"},{"annotations":[115479],"is_not":false,"summary":null,"term":"FYPO:0007780"},{"annotations":[115476],"is_not":false,"summary":null,"term":"FYPO:0003727"},{"annotations":[115478],"is_not":false,"summary":null,"term":"FYPO:0000106"}]},"doi":"10.1016/j.jbiosc.2022.07.014","gene_count":1,"genes_by_uniquename":{"SJAG_04697":null},"genotypes_by_uniquename":{"gms1delta":{"display_name":"gms1delta","display_uniquename":"gms1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04697:allele-1","expression":"Null"}]}]}},"ltp_gene_count":1,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2022","pubmed_entrez_date":"2022-09-04","pubmed_publication_date":"Nov 2022","terms_by_termid":{"FYECO:0000004":null,"FYECO:0000005":null,"FYECO:0000126":null,"FYECO:0000137":null,"FYECO:0000314":null,"FYPO:0000082":null,"FYPO:0000106":null,"FYPO:0003727":null,"FYPO:0007776":null,"FYPO:0007780":null,"FYPO:0008029":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null},"title":"Galactosylation of cell-surface glycoprotein required for hyphal growth and cell wall integrity in Schizosaccharomyces japonicus.","uniquename":"PMID:36058798"}


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:0000088
data:
  {"abstract":"We have created a standard template for classes defining a protein complex by a molecular function as a cellular component. The underlying equivalence axiom template is \"GO:0043234 and 'capable_of' some ?A\", where A is a molecular function.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of protein complex by molecular function in the Gene Ontology","uniquename":"GO_REF:0000088"}


id: GO_REF:0000008
data:
  {"abstract":"The sequence conservation that permits the establishment of orthology between mouse and rat or mouse and human genes is a strong predictor of the conservation of function for the gene product across these species. Therefore, in instances where a mouse gene product has not been functionally characterized, but its human or rat orthologs have, Mouse Genome Informatics (MGI) curators append the GO terms associated with the orthologous gene(s) to the mouse gene. Only those GO terms assigned by experimental determination to the ortholog of the mouse gene will be adopted by MGI. GO terms that are assigned to the ortholog of the mouse gene computationally (i.e. IEA), will not be transferred to the mouse ortholog. The evidence code represented by this citation is Inferred by Sequence Orthology (ISO).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Mouse Genome Informatics scientific curators","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Gene Ontology annotation by the MGI curatorial staff, curated orthology","uniquename":"GO_REF:0000008"}


id: PMID:23145069
data:
  {"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.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Krzyzanowski MK, Kozlowska E, Kozlowski P","authors_abbrev":"Krzyzanowski MK et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Sequence feature or region","citation":"PLoS One 2012;7(11):e49059","cv_annotations":{},"doi":"10.1371/journal.pone.0049059","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2012","pubmed_entrez_date":"2012-11-13","pubmed_publication_date":"2012","terms_by_termid":{},"title":"Identification and functional analysis of the erh1(+) gene encoding enhancer of rudimentary homolog from the fission yeast Schizosaccharomyces pombe.","uniquename":"PMID:23145069"}


id: PMID:8546451
data:
  {"abstract":"The phylogenesis of fungi is controversial due to their simple morphology and poor fossilization. Traditional classification supported by morphological studies and physiological traits placed the fission yeasts in one group with ascomycetous yeasts. The rRNA sequence comparisons, however, revealed an enormous evolutionary gap between Saccharomyces and Schizosaccharomyces. As shown in this review, the protein sequences also show a large gap which is almost as large as that separating Schizosaccharomyces from higher animals. Since the two yeasts share features (both cytological and molecular) in common which are also characteristic of ascomycetous fungi, their separation must have taken place later than the sequence differences may suggest. Possible reasons for the paradox are discussed. The sequence data also suggest a slower evolutionary rate in the Schizosaccharomyces lineage than in the Saccharomyces branch. In the fission yeast lineage two ramifications can be supposed. First S. japonicus (Hasegawaea japonica) branched off, then S. octosporus (Octosporomyces octosporus) separated from S. pombe.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Sipiczki M","authors_abbrev":"Sipiczki M","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Phylogeny and evolutionary studies","citation":"Antonie Van Leeuwenhoek 1995 Aug;68(2):119-49","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1995","pubmed_entrez_date":"1995-08-01","pubmed_publication_date":"Aug 1995","terms_by_termid":{},"title":"Phylogenesis of fission yeasts. Contradictions surrounding the origin of a century old genus.","uniquename":"PMID:8546451"}


id: GO_REF:0000116
data:
  {"abstract":"Rhea (https://www.rhea-db.org/, PMID:30272209) is an expert-curated knowledgebase of chemical and transport reactions of biological interest - and the standard for enzyme and transporter annotation in UniProtKB (PMID:31688925). Rhea uses the chemical dictionary ChEBI (Chemical Entities of Biological Interest) to describe reaction participants and their chemical transformations in a computationally tractable manner. GO terms corresponding to Rhea reactions are assigned a Rhea database cross-reference. The corresponding GO term is automatically applied to all UniProt entries annotated with a Rhea reaction. The mapping file is available at: http://current.geneontology.org/ontology/external2go/rhea2go.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO Central curators, GOA curators, Rhea curators","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Automatic Gene Ontology annotation based on Rhea mapping.","uniquename":"GO_REF:0000116"}


id: GO_REF:0000003
data:
  {"abstract":"Transitive assignment using Enzyme Commission identifiers. This method is used for any database entry, such as a protein record in UniProtKB or TrEMBL, that has had an Enzyme Commission number assigned. The corresponding GO term is determined using the EC cross-references in the GO molecular function ontology. Also see Hill et al., Genomics (2001) 74:121-128. The mapping file is available at http://www.geneontology.org/external2go/ec2go.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GOA curators, MGI curators","canto_curator_role":"JaponicusDB","cv_annotations":{"molecular_function":[{"annotations":[68469],"is_not":false,"summary":null,"term":"GO:0003925"},{"annotations":[58968],"is_not":false,"summary":null,"term":"GO:0043864"},{"annotations":[65165],"is_not":false,"summary":null,"term":"GO:0052832"},{"annotations":[65166],"is_not":false,"summary":null,"term":"GO:0052833"},{"annotations":[68014],"is_not":false,"summary":null,"term":"GO:1990817"},{"annotations":[60879],"is_not":false,"summary":null,"term":"GO:0102389"}]},"gene_count":5,"genes_by_uniquename":{"SJAG_02383":null,"SJAG_02721":null,"SJAG_03739":null,"SJAG_04509":null,"SJAG_04954":null},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{"GO:0003925":null,"GO:0043864":null,"GO:0052832":null,"GO:0052833":null,"GO:0102389":null,"GO:1990817":null},"title":"Gene Ontology annotation based on Enzyme Commission mapping","uniquename":"GO_REF:0000003"}


id: PMID:31380845
data:
  {"abstract":"Lipid metabolism and its regulation are of interest to both basic and applied life sciences and biotechnology. In this regard, various yeast species are used as models in lipid metabolic research or for industrial lipid production. Lipid droplets are highly dynamic storage bodies and their cellular content represents a convenient readout of the lipid metabolic state. Fluorescence microscopy is a method of choice for quantitative analysis of cellular lipid droplets, as it relies on widely available equipment and allows analysis of individual lipid droplets. Furthermore, microscopic image analysis can be automated, greatly increasing overall analysis throughput. Here, we describe an experimental and analytical workflow for automated detection and quantitative description of individual lipid droplets in three different model yeast species: the fission yeasts Schizosaccharomyces pombe and Schizosaccharomyces japonicus, and the budding yeast Saccharomyces cerevisiae. Lipid droplets are visualized with BODIPY 493/503, and cell-impermeable fluorescent dextran is added to the culture media to help identify cell boundaries. Cells are subjected to 3D epifluorescence microscopy in green and blue channels and the resulting z-stack images are processed automatically by a MATLAB pipeline. The procedure outputs rich quantitative data on cellular lipid droplet content and individual lipid droplet characteristics in a tabular format suitable for downstream analyses in major spreadsheet or statistical packages. We provide example analyses of lipid droplet content under various conditions that affect cellular lipid metabolism.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Princová J, Schätz M, Ťupa O, Převorovský M","authors_abbrev":"Princová J et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Method or reagent","citation":"J Vis Exp 2019 07 17;(149)","cv_annotations":{},"doi":"10.3791/59889","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2019","pubmed_entrez_date":"2019-08-06","pubmed_publication_date":"17 07 2019","terms_by_termid":{},"title":"Analysis of Lipid Droplet Content in Fission and Budding Yeasts using Automated Image Processing.","uniquename":"PMID:31380845"}


id: PMID:31956022
data:
  {"abstract":"Membrane function is fundamental to life. Each species explores membrane lipid diversity within a genetically predefined range of possibilities. How membrane lipid composition in turn defines the functional space available for evolution of membrane-centered processes remains largely unknown. We address this fundamental question using related fission yeasts Schizosaccharomyces pombe and Schizosaccharomyces japonicus. We show that, unlike S. pombe that generates membranes where both glycerophospholipid acyl tails are predominantly 16-18 carbons long, S. japonicus synthesizes unusual \"asymmetrical\" glycerophospholipids where the tails differ in length by 6-8 carbons. This results in stiffer bilayers with distinct lipid packing properties. Retroengineered S. pombe synthesizing the S.-japonicus-type phospholipids exhibits unfolded protein response and downregulates secretion. Importantly, our protein sequence comparisons and domain swap experiments support the hypothesis that transmembrane helices co-evolve with membranes, suggesting that, on the evolutionary scale, changes in membrane lipid composition may necessitate extensive adaptation of the membrane-associated proteome.","alleles_by_uniquename":{"SJAG_01458:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01458","name":"acb1delta","uniquename":"SJAG_01458:allele-1"}},"annotation_curators":[{"annotation_count":4,"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":"Makarova M, Peter M, Balogh G, Glatz A, MacRae JI, Lopez Mora N, Booth P, Makeyev E, Vigh L, Oliferenko S","authors_abbrev":"Makarova M et al.","canto_added_date":"2021-05-10 02:37:19","canto_annotation_status":"APPROVED","canto_approved_date":"2021-07-09 13:38:09","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-07-09 13:38:09","canto_session_key":"801e82954edbb6c1","canto_session_submitted_date":"2021-07-09 13:38:00","canto_triage_status":"Curatable","citation":"Curr Biol 2020 02 03;30(3):367-380.e8","cv_annotations":{"cellular_component":[{"annotations":[115489],"is_not":false,"summary":null,"term":"GO:0005801"},{"annotations":[115491],"is_not":false,"summary":null,"term":"GO:0005829"}],"single_locus_phenotype":[{"annotations":[115490],"is_not":false,"summary":null,"term":"FYPO:0000719"}]},"doi":"10.1016/j.cub.2019.11.043","gene_count":4,"genes_by_uniquename":{"SJAG_00816":null,"SJAG_01458":null,"SJAG_04107":null,"SJAG_04972":null},"genotypes_by_uniquename":{"acb1delta":{"display_name":"acb1delta","display_uniquename":"acb1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01458:allele-1","expression":"Null"}]}]}},"ltp_gene_count":4,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[{"evidence":"Co-purification","gene_uniquename":"SJAG_04972","interactor_uniquename":"SJAG_04107","reference_uniquename":"PMID:31956022","throughput":"low"}],"publication_year":"2020","pubmed_entrez_date":"2020-01-21","pubmed_publication_date":"03 02 2020","terms_by_termid":{"FYECO:0000126":null,"FYPO:0000719":null,"GO:0005801":null,"GO:0005829":null},"title":"Delineating the Rules for Structural Adaptation of Membrane-Associated Proteins to Evolutionary Changes in Membrane Lipidome.","uniquename":"PMID:31956022"}


id: PMID:23934997
data:
  {"abstract":"Both budding yeast Saccharomyces cerevisiae and fission yeast Schizosaccahromyces pombe have been very popular organisms used for biological research with eukaryotes for many decades. Judging from the fission yeast Schizosaccharomyces japonicus DNA sequence determined 2 years ago, this species is evolutionarily very much unrelated to the commonly used yeasts for research. Indicating evolutionary divergence, the S. japonicus makes 8-spored asci and mitosis occurs with a partial breakdown of nuclear membrane whereas the other yeasts make 4-spored asci and cells divide without nuclear breakdown. The commonly used yeast species exhibit a generation time between 1.5 and 2.0 hr, and their genetic cross takes a period of more than 7 working d. As described here, a generation time of only 63 min and meiotic analysis completed in just 2.5 d, the S. japonicus fission yeast is predicted to become a choice organism for future research on the biology of eukaryotes. ","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Klar AJ","authors_abbrev":"Klar AJ","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Review or comment","citation":"G3 (Bethesda) 2013 Oct 03;3(10):1869-73","cv_annotations":{},"doi":"10.1534/g3.113.007187","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":"2013-08-13","pubmed_publication_date":"03 Oct 2013","terms_by_termid":{},"title":"Schizosaccharomyces japonicus yeast poised to become a favorite experimental organism for eukaryotic research.","uniquename":"PMID:23934997"}


id: GO_REF:0000118
data:
  {"abstract":"TreeGrafter is a software tool for annotating protein sequences using pre-annotated PANTHER phylogenetic trees. TreeGrafter takes an input query protein sequence, finds the best matching homologous family, and then grafts it to the best location in the tree. It then annotates the query sequence by propagating annotations from the appropriate ancestral node(s) in the reference tree, which were manually annotated using the PAN-GO method (see GOREF_0000033). This method is integrated into InterProScan, which produces annotations to millions of genes across tens of thousands of organisms.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Haiming Tang, Dustin Ebert, Matthias Blum, Robert Finn, Paul Thomas ","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"TreeGrafter-generated GO annotations","uniquename":"GO_REF:0000118"}


id: PMID:17870620
data:
  {"abstract":"In this work, we identify a family of putative adhesins in the fission yeasts Schizosaccharomyces pombe and Schizosaccharomyces japonicus. The members of this family share a conserved tandem repeat related to those found in the Candida albicans Als family of adhesins. Unlike previously characterised adhesins that possess conserved ligand-binding domains at the N-terminus, this group of proteins carry ligand-binding domains at their C-termini. We demonstrate that one such domain--the uncharacterised GLEYA domain, is related to the lectin-like ligand-binding domain found in the Saccharomyces cerevisiae Flo proteins. Unlike the Flo and Als proteins, the fission yeast adhesins do not contain detectable glycosyl phosphatidyl inositol (GPI) membrane anchor signals to mediate their attachment to the cell wall, which may suggest a novel cell wall attachment mechanism. Further sequence analysis identified several putative adhesins in the sub-phylum of Pezizomycotina, where only a few adhesins have been described to date.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Linder T, Gustafsson CM","authors_abbrev":"Linder T et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Sequence feature or region","citation":"Fungal Genet Biol 2008 Apr;45(4):485-97","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2008","pubmed_entrez_date":"2007-09-18","pubmed_publication_date":"Apr 2008","terms_by_termid":{},"title":"Molecular phylogenetics of ascomycotal adhesins--a novel family of putative cell-surface adhesive proteins in fission yeasts.","uniquename":"PMID:17870620"}


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: 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_approver_orcid":"0000-0002-8138-6851","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":[115251],"is_not":false,"summary":null,"term":"FYPO:0007773"},{"annotations":[115234,115235,115244,115266,115267],"is_not":false,"summary":null,"term":"FYPO:0007789"},{"annotations":[115263],"is_not":false,"summary":null,"term":"FYPO:0000584"},{"annotations":[115233,115237,115241],"is_not":false,"summary":null,"term":"FYPO:0001355"},{"annotations":[115265],"is_not":false,"summary":null,"term":"FYPO:0007790"},{"annotations":[115232,115238,115239,115243,115246,115248,115249,115262,115264],"is_not":false,"summary":null,"term":"FYPO:0000280"},{"annotations":[115240,115245,115247,115250,115252,115253,115254,115255,115256,115257,115258,115259,115260,115261],"is_not":false,"summary":null,"term":"FYPO:0000124"},{"annotations":[115231,115236,115242,115268],"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:21905090
data:
  {"abstract":"The construction of diploid cells eases genetic analysis in haploid genetic systems because diploid cells allow for the characterization of essential genes. Here, we report the construction of diploid cells using ade6 point mutants that suppress each other via interallelic complementation in the fission yeast Schizosaccharomyces japonicus var japonicus (Sz. japonicus). We constructed an ade6-domK mutant in addition to the previously described ade6-domE. Phenotypes of both mutants exhibited adenine auxotrophy and red colonies. The mutations complemented the phenotypes in a mutually dependent manner. Diploid zygotes, in which the two mutations were introduced simultaneously into the same cells, were isolated by selecting for adenine independence. Such diploid cells are apparently larger in size than haploid cells, yet have a similar nuclear/cytoplasmic ratio, and thus the nuclear size control that has been reported in Sz. pombe is also present in Sz. japonicus.","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_01081:allele-2":{"allele_type":"amino_acid_mutation","description":"Q262A","gene_uniquename":"SJAG_01081","name":"ade6-domK","uniquename":"SJAG_01081:allele-2"},"SJAG_01081:allele-3":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01081","name":"ade6delta","uniquename":"SJAG_01081:allele-3"}},"annotation_curators":[{"annotation_count":3,"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 13:21:47","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Sho Okamoto","canto_curator_role":"community","canto_first_approved_date":"2022-11-23 13:21:47","canto_session_key":"7c1c894d4ee8d8d3","canto_session_submitted_date":"2022-11-23 13:21:40","canto_triage_status":"Curatable","citation":"Yeast 2011 Oct;28(10):747-54","cv_annotations":{"single_locus_phenotype":[{"annotations":[115484,115485,115486],"is_not":false,"summary":null,"term":"FYPO:0000747"}]},"doi":"10.1002/yea.1898","gene_count":1,"genes_by_uniquename":{"SJAG_01081":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"}]}]},"ade6-domK-Q262A-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"ade6-domK(Q262A aa)","display_uniquename":"ade6-domK-Q262A-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01081:allele-2","expression":"Not assayed or wild type"}]}]},"ade6delta":{"display_name":"ade6delta","display_uniquename":"ade6delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01081:allele-3","expression":"Null"}]}]}},"ltp_gene_count":1,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2011","pubmed_entrez_date":"2011-09-10","pubmed_publication_date":"Oct 2011","terms_by_termid":{"FYPO:0000747":null},"title":"Construction of diploid zygotes by interallelic complementation of ade6 in Schizosaccharomyces japonicus.","uniquename":"PMID:21905090"}


id: PMID:23090706
data:
  {"abstract":"DNA damage response includes DNA repair, nucleotide metabolism and even a control of cell fates including differentiation, cell death pathway or some combination of these. The responses to DNA damage differ from species to species. Here we aim to delineate the checkpoint pathway in the dimorphic fission yeast Schizosaccharomyces japonicus, where DNA damage can trigger a differentiation pathway that is a switch from a bidirectional yeast growth mode to an apical hyphal growth mode, and the switching is regulated via a checkpoint kinase, Chk1. This Chk1-dependent switch to hyphal growth is activated with even low doses of agents that damage DNA; therefore, we reasoned that this switch may depend on other genes orthologous to the components of the classical Sz. pombe Chk1-dependent DNA checkpoint pathway. As an initial test of this hypothesis, we assessed the effects of mutations in Sz. japonicus orthologs of Sz. pombe checkpoint genes on this switch from bidirectional to hyphal growth. The same set of DNA checkpoint genes was confirmed in Sz. japonicus. We tested the effect of each DNA checkpoint mutants on hyphal differentiation by DNA damage. We found that the Sz. japonicus hyphal differentiation pathway was dependent on Sz. japonicus orthologs of Sz. pombe checkpoint genes-(SP)rad3, (SP)rad26, (SP)rad9, (SP)rad1, (SP)rad24, (SP)rad25, (SP)crb2, and (SP)chk1-that function in the DNA damage checkpoint pathway, but was not dependent on orthologs of two Sz. pombe genes-(SP)cds1 or (SP)mrc1-that function in the DNA replication checkpoint pathway. These findings indicated that although the role of each component of the DNA damage checkpoint and DNA replication checkpoint is mostly same between the two fission yeasts, the DNA damage checkpoint was the only pathway that governed DNA damage-dependent hyphal growth. We also examined whether DNA damage checkpoint signaling engaged in functional crosstalk with other hyphal differentiation pathways because hyphal differentiation can also be triggered by nutritional stress. Here, we discovered genetic interactions that indicated that the cAMP pathway engaged in crosstalk with Chk1-dependent signaling.","alleles_by_uniquename":{"SJAG_00364:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00364","name":"rad3delta","uniquename":"SJAG_00364:allele-1"},"SJAG_00429:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00429","name":"rad26delta","uniquename":"SJAG_00429:allele-1"},"SJAG_01205:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01205","name":"crb2delta","uniquename":"SJAG_01205: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"},"SJAG_02266:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02266","name":"rad24delta","uniquename":"SJAG_02266:allele-1"},"SJAG_02576:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02576","name":"rad25delta","uniquename":"SJAG_02576:allele-1"},"SJAG_02771:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02771","name":"rad1delta","uniquename":"SJAG_02771:allele-1"},"SJAG_03720:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03720","name":"tel1delta","uniquename":"SJAG_03720:allele-1"},"SJAG_04287:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04287","name":"cds1delta","uniquename":"SJAG_04287:allele-1"},"SJAG_04671:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04671","name":"mrc1delta","uniquename":"SJAG_04671:allele-1"}},"annotation_curators":[{"annotation_count":28,"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 17:21:20","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Sho Okamoto","canto_curator_role":"community","canto_first_approved_date":"2022-11-21 17:21:20","canto_session_key":"5f68f94ee65a99b7","canto_session_submitted_date":"2022-11-21 17:21:13","canto_triage_status":"Curatable","citation":"Curr Genet 2012 Dec;58(5-6):291-303","cv_annotations":{"multi_locus_phenotype":[{"annotations":[115458],"is_not":false,"summary":null,"term":"FYPO:0007790"},{"annotations":[115464],"is_not":false,"summary":null,"term":"FYPO:0000085"},{"annotations":[115461],"is_not":false,"summary":null,"term":"FYPO:0000088"}],"single_locus_phenotype":[{"annotations":[115449,115450,115451,115452,115453,115454,115456,115457],"is_not":false,"summary":null,"term":"FYPO:0007782"},{"annotations":[115475],"is_not":false,"summary":null,"term":"FYPO:0007774"},{"annotations":[115474],"is_not":false,"summary":null,"term":"FYPO:0001690"},{"annotations":[115448,115455],"is_not":false,"summary":null,"term":"FYPO:0007790"},{"annotations":[115473],"is_not":false,"summary":null,"term":"FYPO:0004693"},{"annotations":[115462,115463,115468,115469,115470],"is_not":false,"summary":null,"term":"FYPO:0000085"},{"annotations":[115459,115460,115465,115466,115467],"is_not":false,"summary":null,"term":"FYPO:0000088"},{"annotations":[115471,115472],"is_not":false,"summary":null,"term":"FYPO:0001234"}]},"doi":"10.1007/s00294-012-0384-4","gene_count":11,"genes_by_uniquename":{"SJAG_00364":null,"SJAG_00429":null,"SJAG_01205":null,"SJAG_01605":null,"SJAG_01680":null,"SJAG_02266":null,"SJAG_02576":null,"SJAG_02771":null,"SJAG_03720":null,"SJAG_04287":null,"SJAG_04671":null},"genotypes_by_uniquename":{"cds1delta":{"display_name":"cds1delta","display_uniquename":"cds1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04287:allele-1","expression":"Null"}]}]},"chk1-P470L-P470L-amino_acid_mutation-expression-not_assayed_or_wild_type__rad24delta":{"display_name":"chk1-P470L(aa) rad24delta","display_uniquename":"chk1-P470L-P470L-amino_acid_mutation-expression-not_assayed_or_wild_type__rad24delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01680:allele-2","expression":"Not assayed or wild type"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_02266:allele-1","expression":"Null"}]}]},"chk1delta":{"display_name":"chk1delta","display_uniquename":"chk1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01680:allele-1","expression":"Null"}]}]},"chk1delta__crb2delta":{"display_name":"chk1delta crb2delta","display_uniquename":"chk1delta__crb2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01680:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_01205:allele-1","expression":"Null"}]}]},"crb2delta":{"display_name":"crb2delta","display_uniquename":"crb2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01205:allele-1","expression":"Null"}]}]},"mrc1delta":{"display_name":"mrc1delta","display_uniquename":"mrc1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04671:allele-1","expression":"Null"}]}]},"rad1delta":{"display_name":"rad1delta","display_uniquename":"rad1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02771:allele-1","expression":"Null"}]}]},"rad24delta":{"display_name":"rad24delta","display_uniquename":"rad24delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02266:allele-1","expression":"Null"}]}]},"rad25delta":{"display_name":"rad25delta","display_uniquename":"rad25delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02576:allele-1","expression":"Null"}]}]},"rad26delta":{"display_name":"rad26delta","display_uniquename":"rad26delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00429:allele-1","expression":"Null"}]}]},"rad3delta":{"display_name":"rad3delta","display_uniquename":"rad3delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00364:allele-1","expression":"Null"}]}]},"rad9delta":{"display_name":"rad9delta","display_uniquename":"rad9delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01605:allele-1","expression":"Null"}]}]},"tel1delta":{"display_name":"tel1delta","display_uniquename":"tel1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03720:allele-1","expression":"Null"}]}]}},"ltp_gene_count":11,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2012","pubmed_entrez_date":"2012-10-24","pubmed_publication_date":"Dec 2012","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:0000088":null,"FYPO:0001234":null,"FYPO:0001690":null,"FYPO:0004693":null,"FYPO:0007774":null,"FYPO:0007782":null,"FYPO:0007790":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null,"FYPO_EXT:0000003":null},"title":"Hyphal differentiation induced via a DNA damage checkpoint-dependent pathway engaged in crosstalk with nutrient stress signaling in Schizosaccharomyces japonicus.","uniquename":"PMID:23090706"}


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_approver_orcid":"0000-0002-8138-6851","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":[115524],"is_not":false,"summary":null,"term":"FYPO:0007773"},{"annotations":[115523],"is_not":false,"summary":null,"term":"FYPO:0001122"},{"annotations":[115525],"is_not":false,"summary":null,"term":"FYPO:0000245"},{"annotations":[115527],"is_not":false,"summary":null,"term":"FYPO:0000097"},{"annotations":[115526],"is_not":false,"summary":null,"term":"FYPO:0000087"},{"annotations":[115528],"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: GO_REF:0000079
data:
  {"abstract":"We have created a standard template for classes describing the assembly or disassembly of a cellular component as a biological process. The underlying equivalence axiom templates are \"GO:0022607 and 'results_in_assembly_of' some C\" (assembly) and \"GO:0022411 and 'results_in_disassembly_of' some C\" (disassembly), where C is a cellular component.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of assembly or disassembly of a cell component as biological process in the Gene Ontology","uniquename":"GO_REF:0000079"}


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: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":"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"},{"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"}],"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: GO_REF:0000114
data:
  {"abstract":"Method for transferring manual annotations to an entry based on a curator's judgment of its similarity to a putative homolog that has annotations that are supported with experimental evidence. Annotations are created when a curator judges that the sequence, composition and function of a complex shows high similarity to another complex that has annotation(s) supported by experimental evidence (and therefore display one of the evidence codes ECO:0000353 [IPI] or ECO:0005543). Annotations resulting from the transfer of GO terms display the ECO:0005610, ECO:0005544 or ECO:0005546 evidence codes and include an accession for the complex from which the annotation was projected in the 'with/from' field (column 8). This field MUST contain a Complex Portal accession identifier. Putative homologs are chosen using information combined from a variety of complementary sources. Potential homologs are initially identified using sequence similarity search programs such as BLAST. Homologous relationships are then verified manually using a combination of resources including sequence analysis tools, phylogenetic and comparative genomics databases such as Ensembl Compara, INPARANOID and OrthoMCL, as well as other specialised databases such as species-specific collections (e.g. HGNC's HCOP). In all cases curators check the alignments for each complex component and use their experience to assess whether similarity is considered to be strong enough to infer that the two proteins have a common function so that they can confidently project an annotation. While there is no fixed cut-off point in percentage sequence similarity, generally proteins which have greater than 70% identity that covers greater than 90% of the length of both proteins are examined further. Whilst we expect subunit composition to be conserved between closely related species, this is not an absolute rule and orthologous complexes may differ if a subunit cannot be traced in one species or is experimentally shown not to be present. When there is evidence of multiple paralogs for a single species, multiple variants of the complex can be inferred.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Birgit Meldal and Sandra Orchard (1). (1) European Bioinformatics Institute (EBI), Hinxton, Cambridgeshire, United Kingdom","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Manual transfer of experimentally-verified manual GO annotation data to homologous complexes by curator judgment of sequence, composition and function similarity","uniquename":"GO_REF:0000114"}


id: PMID:28733401
data:
  {"abstract":"Haploid yeast cells mate to form heterozygotes and subsequently undergo meiosis to form spores. This process can be used to produce gene combinations and variants that are useful for genetic analysis. For example, these spores can be used to generate double mutants or to measure genetic distances in a mutational analysis. Here, we describe mating and spore dissection procedures for  Schizosaccharomyces japonicus  cells. Although the overall procedures resemble those used in  Schizosaccharomyces pombe , some differences exist, including the use of EMM2 medium without nitrogen (EMM-N) for mating and the shorter incubation time of 16-20 h for  S. japonicus  cells. Furthermore, the  S. japonicus  zygotes produce eight spores and thus require an \"octad\" analysis.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Furuya K, Niki H","authors_abbrev":"Furuya K et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Method or reagent","citation":"Cold Spring Harb Protoc 2017 Dec 01;2017(12):pdb.prot091843","cv_annotations":{},"doi":"10.1101/pdb.prot091843","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":"Mating, Spore Dissection, and Selection of Diploid Cells in  Schizosaccharomyces japonicus .","uniquename":"PMID:28733401"}


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_approver_orcid":"0000-0002-8138-6851","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":[115567],"is_not":false,"summary":null,"term":"GO:0032432"},{"annotations":[115566],"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: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: GO_REF:0000083
data:
  {"abstract":"We have created a standard template for classes describing the morphogenesis of a plant structure as a biological process. The underlying equivalence axiom template is \"'anatomical structure morphogenesis' and 'results in morphogenesis of' some P\", where P is a plant anatomical entity (PO:0025131).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of plant morphogenesis as biological process in the Gene Ontology","uniquename":"GO_REF:0000083"}


id: GO_REF:0000059
data:
  {"abstract":"We have created a standard template for the definition of classes for the regulation of a molecular function. This includes the definitions for positive and negative regulation. The equivalence axiom templates are \"GO:0065007 and 'regulates' some X\" (regulation), \"GO:0065007 and 'negatively_regulates' some X\" (negative regulation), and \"GO:0065007 and 'positively_regulates' some X\" (positive regulation), where X is a molecular function.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of regulation in the Gene Ontology (molecular function) ","uniquename":"GO_REF:0000059"}


id: GO_REF:0000110
data:
  {"abstract":"Gene Ontology annotation of Drosophila melanogaster nuclear genes encoding proteins targeted to the mitochondrion based on analysis by MitoDrome (http://mitodrome.ba.itb.cnr.it/) by comparison of human mitochondrial proteins available in SWISSPROT vs. the Drosophila genome, ESTs and cDNA sequences available in the FlyBase database (PMID:12520013).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"FlyBase","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Gene Ontology annotation of Drosophila melanogaster nuclear genes encoding proteins targeted to the mitochondrion.","uniquename":"GO_REF:0000110"}


id: PMID:34198697
data:
  {"abstract":"Mitogen activated protein kinase (MAPK) signaling pathways execute essential functions in eukaryotic organisms by transducing extracellular stimuli into adaptive cellular responses. In the fission yeast model  Schizosaccharomyces pombe  the cell integrity pathway (CIP) and its core effector, MAPK Pmk1, play a key role during regulation of cell integrity, cytokinesis, and ionic homeostasis.  Schizosaccharomyces japonicus , another fission yeast species, shows remarkable differences with respect to  S. pombe , including a robust yeast to hyphae dimorphism in response to environmental changes. We show that the CIP MAPK module architecture and its upstream regulators, PKC orthologs Pck1 and Pck2, are conserved in both fission yeast species. However, some of  S. pombe 's CIP-related functions, such as cytokinetic control and response to glucose availability, are regulated differently in  S. japonicus.  Moreover, Pck1 and Pck2 antagonistically regulate  S. japonicus  hyphal differentiation through fine-tuning of Pmk1 activity. Chimeric MAPK-swapping experiments revealed that  S. japonicus  Pmk1 is fully functional in  S. pombe , whereas  S. pombe  Pmk1 shows a limited ability to execute CIP functions and promote  S. japonicus  mycelial development. Our findings also suggest that a modified N-lobe domain secondary structure within  S. japonicus  Pmk1 has a major influence on the CIP signaling features of this evolutionarily diverged fission yeast.","alleles_by_uniquename":{"SJAG_00610:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00610","name":"pck2delta","uniquename":"SJAG_00610:allele-1"},"SJAG_01787:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01787","name":"pck1delta","uniquename":"SJAG_01787:allele-1"},"SJAG_02592:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02592","name":"sty1delta","uniquename":"SJAG_02592:allele-1"},"SJAG_04551:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04551","name":"pmk1delta","uniquename":"SJAG_04551:allele-1"},"SJAG_04551:allele-2":{"allele_type":"amino_acid_insertion","description":"82-NITCIYDLDIIINPYNFNEVYIYEE-105","gene_uniquename":"SJAG_04551","name":"Pmk1Sj(ins82-105)","uniquename":"SJAG_04551:allele-2"},"SJAG_04551:allele-3":{"allele_type":"other","description":"Pmk1 from S. pombe","gene_uniquename":"SJAG_04551","name":"Pmk1Sp","uniquename":"SJAG_04551:allele-3"},"SJAG_04551:allele-4":{"allele_type":"partial_amino_acid_deletion","description":"Pmk1 from S. pombe with deleted residues 82-105","gene_uniquename":"SJAG_04551","name":"Pmk1Sp(delta82-105)","uniquename":"SJAG_04551:allele-4"}},"annotation_curators":[{"annotation_count":34,"community_curator":true,"file_name":null,"file_type":null,"name":"Elisa Gomez Gil","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-09-14","authors":"Gómez-Gil E, Franco A, Vázquez-Marín B, Prieto-Ruiz F, Pérez-Díaz A, Vicente-Soler J, Madrid M, Soto T, Cansado J","authors_abbrev":"Gómez-Gil E et al.","canto_added_date":"2021-09-14 16:45:58","canto_annotation_status":"APPROVED","canto_approved_date":"2021-09-14 21:32:21","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Elisa Gomez Gil","canto_curator_role":"community","canto_first_approved_date":"2021-09-14 21:32:21","canto_session_key":"0ba747685c452996","canto_session_submitted_date":"2021-09-14 17:59:01","canto_triage_status":"Curatable","citation":"J Fungi (Basel) 2021 Jun 14;7(6)","cv_annotations":{"PSI-MOD":[{"annotations":[115377,115378,115379],"is_not":false,"summary":null,"term":"MOD:00696"}],"cellular_component":[{"annotations":[115376],"is_not":false,"summary":null,"term":"GO:0005737"},{"annotations":[115375],"is_not":false,"summary":null,"term":"GO:0005634"}],"multi_locus_phenotype":[{"annotations":[115393],"is_not":false,"summary":null,"term":"FYPO:0007780"}],"single_locus_phenotype":[{"annotations":[115391,115399],"is_not":false,"summary":null,"term":"FYPO:0002678"},{"annotations":[115398],"is_not":false,"summary":null,"term":"FYPO:0002033"},{"annotations":[115380,115392,115396,115401,115404],"is_not":false,"summary":null,"term":"FYPO:0007776"},{"annotations":[115381,115397,115402,115405],"is_not":false,"summary":null,"term":"FYPO:0007780"},{"annotations":[115390,115394],"is_not":false,"summary":null,"term":"FYPO:0001838"},{"annotations":[115385],"is_not":false,"summary":null,"term":"FYPO:0007775"},{"annotations":[115386],"is_not":false,"summary":null,"term":"FYPO:0007779"},{"annotations":[115387],"is_not":false,"summary":null,"term":"FYPO:0002680"},{"annotations":[115384],"is_not":false,"summary":null,"term":"FYPO:0001038"},{"annotations":[115372],"is_not":false,"summary":null,"term":"FYPO:0004295"},{"annotations":[115382],"is_not":false,"summary":null,"term":"FYPO:0005152"},{"annotations":[115374,115389,115395,115400,115403],"is_not":false,"summary":null,"term":"FYPO:0007521"},{"annotations":[115373,115388],"is_not":false,"summary":null,"term":"FYPO:0000079"},{"annotations":[115383],"is_not":false,"summary":null,"term":"FYPO:0007522"}]},"doi":"10.3390/jof7060482","gene_count":4,"genes_by_uniquename":{"SJAG_00610":null,"SJAG_01787":null,"SJAG_02592":null,"SJAG_04551":null},"genotypes_by_uniquename":{"Pmk1Sj(ins82-105)-82-NITCIYDLDIIINPYNFNEVYIYEE-105-amino_acid_insertion-expression-not_assayed_or_wild_type":{"display_name":"Pmk1Sj(ins82-105)(82-NITCIYDLDIIINPYNFNEVYIYEE-105)","display_uniquename":"Pmk1Sj(ins82-105)-82-NITCIYDLDIIINPYNFNEVYIYEE-105-amino_acid_insertion-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04551:allele-2","expression":"Not assayed or wild type"}]}]},"Pmk1Sp(delta82-105)-Pmk1_from_S._pombe_with_deleted_residues_82-105-partial_amino_acid_deletion-expression-not_assayed_or_wild_type":{"display_name":"Pmk1Sp(delta82-105)(Pmk1 from S. pombe with deleted residues 82-105 Δaa)","display_uniquename":"Pmk1Sp(delta82-105)-Pmk1_from_S._pombe_with_deleted_residues_82-105-partial_amino_acid_deletion-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04551:allele-4","expression":"Not assayed or wild type"}]}]},"Pmk1Sp-Pmk1_from_S._pombe-other-expression-not_assayed_or_wild_type":{"display_name":"Pmk1Sp(Pmk1 from S. pombe)","display_uniquename":"Pmk1Sp-Pmk1_from_S._pombe-other-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04551:allele-3","expression":"Not assayed or wild type"}]}]},"pck1delta":{"display_name":"pck1delta","display_uniquename":"pck1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01787:allele-1","expression":"Null"}]}]},"pck1delta__pmk1delta":{"display_name":"pck1delta pmk1delta","display_uniquename":"pck1delta__pmk1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01787:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_04551:allele-1","expression":"Null"}]}]},"pck2delta":{"display_name":"pck2delta","display_uniquename":"pck2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00610:allele-1","expression":"Null"}]}]},"pmk1delta":{"display_name":"pmk1delta","display_uniquename":"pmk1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04551:allele-1","expression":"Null"}]}]},"sty1delta":{"display_name":"sty1delta","display_uniquename":"sty1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02592:allele-1","expression":"Null"}]}]}},"ltp_gene_count":4,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2021","pubmed_entrez_date":"2021-07-02","pubmed_publication_date":"14 Jun 2021","terms_by_termid":{"FYECO:0000207":null,"FYECO:0000314":null,"FYPO:0000079":null,"FYPO:0001038":null,"FYPO:0001838":null,"FYPO:0002033":null,"FYPO:0002678":null,"FYPO:0002680":null,"FYPO:0004295":null,"FYPO:0005152":null,"FYPO:0007521":null,"FYPO:0007522":null,"FYPO:0007775":null,"FYPO:0007776":null,"FYPO:0007779":null,"FYPO:0007780":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null,"GO:0005634":null,"GO:0005737":null,"GO:0036460":null,"GO:0042149":null,"GO:0071475":null,"GO:0072690":null,"MOD:00696":null},"title":"Specific Functional Features of the Cell Integrity MAP Kinase Pathway in the Dimorphic Fission Yeast  Schizosaccharomyces japonicus .","uniquename":"PMID:34198697"}


id: PMID:26104357
data:
  {"abstract":"Cells of the highly diverged Schizosaccharomyces (S.) pombe and S. japonicus fission yeasts exist in one of two sex/mating types, called P (for plus) or M (for minus), specified by which allele, M or P, resides at mat1. The fission yeasts have evolved an elegant mechanism for switching P or M information at mat1 by a programmed DNA recombination event with a copy of one of the two silent mating-type genes residing nearby in the genome. The switching process is highly cell-cycle and generation dependent such that only one of four grandchildren of a cell switches mating type. Extensive studies of fission yeast established the natural DNA strand chirality at the mat1 locus as the primary basis of asymmetric cell division. The asymmetry results from a unique site- and strand-specific epigenetic \"imprint\" at mat1 installed in one of the two chromatids during DNA replication. The imprint is inherited by one daughter cell, maintained for one cell cycle, and is then used for initiating recombination during mat1 replication in the following cell cycle. This mechanism of cell-type switching is considered to be unique to these two organisms, but determining the operation of such a mechanism in other organisms has not been possible for technical reasons. This review summarizes recent exciting developments in the understanding of mating-type switching in fission yeasts and extends these observations to suggest how such a DNA strand-based epigenetic mechanism of cellular differentiation could also operate in diploid organisms. ","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Klar AJS, Ishikawa K, Moore S","authors_abbrev":"Klar AJS et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Review or comment","citation":"Microbiol Spectr 2014 Oct;2(5)","cv_annotations":{},"doi":"10.1128/microbiolspec.MDNA3-0003-2014","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":"2015-06-25","pubmed_publication_date":"Oct 2014","terms_by_termid":{},"title":"A Unique DNA Recombination Mechanism of the Mating/Cell-type Switching of Fission Yeasts: a Review.","uniquename":"PMID:26104357"}


id: PMID:2021084
data:
  {"abstract":"The genus Schizosaccharomyces comprises a small, somewhat heterogeneous group of yeast species which have in common a unique mode of vegetative reproduction by cross-wall formation without constriction as well as a certain degree of osmophilia, most strains having been isolated from habitats of high sugar concentration. This study evaluated inter- and intraspecific relationships utilizing nDNA/nDNA optical reassociation and by the analysis of physiological profiles of several strains of each species. Results demonstrate that the genus should be divided into three species: Schiz. japonicus, Schiz. octosporus and Schiz. pombe.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Vaughan Martini A","authors_abbrev":"Vaughan Martini A","canto_added_date":"2023-05-04 00:40:04","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"Yeast 1991 Jan;7(1):73-8","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1991","pubmed_entrez_date":"1991-01-01","pubmed_publication_date":"Jan 1991","terms_by_termid":{},"title":"Evaluation of phylogenetic relationships among fission yeast by nDNA/nDNA reassociation and conventional taxonomic criteria.","uniquename":"PMID:2021084"}


id: GO_REF:0000054
data:
  {"abstract":"LIFEdb is a database that was created to manage the experimental data produced by the German Cancer Research Institute (DKFZ) and its collaborators, from work on cDNAs contained in the German cDNA Consortium collection. <br>A novel cloning technology was used to rapidly generate N- and C-terminal green fluorescent protein fusions of cDNAs to examine the intracellular localizations of expressed fusion proteins in living cells. GO Cellular Component terms are manually assigned by curators studying fluorescence microscope images of cells labelled with GFP-fused cDNAs. Protein coding regions of novel full length cDNAs are tagged with the coding sequence of the green fluorescent protein, the fusion proteins are then expressed and analyzed for their subcellular localization. <br>Prior to February 2013, all LIFEdb annotations were referenced by PMID: 11256614 (Simpson et al. 2000 EMBO Rep. 1:287-292), a paper describing the protein subcellular localization pilot study and methodology used by LIFEdb. However, it has been decided that these annotations are more correctly described by a GO reference. <br>Resource URL: http://www.dkfz.de/en/mga/Groups/LIFEdb-Database.html <br>Protein subcellular localization images can be viewed on the LIFEdb website, http://www.dkfz.de/gpcf/lifedb.php","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"LIFEdb","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Gene Ontology annotation based on curation of intracellular localizations of expressed fusion proteins in living cells.","uniquename":"GO_REF:0000054"}


id: PMID:31732056
data:
  {"abstract":"Vitis davidii Föex is widely planted in South China as a potential wine making grape. In this study, yeast communities during the spontaneous fermentations of two varieties of Vitis davidii Föex in Guizhou, China were investigated. Hanseniaspora uvarum, Pichia terricola, Saccharomyces cerevisiae/S. mikatae, and Schizosaccharomyces japonicus were the four main yeast species detected by culture-dependent and high-throughput sequencing approaches. However, the composition of minor yeast species was quite different as revealed by the two approaches. Ten yeast species including Debaryomyces hansenii, Rhodotorula mucilaginosa, Sporidiobolus paraoseus, Starmerella bacillaris, Zygoascus meyerae, etc. were detected by culture-dependent approaches, whereas the other five species were found by high-throughput sequencing analysis. S. japonicus was widely found during spontaneous fermentations and its concentrations were mostly higher than that of S. cerevisiae. The difference in grape varieties and fermentation conditions contributed to yeast diversity. The results of this study provide basic information on indigenous yeast diversity from Vitis davidii Föex in Guizhou, which would help to exploit the potential of non-Saccharomyces yeast species with good oenological attributes.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Wang C, Wu C, Qiu S","authors_abbrev":"Wang C et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Biotech","citation":"Food Res Int 2019 12;126:108582","cv_annotations":{},"doi":"10.1016/j.foodres.2019.108582","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2019","pubmed_entrez_date":"2019-11-17","pubmed_publication_date":"12 2019","terms_by_termid":{},"title":"Yeast diversity investigation of Vitis davidii Föex during spontaneous fermentations using culture-dependent and high-throughput sequencing approaches.","uniquename":"PMID:31732056"}


id: GO_REF:0000024
data:
  {"abstract":"Method for transferring manual annotations to an entry based on a curator's judgment of its similarity to a putative ortholog that has annotations that are supported with experimental evidence. Annotations are created when a curator judges that the sequence of a protein shows high similarity to another protein that has annotation(s) supported by experimental evidence (and therefore display one of the evidence codes EXP, IDA, IGI, IMP, IPI or IEP). Annotations resulting from the transfer of GO terms display the 'ISS' evidence code and include an accession for the protein from which the annotation was projected in the 'with' field (column 8). This field can contain either a UniProtKB accession or an IPI (International Protein Index) identifier. Only annotations with an experimental evidence code and which do not have the 'NOT' qualifier are transferred. Putative orthologs are chosen using information combined from a variety of complementary sources. Potential orthologs are initially identified using sequence similarity search programs such as BLAST. Orthology relationships are then verified manually using a combination of resources including sequence analysis tools, phylogenetic and comparative genomics databases such as Ensembl Compara, INPARANOID and OrthoMCL, as well as other specialised databases such as species-specific collections (e.g. HGNC's HCOP). In all cases curators check each alignment and use their experience to assess whether similarity is considered to be strong enough to infer that the two proteins have a common function so that they can confidently project an annotation. While there is no fixed cut-off point in percentage sequence similarity, generally proteins which have greater than 30% identity that covers greater than 80% of the length of both proteins are examined further. For mammalian proteins this cut-off tends to be higher, with an average of 80% identity over 90% of the length of both proteins. Strict orthologs are desirable but not essential. In general, when there is evidence of multiple paralogs for a single species, annotations using less specific GO terms are transferred to the paralogs, however, annotations using more specific GO terms may be transferred to the most similar paralog in each species, this decision is taken on a case by case basis and may be influenced by statements by researchers in the field. Further detailed information on this procedure, including how ISS annotations are made to protein isoforms, can be found at: http://www.ebi.ac.uk/GOA/ISS_method.html.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"AgBase, BHF-UCL, Parkinson's UK-UCL, dictyBase, HGNC, Roslin Institute, FlyBase and UniProtKB curators.","canto_curator_role":"JaponicusDB","cv_annotations":{"biological_process":[{"annotations":[79353],"is_not":false,"summary":null,"term":"GO:0000122"}],"cellular_component":[{"annotations":[79350],"is_not":false,"summary":null,"term":"GO:0005869"}],"molecular_function":[{"annotations":[79351],"is_not":false,"summary":null,"term":"GO:0001227"},{"annotations":[79352],"is_not":false,"summary":null,"term":"GO:0000978"}]},"gene_count":2,"genes_by_uniquename":{"SJAG_00124":null,"SJAG_01739":null},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{"GO:0000122":null,"GO:0000978":null,"GO:0001227":null,"GO:0005869":null},"title":"Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity.","uniquename":"GO_REF:0000024"}


id: PMID:8590481
data:
  {"abstract":"Fission yeasts form a small but heterogeneous group of ascomycetes and it is still unclear whether they should be subdivided into three genera (Schizosaccharomyces, Octosporomyces, Hasegawaea) or remain a single genus (Schizosaccharomyces). In order to decide whether a new genus Hasegawaea should be established for the species Schizosaccharomyces japonicus and Schizosaccharomyces versatilis, we have characterized the entire rDNA cluster in Schizosaccharomyces japonicus var. versatilis and compared it with the homologous region from Schizosaccharomyces pombe and with complete rRNA gene sequences from other yeast genera. From a phage genomic library a recombinant lambda phage containing the entire rDNA repeat unit was isolated. In this paper we report the primary sequence of the 18s, 5.8s and 25s rRNA coding regions. The S. japonicus var. versatilis rRNA genes are 1823 (18s), 158 (5.8s) and 3422 (25s) nucleotides long. The two sequences of the larger rRNA genes exhibit 95.7% (18s) and 93% (25s) similarity with the homologous genes from S. pombe. The differences between the rRNA genes of S. japonicus and S. pombe, however, are much smaller than the intrageneric differences within the rDNA sequences of other yeast genera. Therefore, subdivision of fission yeasts into the genera Schizosaccharomyces and Hasegawaea does not to seem to be justified.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Naehring J, Kiefer S, Wolf K","authors_abbrev":"Naehring J et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Sequence feature or region","citation":"Curr Genet 1995 Sep;28(4):353-9","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1995","pubmed_entrez_date":"1995-09-01","pubmed_publication_date":"Sep 1995","terms_by_termid":{},"title":"Nucleotide sequence of the Schizosaccharomyces japonicus var. versatilis ribosomal RNA gene cluster and its phylogenetic implications.","uniquename":"PMID:8590481"}


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:22300943
data:
  {"abstract":"The fission yeasts (Schizosaccharomyces) representing a highly divergent phylogenetic branch of Fungi evolved from filamentous ancestors by gradual transition from mycelial growth to yeast morphology. For the transition, a mechanism had been developed that separates the sister cells after the completion of cytokinesis. Numerous components of the separation mechanism have been characterised in Schizosaccharomycespombe, including the zinc-finger transcription factor Ace2p and the fork-head transcription factor Sep1p. Here we show that both regulators have regions conserved within the genus. The most conserved parts contain the DNA-binding domains whose amino-acid sequences perfectly reflect the phylogenetic positions of the species. The less conserved parts of the proteins contain sequence blocks specific for the whole genus or only for the species propagating predominantly or exclusively as yeasts. Inactivation of either gene in the dimorphic species Schizosaccharomycesjaponicus abolished cell separation in the yeast phase conferring hypha-like morphology but did not change the growth pattern to unipolar and did not cause extensive polar vacuolation characteristic of the true mycelium. Neither mutation affected the mycelial phase, but both mutations hampered the hyphal fragmentation at the mycelium-to-yeast transition. Ace2p(Sj) acts downstream of Sep1p(Sj) and regulates the orthologues of the Ace2p-dependent S.pombe genes agn1(+) (1,3-alpha-glucanase) and eng1(+) (1,3-beta-glucanase) but does not regulate the orthologue of cfh4(+) (chitin synthase regulatory factor). These results and the complementation of the cell separation defects of the ace2(-) and sep1(-) mutations of S.pombe by heterologously expressed ace2(Sj) and sep1(Sj) indicate that the cell separation mechanism is conserved in the Schizosaccharomyces genus.","alleles_by_uniquename":{"SJAG_02252:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02252","name":"ace2delta","uniquename":"SJAG_02252:allele-1"},"SJAG_03143:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03143","name":"sep1delta","uniquename":"SJAG_03143:allele-1"}},"annotation_curators":[{"annotation_count":7,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2022-12-09","authors":"Balazs A, Batta G, Miklos I, Acs-Szabo L, Vazquez de Aldana CR, Sipiczki M","authors_abbrev":"Balazs A et al.","canto_added_date":"2022-12-09 17:19:01","canto_annotation_status":"APPROVED","canto_approved_date":"2022-12-09 17:39:12","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2022-12-09 17:39:12","canto_session_key":"f106e12e6366fbad","canto_session_submitted_date":"2022-12-09 17:38:34","canto_triage_status":"Curatable","citation":"Fungal Genet Biol 2012 Mar;49(3):235-49","cv_annotations":{"single_locus_phenotype":[{"annotations":[115343,115344],"is_not":false,"summary":null,"term":"FYPO:0006557"}]},"doi":"10.1016/j.fgb.2012.01.003","gene_count":2,"genes_by_uniquename":{"SJAG_02252":null,"SJAG_03143":null},"genotypes_by_uniquename":{"ace2delta":{"display_name":"ace2delta","display_uniquename":"ace2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02252:allele-1","expression":"Null"}]}]},"sep1delta":{"display_name":"sep1delta","display_uniquename":"sep1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03143:allele-1","expression":"Null"}]}]}},"ltp_gene_count":2,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2012","pubmed_entrez_date":"2012-02-04","pubmed_publication_date":"Mar 2012","terms_by_termid":{"FYECO:0000137":null,"FYPO:0006557":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null},"title":"Conserved regulators of the cell separation process in Schizosaccharomyces.","uniquename":"PMID:22300943"}


id: GO_REF:0000068
data:
  {"abstract":"We have created a standard template for classes each describing the metabolism, catabolism, or biosynthesis of a chemical entity (ChEBI) as a process. The underlying equivalence axiom templates are \"GO:0008152 and 'has participant' some X\" (metabolism), \"GO:0009056 and 'has input' some X\" (catabolism), \"GO:0009058 and 'has output' some X\" and (biosynthesis),  where X is a chemical entity (CHEBI:24431). The approach to combine GO and ChEBI has been described in the following publication: PMID:23895341.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of metabolic triad (metabolism, catabolism, biosynthesis) as biological process in the Gene Ontology","uniquename":"GO_REF:0000068"}


id: GO_REF:0000096
data:
  {"abstract":"Mouse Genome Database (MGD), The HUGO Gene Nomenclature Committee (HGNC), and Rat Genome Database (RGD) have extensive procedures in place, overseen by expert curation, to establish orthology relationships between their genes. The Experimentally based annotations annotated by each group (IDA, IMP IPI, IGI, and EXP) are used to provide annotations  to the respective mouse and rat orthologs, and given the ISO evidence code and an entry in the inferred_from field to indicate the orthologous entity. ","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Mouse Genome Informatics scientific curators","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Automated transfer of experimentally-verified manual GO annotation data to close orthologs.","uniquename":"GO_REF:0000096"}


id: PMID:21733045
data:
  {"abstract":"During open mitosis in higher eukaryotic cells, the nuclear envelope completely breaks down and then mitotic chromosomes are exposed in the cytoplasm. By contrast, mitosis in lower eukaryotes, including fungi, proceeds with the nucleus enclosed in an intact nuclear envelope. The mechanism of mitosis has been studied extensively in yeast, a closed mitosis organism. Here, we describe a form of mitosis in which the nuclear envelope is torn by elongation of the nucleus in the fission yeast Schizosaccharomyces japonicus. The mitotic nucleus of Sz. japonicus adopted a fusiform shape in anaphase, and its following extension caused separation. Finally, a tear in the nuclear envelope occurred in late anaphase. At the same time, a polarized-biased localization of nuclear pores was seen in the fusiform-shaped nuclear envelope, suggesting a compromise in the mechanical integrity of the lipid membrane. It has been known that nuclear membrane remains intact in some metazoan mitosis. We found that a similar tear of the nuclear envelope was also observed in late mitosis of the Caenorhabditis elegans embryo. These findings provide insight into the diversity of mitosis and the biological significance of breakdown of the nuclear envelope.","alleles_by_uniquename":{},"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":"2022-11-21","authors":"Aoki K, Hayashi H, Furuya K, Sato M, Takagi T, Osumi M, Kimura A, Niki H","authors_abbrev":"Aoki K et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2022-11-21 17:28:56","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Sho Okamoto","canto_curator_role":"community","canto_first_approved_date":"2022-11-21 17:28:56","canto_session_key":"6063f08db89b54c7","canto_session_submitted_date":"2022-11-21 17:28:46","canto_triage_status":"Curatable","citation":"Genes Cells 2011 Sep;16(9):911-26","cv_annotations":{"cellular_component":[{"annotations":[115564],"is_not":false,"summary":null,"term":"GO:0070762"},{"annotations":[115565],"is_not":false,"summary":null,"term":"GO:0005816"}]},"doi":"10.1111/j.1365-2443.2011.01540.x","gene_count":1,"genes_by_uniquename":{"SJAG_03200":null},"genotypes_by_uniquename":{},"ltp_gene_count":1,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2011","pubmed_entrez_date":"2011-07-08","pubmed_publication_date":"Sep 2011","terms_by_termid":{"GO:0005816":null,"GO:0070762":null},"title":"Breakage of the nuclear envelope by an extending mitotic nucleus occurs during anaphase in Schizosaccharomyces japonicus.","uniquename":"PMID:21733045"}


id: PMID:23873862
data:
  {"abstract":"Many fungi respond to light and regulate fungal development and behavior. A blue light-activated complex has been identified in Neurospora crassa as the product of the wc-1 and wc-2 genes. Orthologs of WC-1 and WC-2 have hitherto been found only in filamentous fungi and not in yeast, with the exception of the basidiomycete pathogenic yeast Cryptococcus. Here, we report that the fission yeast Schizosaccharomyces japonicus responds to blue light depending on Wcs1 and Wcs2, orthologs of components of the WC complex. Surprisingly, those of ascomycete S. japonicus are more closely related to those of the basidiomycete. S. japonicus reversibly changes from yeast to hyphae in response to environmental stresses. After incubation at 30°C, a colony of yeast was formed, and then hyphal cells extended from the periphery of the colony. When light cycles were applied, distinct dark- and bright-colored hyphal cell stripes were formed because the growing hyphal cells had synchronously activated cytokinesis. In addition, temperature cycles of 30°C for 12 h and 35°C for 12 h or of 25°C for 12 h and 30°C for 12 h during incubation in the dark induced a response in the hyphal cells similar to that of light. The stripe formation of the temperature cycles was independent of the wcs genes. Both light and temperature, which are daily external cues, have the same effect on growing hyphal cells. A dual sensing mechanism of external cues allows organisms to adapt to daily changes of environmental alteration. ","alleles_by_uniquename":{"SJAG_02860:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02860","name":"wcs1delta","uniquename":"SJAG_02860:allele-1"},"SJAG_05242:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_05242","name":"wcs2delta","uniquename":"SJAG_05242:allele-1"}},"annotation_curators":[{"annotation_count":7,"community_curator":true,"file_name":null,"file_type":null,"name":"Sho Okamoto","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2022-12-01","authors":"Okamoto S, Furuya K, Nozaki S, Aoki K, Niki H","authors_abbrev":"Okamoto S et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2022-12-01 10:29:08","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Sho Okamoto","canto_curator_role":"community","canto_first_approved_date":"2022-12-01 10:29:08","canto_session_key":"0e71b7054e7d7754","canto_session_submitted_date":"2022-12-01 10:28:58","canto_triage_status":"Curatable","citation":"Eukaryot Cell 2013 Sep;12(9):1235-43","cv_annotations":{"biological_process":[{"annotations":[115569,115570],"is_not":false,"summary":null,"term":"GO:0071483"}],"molecular_function":[{"annotations":[115568],"is_not":false,"summary":null,"term":"GO:0009882"}],"single_locus_phenotype":[{"annotations":[115571,115572],"is_not":false,"summary":null,"term":"FYPO:0008031"},{"annotations":[115573,115574],"is_not":false,"summary":null,"term":"FYPO:0008046"}]},"doi":"10.1128/EC.00109-13","gene_count":2,"genes_by_uniquename":{"SJAG_02860":null,"SJAG_05242":null},"genotypes_by_uniquename":{"wcs1delta":{"display_name":"wcs1delta","display_uniquename":"wcs1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02860:allele-1","expression":"Null"}]}]},"wcs2delta":{"display_name":"wcs2delta","display_uniquename":"wcs2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_05242:allele-1","expression":"Null"}]}]}},"ltp_gene_count":2,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2013","pubmed_entrez_date":"2013-07-23","pubmed_publication_date":"Sep 2013","terms_by_termid":{"FYECO:0000005":null,"FYECO:0000126":null,"FYPO:0008031":null,"FYPO:0008046":null,"FYPO_EXT:0000001":null,"GO:0009882":null,"GO:0071483":null},"title":"Synchronous activation of cell division by light or temperature stimuli in the dimorphic yeast Schizosaccharomyces japonicus.","uniquename":"PMID:23873862"}


id: PMID:10379403
data:
  {"abstract":"The order Schizosaccharomycetales contains a dimorphic and two yeast species. Sch. japonicus can form both yeast cells and mycelium, depending on the substrate and the culturing conditions. Sch. pombe is a strictly unicellular organism, but it can be forced to form mycelial cell chains by inactivating members of the sep gene family. The mutations in most of the sep genes confer pleitropic phenotypes indicating functional involvement in MAP-kinase-mediated signalling pathways. Two of them were found to encode transcription factor homologues of other eukaryotes.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Sipiczki M, Grallert A, Miklós I, Zilahi E, Bozsik A, Szilágyi Z","authors_abbrev":"Sipiczki M et al.","canto_added_date":"2023-05-04 00:40:04","canto_annotation_status":"SESSION_CREATED","canto_curator_role":"JaponicusDB","canto_session_key":"eb5db4e2ead0caf4","canto_triage_status":"Cell composition or WT feature","citation":"Acta Microbiol Immunol Hung 1999;46(2-3):297-302","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1999","pubmed_entrez_date":"1999-06-24","pubmed_publication_date":"1999","terms_by_termid":{},"title":"Genetics, physiology and cytology of yeast-mycelial dimorphism in fission yeasts.","uniquename":"PMID:10379403"}


id: GO_REF:0000062
data:
  {"abstract":"We have created a standard template for classes describing processes occurring in parts of the cell. The underlying equivalence axiom template is \"P and 'occurs in' some C\", where P is a biological process and C is a cellular component.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of processes occurring in parts of the cell in the Gene Ontology","uniquename":"GO_REF:0000062"}


id: GO_REF:0000086
data:
  {"abstract":"We have created a standard template for classes describing the differentiation process for a cell type as a biological process. The underlying equivalence axiom template is \"GO:0030154 and 'results in acquisition of features of' some C\", where C is a native cell (CL:0000003).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of cell differentiation as biological process in the Gene Ontology","uniquename":"GO_REF:0000086"}


