# refs

id: GO_REF:0000071
data:
  {"abstract":"We have created a standard template for classes describing the response to and cellular response to a chemical entity (ChEBI) as a biological process. The underlying equivalence axiom templates are \"GO:0050896 and 'has input' some X\" (response to) and \"GO:0070887 and 'has input' some X\" (cellular response to), 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 response to and cellular response to a chemical as biological process in the Gene Ontology","uniquename":"GO_REF:0000071"}


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_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":[115560],"is_not":false,"summary":null,"term":"MOD:00696"}],"single_locus_phenotype":[{"annotations":[115559],"is_not":false,"summary":null,"term":"FYPO:0002998"},{"annotations":[115557,115558],"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: GO_REF:0000041
data:
  {"abstract":"Transitive assignment of GO terms based on the UniPathway pathway vocabulary. UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways. Descriptions of the pathway(s) that a particular protein is involved in are included in UniProtKB records.<br>UniPathway data are cross-linked to existing pathway resources such as KEGG and MetaCyc. Further information on the UniPathway resource is available at http://www.unipathway.org/obiwarehouse/unipathway.<br>When a UniPathway pathway describes a concept that is within the scope of the Gene Ontology, it is investigated to determine whether it is appropriate to map the term to an equivalent term in GO. The mapping between UniPathway terms and GO terms is carried out manually. Definitions and hierarchies of the terms in the two resources are compared and the mapping generated will reflect the most correct correspondence. The translation table between GO terms and UniPathway pathways is maintained by the UniPathway team and is available at http://www.grenoble.prabi.fr/dev/obiwarehouse/download/unipathway/public/unipathway2go.tsv.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"UniProt-GOA","canto_curator_role":"JaponicusDB","cv_annotations":{"biological_process":[{"annotations":[65186],"is_not":false,"summary":null,"term":"GO:0006021"},{"annotations":[66654],"is_not":false,"summary":null,"term":"GO:0006782"},{"annotations":[57740],"is_not":false,"summary":null,"term":"GO:0006048"}]},"gene_count":3,"genes_by_uniquename":{"SJAG_00097":null,"SJAG_00519":null,"SJAG_03739":null},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{"GO:0006021":null,"GO:0006048":null,"GO:0006782":null},"title":"Gene Ontology annotation based on UniPathway vocabulary mapping. ","uniquename":"GO_REF:0000041"}


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_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: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: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: PMID:2197287
data:
  {"abstract":"Changes in the distribution of microtubules and F-actin through the cell division cycle of the fission yeast Schizosaccharomyces japonicus var. versatilis were investigated by fluorescence microscopy. The fluorescence images obtained with S. japonicus were markedly superior to those previously reported for S. pombe and revealed new details of cytoskeletal organization in this important genus. As in S. pombe, F-actin in S. japonicus was present as a concentration of 'dots' at the growing poles of interphase cells and as a filamentous equatorial ring directing the deposition of the cytokinetic septum. The transition between these two states occurred at late anaphase, in contrast to the situation in S. pombe where the appearance of the equatorial actin ring is tightly coupled to the early events of mitosis. During the course of cytokinesis in S. japonicus the actin ring constricted and broadened, suggesting that it is contractile. Microtubule organization in S. japonicus also revealed interesting differences from S. pombe. Whereas in S. pombe cytoplasmic microtubules are reinitiated from a pair of microtubule organizing centres (MTOCs) at the cell equator, in S. japonicus they arise by extensive microtubule growth from the spindle poles. Western blots of cell extracts enriched for tubulin by DEAE-Sephadex chromatography showed that, like S. pombe, S. japonicus contains two alpha-tubulins and a single beta-tubulin. Whilst the alpha 1- and beta-tubulins from the two species comigrated on one-dimensional polyacrylamide gels, the alpha 2 species were electrophoretically distinct. Although fundamental differences clearly exist between the two species, S. japonicus could prove to be a useful tool in basic studies of fission yeast cell biology.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Alfa CE, Hyams JS","authors_abbrev":"Alfa CE et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"J Cell Sci 1990 May;96 ( Pt 1):71-7","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1990","pubmed_entrez_date":"1990-05-01","pubmed_publication_date":"May 1990","terms_by_termid":{},"title":"Distribution of tubulin and actin through the cell division cycle of the fission yeast Schizosaccharomyces japonicus var. versatilis: a comparison with Schizosaccharomyces pombe.","uniquename":"PMID:2197287"}


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: 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:2226803
data:
  {"abstract":"In the fission yeast Schizosaccharomyces pombe, the enzyme RNAse P copurifies with two RNAs, K1- and K2-RNA, which are identical except for their termini [1] and which are encoded by a single gene [2]. We have undertaken the cloning of the K-RNA genes in related organisms in order to gain comparative structural information. Because the K-RNA sequence is poorly conserved across species, we have cloned the K-RNA genes in the Schizosaccharomyces species S. malidevorans, S. japonicus, S. versatilis, and S. octosporus. Of the 4 species, only S. octosporus contains a K-RNA gene different from that in S. pombe; the gene diverges by 20%. Based on the two sequences, nuclease protection data and computer analysis, we have proposed a secondary structure model for the K-RNA. Northern analysis shows the K-RNA genes in all four Schizosaccharomyces species to be expressed as two RNAs, as in S. pombe.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Zimmerly S, Gamulin V, Burkard U, Söll D","authors_abbrev":"Zimmerly S et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Sequence feature or region","citation":"FEBS Lett 1990 Oct 01;271(1-2):189-93","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1990","pubmed_entrez_date":"1990-10-01","pubmed_publication_date":"01 Oct 1990","terms_by_termid":{},"title":"The RNA component of RNase P in Schizosaccharomyces species.","uniquename":"PMID:2226803"}


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: GO_REF:0000047
data:
  {"abstract":"This describes a method for supplying a NOT-qualified, IKR-evidenced GO annotation to a gene product, when general sequence homology considerations would suggest a function or location, or a role in a biological process, but where a curator has determined that the absence of key sequence residues, known to be required for an expected activity or location, indicating the gene product is unlikely to be able to carry out the implied activity, involvement in a process or cellular component location. This reference should only be used used when an IKR-evidenced annotation is made based on curator judgement from manually reviewing the sequence of the gene product and where no publication can be found to support the curators conclusion. It is preferable to cite a peer-reviewed publication (such as a PubMed identifier) for IKR-evidenced annotations whenever possible. Curators will have carefully reviewed the sequence of the annotated protein, and established that the key residues known to be required for an expected activity or location are not present. Inclusion of an identifier in the 'with/from' field, that highlights to the user the lacking residues(e.g. an alignment, domain or rule identifier) is absolutely required when annotating to IKR with this GO_REF. Documentation on the GOC website provides more details on the <a href = \"http://www.geneontology.org/GO.evidence.shtml#ikr\">correct use of the IKR evidence code</a>.","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":"Gene Ontology annotation based on absence of key sequence residues.","uniquename":"GO_REF:0000047"}


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


id: GO_REF:0000113
data:
  {"abstract":"The TFClass (http://tfclass.bioinf.med.uni-goettingen.de/index.jsf) database provides a comprehensive classification of mammalian DNA binding transcription factors (DbTFs) based on their DNA binding domains (DBDs) (PMID:29087517). TFClass classifies mammalian DbTFs by a five-level classification in which the four highest levels represent groups defined by structural and sequence similarities (superclass, class, family, subfamily, and genera) (more details at http://www.edgar-wingender.de/TFClass_schema.html). This classification is based on the combination of background knowledge of the molecular structural features of DBDs (PMID:9340487, PMID:23427989) and phylogenetic trees constructed via multiple sequence alignment with hierarchical clustering of manually validated DBDs and/or full-length protein sequences retrieved from UniProt (PMID:23427989, PMID:23180794, PMID:23427989). ","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Marcio Luis Acencio (1), George Georghiou (2), Sandra Orchard (2), Liv Thommensen (1), Martin Kuiper (1) and Astrid Lægreid (1). (1) Norwegian University of Science and Technology (NTNU), Trondheim, Norway; (2) 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":"Gene Ontology annotation of human sequence-specific DNA binding transcription factors (DbTFs) based on the TFClass database","uniquename":"GO_REF:0000113"}


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_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":[115392,115398],"is_not":false,"summary":null,"term":"GO:0097753"}],"cellular_component":[{"annotations":[115393,115394],"is_not":false,"summary":null,"term":"GO:0032541"},{"annotations":[115395,115396],"is_not":false,"summary":null,"term":"GO:0005643"}],"single_locus_phenotype":[{"annotations":[115397],"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: 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: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: 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_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":[115321],"is_not":false,"summary":null,"term":"GO:0070762"},{"annotations":[115322],"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: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_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":[115512,115513],"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: 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:32265131
data:
  {"abstract":"The N- and O-linked oligosaccharides from fission yeast Schizosaccharomyces pombe not only contain large amounts of d-mannose (Man) but also contain large amounts of d-galactose (Gal). Although the galactomannans of S. pombe are mainly composed of α1,2- or α1,3-linked Gals, some of the terminal α1,2-linked Gals are found to be linked to pyruvylated β1,3-linked galactose (PvGal). We have determined the structural characteristics of the N-glycans and O-glycans in three Schizosaccharomyces species (S. japonicus, S. octosporus, and S. cryophilus) using lectin blot,  1 H NMR spectroscopy, and size-fractionation high performance liquid chromatography (HPLC), and found that the galactosylation of oligosaccharides was a common feature in fission yeasts. In addition, each of the terminal Galα1,2-, Galβ1,3- and non-substituted Man residues exhibited distinct characteristics. A BLAST search of gene databases in Schizosaccharomyces identified genes homologous to pvg1 encoding pyruvyltransferase of S. pombe. These genes, when expressed in an S. pombe pvg1Δ strains, led to the pyruvylation of non-reducing terminal β-linked Gal, suggesting the biosynthetic pathway of PvGal-containing oligosaccharides is highly conserved in fission yeasts.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Fukunaga T, Tanaka N, Furumoto T, Nakakita S, Ohashi T, Higuchi Y, Maekawa H, Takegawa K","authors_abbrev":"Fukunaga T et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"J Biosci Bioeng 2020 Aug;130(2):128-136","cv_annotations":{},"doi":"10.1016/j.jbiosc.2020.03.008","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2020","pubmed_entrez_date":"2020-04-09","pubmed_publication_date":"Aug 2020","terms_by_termid":{},"title":"Characterization of N- and O-linked galactosylated oligosaccharides from fission yeast species.","uniquename":"PMID:32265131"}


id: PMID:28954740
data:
  {"abstract":"After mitosis, nuclear reorganization occurs together with decondensation of mitotic chromosomes and reformation of the nuclear envelope, thereby restoring the Ran-GTP gradient between the nucleus and cytoplasm. The Ran-GTP gradient is dependent on Pim1/RCC1. Interestingly, a defect in Pim1/RCC1 in  Schizosaccharomyces pombe  causes postmitotic condensation of chromatin, namely hypercondensation, suggesting a relationship between the Ran-GTP gradient and chromosome decondensation. However, how Ran-GTP interacts with chromosome decondensation is unresolved. To examine this interaction, we used  Schizosaccharomyces japonicus , which is known to undergo partial breakdown of the nuclear membrane during mitosis. We found that Pim1/RCC1 was localized on nuclear pores, but this localization failed in a temperature-sensitive mutant of Pim1/RCC1. The mutant cells exhibited hypercondensed chromatin after mitosis due to prolonged association of condensin on the chromosomes. Conceivably, a condensin-dephosphorylation defect might cause hypercondensed chromatin, since chromosomal localization of condensin is dependent on phosphorylation by cyclin-dependent kinase (CDK). Indeed, CDK-phospho-mimic mutation of condensin alone caused untimely condensin localization, resulting in hypercondensed chromatin. Together, these results suggest that dephosphorylation of CDK sites of condensin might require the Ran-GTP gradient produced by nuclear pore-localized Pim1/RCC1.","alleles_by_uniquename":{"SJAG_00871:allele-1":{"allele_type":"amino_acid_mutation","description":"cut3-T19E","gene_uniquename":"SJAG_00871","name":"cut3-T19E","uniquename":"SJAG_00871:allele-1"},"SJAG_04284:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04284","name":"nup61delta","uniquename":"SJAG_04284:allele-1"},"SJAG_04464:allele-1":{"allele_type":"amino_acid_mutation","description":"R152C","gene_uniquename":"SJAG_04464","name":"pim1-R152C","synonyms":[{"name":"Inferred CDK-phospho-mimic mutation","reference":"PMID:28954740","type":"exact"}],"uniquename":"SJAG_04464:allele-1"}},"annotation_curators":[{"annotation_count":12,"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":"Aoki K, Niki H","authors_abbrev":"Aoki K et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2022-11-23 15:00:26","canto_curator_name":"Sho Okamoto","canto_curator_role":"community","canto_first_approved_date":"2022-11-23 15:00:26","canto_session_key":"7c26b8235c98c3eb","canto_session_submitted_date":"2022-11-23 15:00:18","canto_triage_status":"Curatable","citation":"Biol Open 2017 Nov 15;6(11):1614-1628","cv_annotations":{"biological_process":[{"annotations":[115311],"is_not":false,"summary":null,"term":"GO:0101024"},{"annotations":[115316],"is_not":false,"summary":null,"term":"GO:0006998"}],"cellular_component":[{"annotations":[115315],"is_not":false,"summary":null,"term":"GO:0120321"}],"multi_locus_phenotype":[{"annotations":[115318],"is_not":false,"summary":null,"term":"FYPO:0000619"},{"annotations":[115317],"is_not":false,"summary":null,"term":"FYPO:0001489"}],"single_locus_phenotype":[{"annotations":[115319],"is_not":false,"summary":null,"term":"FYPO:0000619"},{"annotations":[115313],"is_not":false,"summary":null,"term":"FYPO:0003738"},{"annotations":[115320],"is_not":false,"summary":null,"term":"FYPO:0000815"},{"annotations":[115312],"is_not":false,"summary":null,"term":"FYPO:0000082"},{"annotations":[115314],"is_not":false,"summary":null,"term":"FYPO:0003976"},{"annotations":[115310],"is_not":false,"summary":null,"term":"FYPO:0001387"}]},"doi":"10.1242/bio.027193","gene_count":4,"genes_by_uniquename":{"SJAG_00471":null,"SJAG_00871":null,"SJAG_04284":null,"SJAG_04464":null},"genotypes_by_uniquename":{"cut3-T19E-cut3-T19E-amino_acid_mutation-expression-not_assayed_or_wild_type__pim1-R152C-R152C-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"cut3-T19E(aa) pim1-R152C(aa)","display_uniquename":"cut3-T19E-cut3-T19E-amino_acid_mutation-expression-not_assayed_or_wild_type__pim1-R152C-R152C-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00871:allele-1","expression":"Not assayed or wild type"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_04464:allele-1","expression":"Not assayed or wild type"}]}]},"nup61delta":{"display_name":"nup61delta","display_uniquename":"nup61delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04284:allele-1","expression":"Null"}]}]},"pim1-R152C-R152C-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"pim1-R152C(aa)","display_uniquename":"pim1-R152C-R152C-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04464:allele-1","expression":"Not assayed or wild type"}]}]}},"ltp_gene_count":4,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[{"evidence":"Affinity Capture-Western","gene_uniquename":"SJAG_04464","interactor_uniquename":"SJAG_00471","reference_uniquename":"PMID:28954740","throughput":"low"}],"publication_year":"2017","pubmed_entrez_date":"2017-09-29","pubmed_publication_date":"15 Nov 2017","references_by_uniquename":{"PMID:28954740":null},"terms_by_termid":{"FYECO:0000004":null,"FYECO:0000005":null,"FYECO:0000137":null,"FYPO:0000082":null,"FYPO:0000619":null,"FYPO:0000815":null,"FYPO:0001387":null,"FYPO:0001489":null,"FYPO:0003738":null,"FYPO:0003976":null,"FYPO_EXT:0000001":null,"GO:0006998":null,"GO:0101024":null,"GO:0120321":null},"title":"Release of condensin from mitotic chromosomes requires the Ran-GTP gradient in the reorganized nucleus.","uniquename":"PMID:28954740"}


id: PMID:37233261
data:
  {"abstract":"Gene targeting is a commonly used method to reveal the function of genes. Although it is an attractive tool for molecular studies, it can frequently be a challenge because its efficiency can be low and it requires the screening of a large number of transformants. Generally, these problems originate from the elevated level of ectopic integration caused by non-homologous DNA end joining (NHEJ). To eliminate this problem, NHEJ-related genes are frequently deleted or disrupted. Although these manipulations can improve gene targeting, the phenotype of the mutant strains raised the question of whether mutations have side effects. The aim of this study was to disrupt the  lig4  gene in the dimorphic fission yeast,  S. japonicus , and investigate the phenotypic changes of the mutant strain. The mutant cells have shown various phenotypic changes, such as increased sporulation on complete medium, decreased hyphal growth, faster chronological aging, and higher sensitivity to heat shock, UV light, and caffeine. In addition, higher flocculation capacity has been observed, especially at lower sugar concentrations. These changes were supported by transcriptional profiling. Many genes belonging to metabolic and transport processes, cell division, or signaling had altered mRNA levels compared to the control strain. Although the disruption improved the gene targeting, we assume that the  lig4  inactivation can cause unexpected physiological side effects, and we have to be very careful with the manipulations of the NHEJ-related genes. To reveal the exact mechanisms behind these changes, further investigations are required.","alleles_by_uniquename":{"SJAG_02527:allele-1":{"allele_type":"disruption","description":"RNA sequencing revealed that only the 5' end of the disrupted allele showed low RNA expression and coverage","gene_uniquename":"SJAG_02527","name":"lig4::KanMX6","uniquename":"SJAG_02527:allele-1"}},"annotation_curators":[{"annotation_count":7,"community_curator":true,"file_name":null,"file_type":null,"name":"Ida Miklos","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2023-08-08","authors":"Acs-Szabo L, Papp LA, Takacs S, Miklos I","authors_abbrev":"Acs-Szabo L et al.","canto_added_date":"2023-05-27 00:40:04","canto_annotation_status":"APPROVED","canto_approved_date":"2023-08-08 20:07:33","canto_curator_name":"Ida Miklos","canto_curator_role":"community","canto_first_approved_date":"2023-08-08 20:07:33","canto_session_key":"c74bdd0a67b132f8","canto_session_submitted_date":"2023-08-08 20:07:15","canto_triage_status":"Curatable","citation":"J Fungi (Basel) 2023 May 10;9(5)","cv_annotations":{"single_locus_phenotype":[{"annotations":[115354],"is_not":false,"summary":null,"term":"FYPO:0007776"},{"annotations":[115356],"is_not":false,"summary":null,"term":"FYPO:0009111"},{"annotations":[115353],"is_not":false,"summary":null,"term":"FYPO:0000588"},{"annotations":[115359],"is_not":false,"summary":null,"term":"FYPO:0005705"},{"annotations":[115357],"is_not":false,"summary":null,"term":"FYPO:0005231"},{"annotations":[115355],"is_not":false,"summary":null,"term":"FYPO:0000097"},{"annotations":[115358],"is_not":false,"summary":null,"term":"FYPO:0001408"}]},"doi":"10.3390/jof9050550","gene_count":1,"genes_by_uniquename":{"SJAG_02527":null},"genotypes_by_uniquename":{"lig4::KanMX6-RNA_sequencing_revealed_that_only_the_5'_end_of_the_disrupted_allele_showed_low_RNA_expression_and_coverage-disruption-expression-knockdown":{"display_name":"lig4::KanMX6(RNA sequencing revealed that only the 5' end of the disrupted allele showed low RNA expression and coverage)[Knockdown]","display_uniquename":"lig4::KanMX6-RNA_sequencing_revealed_that_only_the_5'_end_of_the_disrupted_allele_showed_low_RNA_expression_and_coverage-disruption-expression-knockdown","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02527:allele-1","expression":"Knockdown"}]}]}},"ltp_gene_count":1,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2023","pubmed_entrez_date":"2023-05-26","pubmed_publication_date":"10 May 2023","terms_by_termid":{"FYECO:0000005":null,"FYECO:0000081":null,"FYECO:0000117":null,"FYECO:0000126":null,"FYECO:0000137":null,"FYECO:0000315":null,"FYPO:0000097":null,"FYPO:0000588":null,"FYPO:0001408":null,"FYPO:0005231":null,"FYPO:0005705":null,"FYPO:0007776":null,"FYPO:0009111":null},"title":"Disruption of the  Schizosaccharomyces japonicus lig4  Disturbs Several Cellular Processes and Leads to a Pleiotropic Phenotype.","uniquename":"PMID:37233261"}


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: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_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":[115596],"is_not":false,"summary":null,"term":"GO:0005801"},{"annotations":[115598],"is_not":false,"summary":null,"term":"GO:0005829"}],"single_locus_phenotype":[{"annotations":[115597],"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: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_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":[115253],"is_not":false,"summary":null,"term":"GO:0005730"}],"multi_locus_phenotype":[{"annotations":[115267,115268,115269,115271],"is_not":false,"summary":null,"term":"FYPO:0000674"}],"single_locus_phenotype":[{"annotations":[115254,115255,115256,115270],"is_not":false,"summary":null,"term":"FYPO:0000080"},{"annotations":[115263,115264,115265],"is_not":false,"summary":null,"term":"FYPO:0000618"},{"annotations":[115272,115273,115274],"is_not":false,"summary":null,"term":"FYPO:0001327"},{"annotations":[115260,115261,115262],"is_not":false,"summary":null,"term":"FYPO:0001387"},{"annotations":[115257,115258,115259],"is_not":false,"summary":null,"term":"FYPO:0000324"},{"annotations":[115266],"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: 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: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: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:0000101
data:
  {"abstract":"This reference is used to describe functional annotations transferred from one or more reference (\"source\") organisms to a newly annotated (\"target\") organism on the basis of ortholog cluster membership. In detail, predicted (e.g. by AUGUSTUS, see doi:10.1186/1471-2105-7-62) or transferred (e.g. via RATT, see doi:10:1093/nar/gkg1268) gene models in the target genome are translated and processed by OrthoMCL 1.4 together with reference protein sequences to produce clusters of gene products derived from orthologous genes. For each cluster, GO terms are automatically transferred from source products to the target gene products if they are experimentally verified (IDA (ECO:0000314), IMP (ECO:0000315), IPI (ECO:0000353), IGI (ECO:0000316), (EXP ECO:0000269). They are tagged with the ISO evidence code and the \"with/from\" is populated with the source feature references (e.g. \"GeneDB:LmjF.28.0960\"). OrthoMCL runs are done using the parameterization suggested in the OrthoMCL algorithm document (blastall -F 'm S' -e 1e-5).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Sascha Steinbiss, GeneDB 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 GO annotation data to close orthologs","uniquename":"GO_REF:0000101"}


id: PMID:28342076
data:
  {"abstract":"Environmental glucose is an important regulator of biological processes, as it can launch different cell processes depending on its concentration. Thus, low glucose concentration can induce entry into quiescence, which ensures long-term viability for the cells or in other cases mycelial growth in the dimorphic species, which, in turn, provides the cells with fresh nutrients. Several genes, such as the genes of cAMP cascade, are involved in glucose sensing and response. Since this signal transduction pathway seemed to be an evolutionarily conserved process, we assumed that its genes were also conserved and preserved their functional homology. To obtain evidence, Schizosaccharomyces pombe rsv1 and its orthologous genes were investigated using in silico and experimental approaches. Our results supported that the Rsv1 zinc-finger transcription factors of Schizosaccharomyces japonicus and Schizosaccharomyces octosporus and the Candida albicans cas5p were really functional homologues of the S. pombe Rsv1. Namely, the homologous proteins were able to restore mutant phenotype of the S. pombe rsv1-deleted cells. Bioinformatic anaysis revealed that the most conserved parts of the proteins always contained the C2H2 domains and the complementation abilities of the counterpart genes were not uniform regarding the investigated features, which can be in connection with the conserved regions outside C2H2.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Pataki E, Sipiczki M, Miklos I","authors_abbrev":"Pataki E et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Sequence feature or region","citation":"Curr Microbiol 2017 Jun;74(6):710-717","cv_annotations":{},"doi":"10.1007/s00284-017-1227-9","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":"2017-03-26","pubmed_publication_date":"Jun 2017","terms_by_termid":{},"title":"Schizosaccharomyces pombe rsv1 Transcription Factor and its Putative Homologues Preserved their Functional Homology and are Evolutionarily Conserved.","uniquename":"PMID:28342076"}


id: GO_REF:0000108
data:
  {"abstract":"GO terms are automatically assigned based on inter-ontology links to generate inferred annotations. Annotations from Molecular Function to Biological Process can be propagated, as well as between Biological Process and Cellular Component. Annotations that are created using this inference method receive either the evidence code ECO:0000366 (evidence based on logical inference from automatic annotation used in automatic assertion) or ECO:0000364 (evidence based on logical inference from manual annotation used in automatic assertion), depending on whether the source annotation has a manual or automatic evidence code. 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id: GO_REF:0000119
data:
  {"abstract":"The Alliance of Genome Resources (https://www.alliancegenome.org/) has procedures in place to establish orthology relationships","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"The Gene Ontology Consortium","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 mouse-human orthologs","uniquename":"GO_REF:0000119"}


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:0000050
data:
  {"abstract":"Transitive assignment of GO terms to a gene based on a curator's judgment of its match to a sequence model,such as a Pfam or InterPro entry, that has manually curated GO annotations, mappings to GO terms, or a description from which GO terms can be inferred. A statistical model of a sequence or group of sequences is used to make a prediction about the function of a protein or RNA. Annotations are created when a curator evaluates the results, using criteria that include excluding false positives and ensuring that the annotation is accurate for all matches. Statistical scores (such as e values and cutoff scores) and the functional specificity of the model may also be (but are not always) considered. Annotations resulting from the transfer of GO terms use the 'ISM' evidence code and include an accession for the model from which the annotation was projected in the 'with' field (column 8).","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":"Manual transfer of GO annotation data to genes by curator judgment of sequence model","uniquename":"GO_REF:0000050"}


id: PMID:28228545
data:
  {"abstract":"Inactivation of retrotransposons is accompanied by the emergence of centromere-binding protein-B (CENPB) in  Schizosaccharomyces , as well as in metazoans. The RNA interference (RNAi)-induced transcriptional silencing (RITS) complex, comprising chromodomain protein-1 (Chp1), Tas3 (protein with unknown function), and Argonaute (Ago1), plays an important role in RNAi-mediated heterochromatinization. We find that whereas the Ago1 subunit of the RITS complex is highly conserved, Tas3 is lost and Chp1 is truncated in  Schizosaccharomyces cryophilus  and  Schizosaccharomyces octosporus  We show that truncated Chp1 loses the property of heterochromatin localization and silencing when transformed in  Schizosaccharomyces pombe  Furthermore, multiple copies of CENPB, related to  Tc1/mariner and Tc5  transposons, occur in all  Schizosaccharomyces  species, as well as in humans, but with loss of transposase function (except  Schizosaccharomyces japonicus ). We propose that acquisition of  Tc1/mariner and Tc5  elements by horizontal transfer in  S. pombe  (and humans) is accompanied by alteration of their function from a transposase/endonuclease to a heterochromatin protein, designed to suppress transposon expression and recombination. The resulting redundancy of RITS may have eased the selection pressure, resulting in progressive loss or truncation of  tas3  and  chp1  genes in  S. octosporus  and  S. cryophilus  and triggered similar evolutionary dynamics in the metazoan orthologues.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Upadhyay U, Srivastava S, Khatri I, Nanda JS, Subramanian S, Arora A, Singh J","authors_abbrev":"Upadhyay U et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Phylogeny and evolutionary studies","citation":"Mol Biol Cell 2017 Apr 15;28(8):1132-1146","cv_annotations":{},"doi":"10.1091/mbc.E16-07-0485","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":"2017-02-24","pubmed_publication_date":"15 Apr 2017","terms_by_termid":{},"title":"Ablation of RNA interference and retrotransposons accompany acquisition and evolution of transposases to heterochromatin protein CENPB.","uniquename":"PMID:28228545"}


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: 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: 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: PMID:33022982
data:
  {"abstract":"Nowadays commercial preparations of yeast polysaccharides (PSs), in particular mannoproteins, are widely used for wine colloidal and tartrate salt stabilization. In this context, the industry has developed different processes for the isolation and purification of PSs from the cell wall of  Saccharomyces cerevisiae . This yeast releases limited amounts of mannoproteins in the growth medium, thus making their direct isolation from the culture broth not economically feasible. On the contrary,  Schizosaccharomyces japonicus , a non- Saccharomyces  yeast isolated from wine, releases significant amounts of PSs during the alcoholic fermentation. In the present work, PSs released by  Sch. japonicus  were recovered from the growth medium by ultrafiltration and their impact on the wine colloidal stability was evaluated. Interestingly, these PSs contribute positively to the wine protein stability. The visible haziness of the heat-treated wine decreases as the concentration of added PSs increases. SDS-PAGE Gel electrophoresis results of the haze and of the supernatant after the heat stability test are consistent with the turbidity measurements. Moreover, particle size distributions of the heat-treated wines, as obtained by Dynamic Light Scattering (DLS), show a reduction in the average dimension of the protein aggregates as the concentration of added PSs increases.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Millarini V, Ignesti S, Cappelli S, Ferraro G, Adessi A, Zanoni B, Fratini E, Domizio P","authors_abbrev":"Millarini V et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Biotech","citation":"Foods 2020 Oct 03;9(10)","cv_annotations":{},"doi":"10.3390/foods9101407","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2020","pubmed_entrez_date":"2020-10-07","pubmed_publication_date":"03 Oct 2020","terms_by_termid":{},"title":"Protection of Wine from Protein Haze Using  Schizosaccharomyces japonicus  Polysaccharides.","uniquename":"PMID:33022982"}


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 L327S","gene_uniquename":"SJAG_03892","name":"vps4-ts","uniquename":"SJAG_03892:allele-3"},"SJAG_04349:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04349","name":"vps28delta","uniquename":"SJAG_04349:allele-1"},"SJAG_04489:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04489","name":"did4delta","uniquename":"SJAG_04489:allele-1"},"SJAG_04912:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04912","name":"vps25delta","uniquename":"SJAG_04912: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":53,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-06-17","authors":"Pieper 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_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 06;53(1):27-41.e6","cv_annotations":{"cellular_component":[{"annotations":[115664],"is_not":false,"summary":null,"term":"GO:0000781"},{"annotations":[115662],"is_not":false,"summary":null,"term":"GO:0005783"},{"annotations":[115684],"is_not":false,"summary":null,"term":"GO:0000792"},{"annotations":[115689],"is_not":false,"summary":null,"term":"GO:1990343"},{"annotations":[115646],"is_not":false,"summary":null,"term":"GO:0000776"},{"annotations":[115666],"is_not":false,"summary":null,"term":"GO:0005771"},{"annotations":[115668],"is_not":false,"summary":null,"term":"GO:0032585"},{"annotations":[115667,115669],"is_not":false,"summary":null,"term":"GO:0031965"},{"annotations":[115690],"is_not":false,"summary":null,"term":"GO:0005643"},{"annotations":[115647,115652,115670],"is_not":false,"summary":null,"term":"GO:0005816"}],"molecular_function":[{"annotations":[115645],"is_not":false,"summary":null,"term":"GO:0043515"}],"multi_locus_phenotype":[{"annotations":[115675],"is_not":false,"summary":null,"term":"FYPO:0007771"},{"annotations":[115686],"is_not":false,"summary":null,"term":"FYPO:0001132"}],"single_locus_phenotype":[{"annotations":[115671,115672,115673],"is_not":false,"summary":null,"term":"FYPO:0001440"},{"annotations":[115682,115683],"is_not":false,"summary":null,"term":"FYPO:0001370"},{"annotations":[115685],"is_not":false,"summary":null,"term":"FYPO:0004718"},{"annotations":[115650,115651,115657,115658,115660,115661,115674,115676,115677,115678,115679,115680,115681],"is_not":false,"summary":null,"term":"FYPO:0007771"},{"annotations":[115663],"is_not":false,"summary":null,"term":"FYPO:0004318"},{"annotations":[115654],"is_not":false,"summary":null,"term":"FYPO:0007073"},{"annotations":[115648,115649,115655,115656],"is_not":false,"summary":null,"term":"FYPO:0007772"},{"annotations":[115659],"is_not":false,"summary":null,"term":"FYPO:0007770"},{"annotations":[115665],"is_not":false,"summary":null,"term":"FYPO:0003780"},{"annotations":[115653],"is_not":false,"summary":null,"term":"FYPO:0003657"},{"annotations":[115687,115688],"is_not":false,"summary":null,"term":"FYPO:0001234"}]},"doi":"10.1016/j.devcel.2020.01.028","gene_count":15,"genes_by_uniquename":{"SJAG_00684":null,"SJAG_01050":null,"SJAG_01242":null,"SJAG_01330":null,"SJAG_01601":null,"SJAG_01745":null,"SJAG_01777":null,"SJAG_03250":null,"SJAG_03299":null,"SJAG_03783":null,"SJAG_03892":null,"SJAG_04349":null,"SJAG_04489":null,"SJAG_04912":null,"SJAG_05207":null},"genotypes_by_uniquename":{"Vps4-EQ-E233Q-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"Vps4-EQ(E233Q aa)","display_uniquename":"Vps4-EQ-E233Q-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03892:allele-2","expression":"Not assayed or wild type"}]}]},"cmp7delta":{"display_name":"cmp7delta","display_uniquename":"cmp7delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_05207:allele-1","expression":"Null"}]}]},"cmp7delta__vps4-ts-I307T_L327S-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"cmp7delta vps4-ts(I307T L327S aa)","display_uniquename":"cmp7delta__vps4-ts-I307T_L327S-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_05207:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_03892:allele-3","expression":"Not assayed or wild type"}]}]},"did4delta":{"display_name":"did4delta","display_uniquename":"did4delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04489:allele-1","expression":"Null"}]}]},"lem2delta":{"display_name":"lem2delta","display_uniquename":"lem2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01745:allele-1","expression":"Null"}]}]},"mad2delta":{"display_name":"mad2delta","display_uniquename":"mad2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01330:allele-1","expression":"Null"}]}]},"nur1delta":{"display_name":"nur1delta","display_uniquename":"nur1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01050:allele-1","expression":"Null"}]}]},"nur1delta__vps4delta":{"display_name":"nur1delta vps4delta","display_uniquename":"nur1delta__vps4delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01050:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_03892:allele-1","expression":"Null"}]}]},"sst4delta":{"display_name":"sst4delta","display_uniquename":"sst4delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03250:allele-1","expression":"Null"}]}]},"vps24delta":{"display_name":"vps24delta","display_uniquename":"vps24delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03783:allele-1","expression":"Null"}]}]},"vps25delta":{"display_name":"vps25delta","display_uniquename":"vps25delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04912:allele-1","expression":"Null"}]}]},"vps28delta":{"display_name":"vps28delta","display_uniquename":"vps28delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04349:allele-1","expression":"Null"}]}]},"vps32delta":{"display_name":"vps32delta","display_uniquename":"vps32delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01242:allele-1","expression":"Null"}]}]},"vps4-ts-I307T_L327S-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"vps4-ts(I307T 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: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_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":[115292],"is_not":false,"summary":null,"term":"FYPO:0007790"},{"annotations":[115298],"is_not":false,"summary":null,"term":"FYPO:0000085"},{"annotations":[115295],"is_not":false,"summary":null,"term":"FYPO:0000088"}],"single_locus_phenotype":[{"annotations":[115283,115284,115285,115286,115287,115288,115290,115291],"is_not":false,"summary":null,"term":"FYPO:0007782"},{"annotations":[115309],"is_not":false,"summary":null,"term":"FYPO:0007774"},{"annotations":[115308],"is_not":false,"summary":null,"term":"FYPO:0001690"},{"annotations":[115282,115289],"is_not":false,"summary":null,"term":"FYPO:0007790"},{"annotations":[115307],"is_not":false,"summary":null,"term":"FYPO:0004693"},{"annotations":[115296,115297,115302,115303,115304],"is_not":false,"summary":null,"term":"FYPO:0000085"},{"annotations":[115293,115294,115299,115300,115301],"is_not":false,"summary":null,"term":"FYPO:0000088"},{"annotations":[115305,115306],"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:9720056
data:
  {"abstract":"The cells of Schizosaccharomyces japonicus var. versatilis responded to the presence of cytochalasin D (CD), an inhibitor of actin polymerization, by the disappearance of contractile actin rings (ARs) that had already formed and by inhibition of new ring formation. Actin cables disappeared. Actin patches remained preserved and became co-localized with regions of actual cell wall formation (at cell poles and at the site of septum development). Removal of the AR arrested formation of the primary septum and led to the production of aberrant septum protrusions in that region. Nuclear division was accomplished in the presence of CD but new ARs were not produced. The wall (septum) material was deposited in the form of a wide band at the inner surface of the lateral cell wall in the cell centre. This layer showed a thin fibrillar structure. The removal of CD resulted in rapid formation of new ARs in the equatorial region of the cells. This implies that the signal for AR localization was not abolished either by CD effects or by removal of an AR already formed. Some of the newly developed ARs showed atypical localization and orientation. In addition, redundant, subcortically situated actin bundles were produced. The removal of CD was quickly followed by the development of primary septa co-localized with ARs. Wall protrusions occurred co-localized with the redundant actin bundles. If these were completed in a circle, redundant septa developed. The AR is a mechanism which, in time and space, triggers cytokinesis by building a septum sequentially dependent on the AR. Aberrant septa were not capable of separating daughter cells. However, non-separated daughter cells subsequently gave rise to normal cells.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Gabriel M, Horký D, Svoboda A, Kopecká M","authors_abbrev":"Gabriel M et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"Microbiology (Reading) 1998 Aug;144 ( Pt 8):2331-2344","cv_annotations":{},"doi":"10.1099/00221287-144-8-2331","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":"1998-08-28","pubmed_publication_date":"Aug 1998","terms_by_termid":{},"title":"Cytochalasin D interferes with contractile actin ring and septum formation in Schizosaccharomyces japonicus var. versatilis.","uniquename":"PMID:9720056"}


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:7214237
data:
  {"abstract":"Hybridization studies based on the prototrophic selection technique, involving the use of auxotrophic mutants of strains of five accepted species of the genus Schizosaccharomyces, are reported. Intrastrain recombinants were recovered in five out of six tested parental pairs. Interstrain recombinants were recovered from crosses involving strains of S. japonicus and strains of S. pombe. No recombinants were recovered in 62 interspecific crosses involving all possible combinations of the six representatives of the genus.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Johannsen E","authors_abbrev":"Johannsen E","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 1981 Feb;27(2):184-91","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1981","pubmed_entrez_date":"1981-02-01","pubmed_publication_date":"Feb 1981","terms_by_termid":{},"title":"Hybridization studies within the genus Schizosaccharomyces Lindner.","uniquename":"PMID:7214237"}


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:24699070
data:
  {"abstract":"The post-cytokinetic separation of cells in cell-walled organisms involves enzymic processes that degrade a specific layer of the division septum and the region of the mother cell wall that edges the septum. In the fission yeast Schizosaccharomyces pombe, the 1,3-α-glucanase Agn1p, originally identified as a mutanase-like glycoside hydrolase family 71 (GH71) enzyme, dissolves the mother cell wall around the septum edge. Our search in the genomes of completely sequenced fungi identified GH71 hydrolases in Basidiomycota, Taphrinomycotina and Pezizomycotina, but not in Saccharomycotina. The most likely Agn1p orthologues in Pezizomycotina species are not mutanases having mutanase-binding domains, but experimentally non-characterized hypothetical proteins that have no carbohydrate-binding domains. The analysis of the GH71 domains corroborated the phylogenetic relationships of the Schizosaccharomyces species determined by previous studies, but suggested a closer relationship to the Basidiomycota proteins than to the Ascomycota proteins. In the Schizosaccharomyces genus, the Agn1p proteins are structurally conserved: their GH71 domains are flanked by N-terminal secretion signals and C-terminal sequences containing the conserved block YNFNA(Y)/HTG. The inactivation of the agn1(Sj) gene in Schizosaccharomyces japonicus, the only true dimorphic member of the genus, caused a severe cell-separation defect in its yeast phase, but had no effect on the hyphal growth and yeast-to-mycelium transition. It did not affect the mycelium-to-yeast transition either, only delaying the separation of the yeast cells arising from the fragmenting hyphae. The heterologous expression of agn1(Sj) partially rescued the separation defect of the agn1Δ cells of Schizosaccharomyces pombe. The results presented indicate that the fission yeast Agn1p 1,3-α-glucanases of Schizosaccharomyces japonicus and Schizosaccharomyces pombe share conserved functions in the yeast phase. ","alleles_by_uniquename":{"SJAG_03444:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03444","name":"agn1delta","uniquename":"SJAG_03444:allele-1"}},"annotation_curators":[{"annotation_count":1,"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":"2021-07-09","authors":"Sipiczki M, Balazs A, Monus A, Papp L, Horvath A, Sveiczer A, Miklos I","authors_abbrev":"Sipiczki M et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-09-01 07:35:20","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-07-09 13:16:43","canto_session_key":"b8bc1733e6f2c600","canto_session_submitted_date":"2021-07-09 13:16:35","canto_triage_status":"Curatable","citation":"Microbiology (Reading) 2014 Jun;160(Pt 6):1063-1074","cv_annotations":{"biological_process":[{"annotations":[115248],"is_not":false,"summary":null,"term":"GO:0030995"}],"single_locus_phenotype":[{"annotations":[115247],"is_not":false,"summary":null,"term":"FYPO:0001971"}]},"doi":"10.1099/mic.0.077511-0","gene_count":1,"genes_by_uniquename":{"SJAG_03444":null},"genotypes_by_uniquename":{"agn1delta":{"display_name":"agn1delta","display_uniquename":"agn1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03444:allele-1","expression":"Null"}]}]}},"ltp_gene_count":1,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2014","pubmed_entrez_date":"2014-04-05","pubmed_publication_date":"Jun 2014","terms_by_termid":{"FYPO:0001971":null,"GO:0030995":null},"title":"Phylogenetic and comparative functional analysis of the cell-separation α-glucanase Agn1p in Schizosaccharomyces.","uniquename":"PMID:24699070"}


id: PMID:28733395
data:
  {"abstract":" Schizosaccharomyces japonicus  is a dimorphic yeast. Depending on the nutrient conditions, the transition between growth as yeast cells and growth as hyphal cells can be reversibly induced. In addition to nutrient stress, induced DNA lesions, such as those produced by camptothecin, also induce hyphal growth regardless of the nutrient status. This protocol describes both methods of induction.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Niki H","authors_abbrev":"Niki H","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Method or reagent","citation":"Cold Spring Harb Protoc 2017 Dec 01;2017(12):pdb.prot091868","cv_annotations":{},"doi":"10.1101/pdb.prot091868","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":"Induction of Hyphal Growth in  Schizosaccharomyces japonicus .","uniquename":"PMID:28733395"}


id: PMID:33232355
data:
  {"abstract":"Coenzyme Q (CoQ, ubiquinone) is an essential component of the electron transport system in aerobic organisms. Human type CoQ10, which has 10 units of isoprene in its quinone structure, is especially valuable as a food supplement. Therefore, studying the biosynthesis of CoQ10 is important not only for increasing metabolic knowledge, but also for improving biotechnological production. Herein, we show that Schizosaccharomyces pombe utilizes p-aminobenzoate (PABA) in addition to p-hydroxybenzoate (PHB) as a precursor for CoQ10 synthesis. We explored compounds that affect the synthesis of CoQ10 and found benzoic acid (Bz) at >5 μg/mL inhibited CoQ biosynthesis without accumulation of apparent CoQ intermediates. This inhibition was counteracted by incubation with a 10-fold lower amount of PABA or PHB. Overexpression of PHB-polyprenyl transferase encoded by ppt1 (coq2) also overcame the inhibition of CoQ biosynthesis by Bz. Inhibition by Bz was efficient in S. pombe and Schizosaccharomyces japonicus, but less so in Saccharomyces cerevisiae, Aureobasidium pullulans, and Escherichia coli. Bz also inhibited a S. pombe ppt1 (coq2) deletion strain expressing human COQ2, and this strain also utilized PABA as a precursor of CoQ10. Thus, Bz is likely to inhibit prenylation reactions involving PHB or PABA catalyzed by Coq2.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Nishida I, Yanai R, Matsuo Y, Kaino T, Kawamukai M","authors_abbrev":"Nishida I et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"PLoS One 2020;15(11):e0242616","cv_annotations":{},"doi":"10.1371/journal.pone.0242616","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2020","pubmed_entrez_date":"2020-11-24","pubmed_publication_date":"2020","terms_by_termid":{},"title":"Benzoic acid inhibits Coenzyme Q biosynthesis in Schizosaccharomyces pombe.","uniquename":"PMID:33232355"}


id: GO_REF:0000105
data:
  {"abstract":"Gene Ontology annotation based on predicted cytoplasmic tRNAs using tRNAscan-SE analysis (doi: 10.1093/nar/25.5.0955) of the Drosophila melanogaster genome (2002). Annotations have been reviewed by FlyBase (2015) and found to be consistent when compared with the most recent tRNAscan-SE analysis of the genome (http://gtrnadb.ucsc.edu/genomes/eukaryota/Dmela6/).","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 transfer RNAs based on tRNAscan-SE analysis of the Drosophila melanogaster genome (2002).","uniquename":"GO_REF:0000105"}


id: PMID:27734801
data:
  {"abstract":"Many eukaryotes assemble a ring-shaped actomyosin network that contracts to drive cytokinesis. Unlike actomyosin in sarcomeres, which cycles through contraction and relaxation, the cytokinetic ring disassembles during contraction through an unknown mechanism. Here we find in  Schizosaccharomyces japonicus  and  Schizosaccharomyces pombe  that, during actomyosin ring contraction, actin filaments associated with actomyosin rings are expelled as micron-scale bundles containing multiple actomyosin ring proteins. Using functional isolated actomyosin rings we show that expulsion of actin bundles does not require continuous presence of cytoplasm. Strikingly, mechanical compression of actomyosin rings results in expulsion of bundles predominantly at regions of high curvature. Our work unprecedentedly reveals that the increased curvature of the ring itself promotes its disassembly. It is likely that such a curvature-induced mechanism may operate in disassembly of other contractile networks.","alleles_by_uniquename":{},"annotation_curators":[{"annotation_count":2,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-07-09","authors":"Huang J, Chew TG, Gu Y, Palani S, Kamnev A, Martin DS, Carter NJ, Cross RA, Oliferenko S, Balasubramanian MK","authors_abbrev":"Huang J et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-07-09 15:10:46","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-07-09 15:10:46","canto_session_key":"f47401f00ac444e0","canto_session_submitted_date":"2021-07-09 15:10:39","canto_triage_status":"Curatable","citation":"Elife 2016 10 13;5","cv_annotations":{"cellular_component":[{"annotations":[115621],"is_not":false,"summary":null,"term":"GO:0032432"},{"annotations":[115620],"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: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:0000033
data:
  {"abstract":"The Phylogenetic ANnotation using Gene Ontology (PAN-GO) method annotates evolutionary trees from the PANTHER database with GO terms describing molecular function, biological process and cellular component. The GO terms are manually selected by a curator and used to annotate ancestral genes in the phylogenetic tree using the evidence code IBA (Inferred from Biological Ancestor). All supporting annotations must be based on experimental data from the scientific literature. The PAN-GO annotations are fully traceable from the data in the 'with/from' column of the annotation, which provides the PANTHER node ID (PTN) from which the annotation is derived, as well as all descendants sequences that support the annotation of the ancestral node. 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id: GO_REF:0000094
data:
  {"abstract":"We have created a standard template for classes describing the development of a metazoan structure as a biological process. The underlying equivalence axiom template is \"'anatomical structure development' and 'results in development of' some E\", where E is a anatomical entity (UBERON:0001062).","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 metazoan development as biological process in the Gene Ontology","uniquename":"GO_REF:0000094"}


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:37164017
data:
  {"abstract":"Most eukaryotes respire oxygen, using it to generate biomass and energy. However, a few organisms have lost the capacity to respire. Understanding how they manage biomass and energy production may illuminate the critical points at which respiration feeds into central carbon metabolism and explain possible routes to its optimization. Here, we use two related fission yeasts, Schizosaccharomyces pombe and Schizosaccharomyces japonicus, as a comparative model system. We show that although S. japonicus does not respire oxygen, unlike S. pombe, it is capable of efficient NADH oxidation, amino acid synthesis, and ATP generation. We probe possible optimization strategies through the use of stable isotope tracing metabolomics, mass isotopologue distribution analysis, genetics, and physiological experiments. S. japonicus appears to have optimized cytosolic NADH oxidation via glycerol-3-phosphate synthesis. It runs a fully bifurcated TCA pathway, sustaining amino acid production. Finally, we propose that it has optimized glycolysis to maintain high ATP/ADP ratio, in part by using the pentose phosphate pathway as a glycolytic shunt, reducing allosteric inhibition of glycolysis and supporting biomass generation. By comparing two related organisms with vastly different metabolic strategies, our work highlights the versatility and plasticity of central carbon metabolism in eukaryotes, illuminating critical adaptations supporting the preferential use of glycolysis over oxidative phosphorylation.","alleles_by_uniquename":{"SJAG_00409:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00409","name":"gpd1delta","uniquename":"SJAG_00409:allele-1"},"SJAG_00601:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00601","name":"rip1delta","uniquename":"SJAG_00601:allele-1"},"SJAG_01355:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01355","name":"cox6delta","uniquename":"SJAG_01355:allele-1"},"SJAG_01753:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01753","name":"mdh1delta","uniquename":"SJAG_01753:allele-1"},"SJAG_02796:allele-1":{"allele_type":"amino_acid_mutation","description":"A343T","gene_uniquename":"SJAG_02796","name":"pyk1-A343T","uniquename":"SJAG_02796:allele-1"},"SJAG_03920:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03920","name":"sdh3delta","uniquename":"SJAG_03920:allele-1"},"SJAG_04843:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04843","name":"fum1delta","uniquename":"SJAG_04843:allele-1"}},"annotation_curators":[{"annotation_count":20,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2023-05-18","authors":"Alam S, Gu Y, Reichert P, Bähler J, Oliferenko S","authors_abbrev":"Alam S et al.","canto_added_date":"2023-05-12 00:40:04","canto_annotation_status":"APPROVED","canto_approved_date":"2023-05-18 12:11:55","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2023-05-18 12:11:54","canto_session_key":"94bcbfb72cf94809","canto_session_submitted_date":"2023-05-18 12:11:43","canto_triage_status":"Curatable","citation":"Curr Biol 2023 Apr 30;","cv_annotations":{"single_locus_phenotype":[{"annotations":[115238],"is_not":false,"summary":null,"term":"FYPO:0007363"},{"annotations":[115236],"is_not":false,"summary":null,"term":"FYPO:0000026"},{"annotations":[115235],"is_not":false,"summary":null,"term":"FYPO:0001355"},{"annotations":[115237],"is_not":false,"summary":null,"term":"FYPO:0001489"},{"annotations":[115239],"is_not":false,"summary":null,"term":"FYPO:0004165"},{"annotations":[115233,115234],"is_not":false,"summary":null,"term":"FYPO:0007790"},{"annotations":[115227,115230],"is_not":false,"summary":null,"term":"FYPO:0000760"},{"annotations":[115229,115232],"is_not":false,"summary":null,"term":"FYPO:0000579"},{"annotations":[115228,115231],"is_not":false,"summary":null,"term":"FYPO:0000590"},{"annotations":[115224,115225,115226],"is_not":false,"summary":null,"term":"FYPO:0001357"},{"annotations":[115223],"is_not":false,"summary":null,"term":"FYPO:0001234"},{"annotations":[115240,115241,115242],"is_not":false,"summary":null,"term":"FYPO:0002058"}]},"doi":"10.1016/j.cub.2023.04.046","gene_count":7,"genes_by_uniquename":{"SJAG_00409":null,"SJAG_00601":null,"SJAG_01355":null,"SJAG_01753":null,"SJAG_02796":null,"SJAG_03920":null,"SJAG_04843":null},"genotypes_by_uniquename":{"cox6delta":{"display_name":"cox6delta","display_uniquename":"cox6delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01355:allele-1","expression":"Null"}]}]},"fum1delta":{"display_name":"fum1delta","display_uniquename":"fum1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04843:allele-1","expression":"Null"}]}]},"gpd1delta":{"display_name":"gpd1delta","display_uniquename":"gpd1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00409:allele-1","expression":"Null"}]}]},"mdh1delta":{"display_name":"mdh1delta","display_uniquename":"mdh1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01753:allele-1","expression":"Null"}]}]},"pyk1-A343T-A343T-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"pyk1-A343T(aa)","display_uniquename":"pyk1-A343T-A343T-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02796:allele-1","expression":"Not assayed or wild type"}]}]},"rip1delta":{"display_name":"rip1delta","display_uniquename":"rip1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00601:allele-1","expression":"Null"}]}]},"sdh3delta":{"display_name":"sdh3delta","display_uniquename":"sdh3delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03920:allele-1","expression":"Null"}]}]}},"ltp_gene_count":7,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2023","pubmed_entrez_date":"2023-05-10","pubmed_publication_date":"30 Apr 2023","terms_by_termid":{"FYECO:0000005":null,"FYECO:0000015":null,"FYECO:0000126":null,"FYECO:0000137":null,"FYPO:0000026":null,"FYPO:0000579":null,"FYPO:0000590":null,"FYPO:0000760":null,"FYPO:0001234":null,"FYPO:0001355":null,"FYPO:0001357":null,"FYPO:0001489":null,"FYPO:0002058":null,"FYPO:0004165":null,"FYPO:0007363":null,"FYPO:0007790":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null,"FYPO_EXT:0000003":null},"title":"Optimization of energy production and central carbon metabolism in a non-respiring eukaryote.","uniquename":"PMID:37164017"}


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: 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: 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-2":{"allele_type":"amino_acid_mutation","description":"T582G","gene_uniquename":"SJAG_04280","name":"wee1-as8","uniquename":"SJAG_04280:allele-2"},"SJAG_04280:allele-3":{"allele_type":"amino_acid_mutation","description":"G788E","gene_uniquename":"SJAG_04280","name":"wee1-G788E","uniquename":"SJAG_04280:allele-3"},"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_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":[115427],"is_not":false,"summary":null,"term":"GO:0061171"},{"annotations":[115428,115429],"is_not":false,"summary":null,"term":"GO:0008360"}],"multi_locus_phenotype":[{"annotations":[115415,115420],"is_not":false,"summary":null,"term":"FYPO:0007783"},{"annotations":[115426],"is_not":false,"summary":null,"term":"FYPO:0004105"},{"annotations":[115417],"is_not":false,"summary":null,"term":"FYPO:0001369"},{"annotations":[115419],"is_not":false,"summary":null,"term":"FYPO:0004293"}],"single_locus_phenotype":[{"annotations":[115421],"is_not":false,"summary":null,"term":"FYPO:0000198"},{"annotations":[115422,115423,115425],"is_not":false,"summary":null,"term":"FYPO:0005503"},{"annotations":[115416],"is_not":false,"summary":null,"term":"FYPO:0007783"},{"annotations":[115410],"is_not":false,"summary":null,"term":"FYPO:0004105"},{"annotations":[115424],"is_not":false,"summary":null,"term":"FYPO:0002870"},{"annotations":[115418],"is_not":false,"summary":null,"term":"FYPO:0001369"},{"annotations":[115411],"is_not":false,"summary":null,"term":"FYPO:0001234"},{"annotations":[115405,115406,115409],"is_not":false,"summary":null,"term":"FYPO:0000648"},{"annotations":[115407,115408,115414],"is_not":false,"summary":null,"term":"FYPO:0001877"},{"annotations":[115412,115413],"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-3","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-2","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-2","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-3","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-2","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: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:0000036
data:
  {"abstract":"The Gene Ontology Consortium uses the IC (Inferred by Curator) evidence code when an annotation cannot be supported by any direct evidence, but can be inferred by GO annotations that have been annotated to the same gene/gene product identifier in conjunction with the curator's knowledge of biology (supporting GO annotations must not be IC-evidenced). In many cases an IC-evidenced annotation simply applies the same reference that was used in the supporting GO annotation.  The use of IC evidence code in an annotation with reference GO_REF:0000036 signifies a curator inferred the GO term based on evidence from multiple sources of evidence/GO annotations. The 'with/from' field in these annotations will therefore supply more than one GO identifier, obtained from the set of supporting GO annotations assigned to the same gene/gene product identifier which cite publicly-available references.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO Annotation working group","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 annotations that require more than one source of functional data to support the assignment of the associated GO term","uniquename":"GO_REF:0000036"}


id: GO_REF:0000109
data:
  {"abstract":"Trypanosomes are exquisitely structured cells in which protein localisation can be extremely informative for likely function. TrypTag is a project using expression of N- and C-terminal mNeonGreen fusion proteins from the endogenous loci to determine the subcellular localisation of every gene in the Trypanosoma brucei genome. GO Cellular Component terms are manually assigned by curators studying fluorescence microscope images of the resulting cells labelled with mNeonGreen fusion proteins. As trypanosomes are a pathogenic basal eukaryote, this will indicate likely function of both highly conserved eukaryote genes and parasite-specific genes. Resource URL: http://www.tryptag.org Protein subcellular localisation images can be viewed on the Tryptag website, e.g. http://www.tryptag.org?id=Tb927.8.1550","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"TrypTag","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 genome-wide subcellular localisation of proteins using fluorescent protein tagging in Trypanosoma brucei","uniquename":"GO_REF:0000109"}


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


id: PMID: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_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":[115520,115521,115522,115523],"is_not":false,"summary":null,"term":"MOD:00046"}],"multi_locus_phenotype":[{"annotations":[115548],"is_not":false,"summary":null,"term":"FYPO:0007779"}],"single_locus_phenotype":[{"annotations":[115516,115528],"is_not":false,"summary":null,"term":"FYPO:0004481"},{"annotations":[115544],"is_not":false,"summary":null,"term":"FYPO:0007778"},{"annotations":[115543,115546],"is_not":false,"summary":null,"term":"FYPO:0007776"},{"annotations":[115527],"is_not":false,"summary":null,"term":"FYPO:0000708"},{"annotations":[115545,115547],"is_not":false,"summary":null,"term":"FYPO:0007780"},{"annotations":[115549,115550],"is_not":false,"summary":null,"term":"FYPO:0007824"},{"annotations":[115514,115526],"is_not":false,"summary":null,"term":"FYPO:0001122"},{"annotations":[115538,115542],"is_not":false,"summary":null,"term":"FYPO:0007777"},{"annotations":[115537,115541],"is_not":false,"summary":null,"term":"FYPO:0007775"},{"annotations":[115536,115540],"is_not":false,"summary":null,"term":"FYPO:0007774"},{"annotations":[115539],"is_not":false,"summary":null,"term":"FYPO:0007779"},{"annotations":[115519,115531],"is_not":false,"summary":null,"term":"FYPO:0000097"},{"annotations":[115518,115530],"is_not":false,"summary":null,"term":"FYPO:0000726"},{"annotations":[115517,115529],"is_not":false,"summary":null,"term":"FYPO:0000271"},{"annotations":[115532],"is_not":false,"summary":null,"term":"FYPO:0000841"},{"annotations":[115515],"is_not":false,"summary":null,"term":"FYPO:0000280"},{"annotations":[115535],"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:29173643
data:
  {"abstract":"In the beverage fermentation industry, especially at the craft or micro level, there is a movement to incorporate as many local ingredients as possible to both capture terroir and stimulate local economies. In the case of craft beer, this has traditionally only encompassed locally sourced barley, hops, and other agricultural adjuncts. The identification and use of novel yeasts in brewing lags behind. We sought to bridge this gap by bio-prospecting for wild yeasts, with a focus on the American Midwest. We isolated 284 different strains from 54 species of yeast and have begun to determine their fermentation characteristics. During this work, we found several isolates of five species that produce lactic acid and ethanol during wort fermentation: Hanseniaspora vineae, Lachancea fermentati, Lachancea thermotolerans, Schizosaccharomyces japonicus, and Wickerhamomyces anomalus. Tested representatives of these species yielded excellent attenuation, lactic acid production, and sensory characteristics, positioning them as viable alternatives to lactic acid bacteria (LAB) for the production of sour beers. Indeed, we suggest a new LAB-free paradigm for sour beer production that we term \"primary souring\" because the lactic acid production and resultant pH decrease occurs during primary fermentation, as opposed to kettle souring or souring via mixed culture fermentation.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Osburn K, Amaral J, Metcalf SR, Nickens DM, Rogers CM, Sausen C, Caputo R, Miller J, Li H, Tennessen JM, Bochman ML","authors_abbrev":"Osburn K et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Biotech","citation":"Food Microbiol 2018 Apr;70:76-84","cv_annotations":{},"doi":"10.1016/j.fm.2017.09.007","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2018","pubmed_entrez_date":"2017-11-28","pubmed_publication_date":"Apr 2018","terms_by_termid":{},"title":"Primary souring: A novel bacteria-free method for sour beer production.","uniquename":"PMID:29173643"}


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


id: PMID: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: GO_REF:0000091
data:
  {"abstract":"We have created a standard template for classes describing the cell migration process for a cell type as a biological process. The underlying equivalence axiom template is \"'cell migration' and 'alters_location_of' some C\", where C is a native cell (CL:0000004).","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 migration as biological processes in the Gene Ontology","uniquename":"GO_REF:0000091"}


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:24184107
data:
  {"abstract":"During cellular proliferation, the mother nucleus divides into two daughters, each carrying a full complement of chromosomes and capable of driving the next cell cycle. Mitotic chromosome segregation must be coordinated with remodeling of other nuclear components, including the nuclear envelope (NE) and the non-membrane-bound nucleolus. Here, we show that in the fission yeast Schizosaccharomyces japonicus, which breaks and reforms the NE during mitosis, the evolutionary conserved LEM-domain protein Man1 promotes equal partitioning of the nuclear membrane, nucleolar remodeling, and efficient inheritance of the nuclear pore complexes (NPCs) by the daughter nuclei. Analyses of man1 mutants and results obtained using an artificial chromatin-nuclear pore tether suggest that Man1 may exert its function by linking the NPCs to segregating chromatin. By integrating the partitioning of the nuclear membrane and nucleolar material with chromosome segregation, cells build two nearly identical copies of the original nucleus.","alleles_by_uniquename":{"SJAG_01834:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01834","name":"pom152delta","uniquename":"SJAG_01834:allele-1"},"SJAG_03449:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03449","name":"man1delta","uniquename":"SJAG_03449:allele-1"},"SJAG_03449:allele-2":{"allele_type":"partial_amino_acid_deletion","description":"man1DHEH","gene_uniquename":"SJAG_03449","name":"Man1DHEH","uniquename":"SJAG_03449:allele-2"},"SJAG_03449:allele-3":{"allele_type":"amino_acid_insertion_and_deletion","description":"man1-1-488","gene_uniquename":"SJAG_03449","name":"man1-1-488","uniquename":"SJAG_03449:allele-3"}},"annotation_curators":[{"annotation_count":17,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"},{"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":"2021-07-27","authors":"Yam C, Gu Y, Oliferenko S","authors_abbrev":"Yam C et al.","canto_added_date":"2021-05-10 02:38:18","canto_annotation_status":"APPROVED","canto_approved_date":"2021-09-01 07:25:17","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-07-27 11:54:17","canto_session_key":"0f2dda384385121f","canto_session_submitted_date":"2021-07-27 11:54:10","canto_triage_status":"Curatable","citation":"Curr Biol 2013 Nov 18;23(22):2303-2310","cv_annotations":{"biological_process":[{"annotations":[115643],"is_not":false,"summary":null,"term":"GO:0101024"}],"cellular_component":[{"annotations":[115628],"is_not":false,"summary":null,"term":"GO:0000781"},{"annotations":[115627],"is_not":false,"summary":null,"term":"GO:0140573"},{"annotations":[115630],"is_not":false,"summary":null,"term":"GO:0005643"},{"annotations":[115629],"is_not":false,"summary":null,"term":"GO:0030875"}],"molecular_function":[{"annotations":[115644],"is_not":false,"summary":null,"term":"GO:0062239"}],"single_locus_phenotype":[{"annotations":[115631,115636,115638],"is_not":false,"summary":null,"term":"FYPO:0003779"},{"annotations":[115640,115641,115642],"is_not":false,"summary":null,"term":"FYPO:0000671"},{"annotations":[115633,115634,115635,115637],"is_not":false,"summary":null,"term":"FYPO:0004890"},{"annotations":[115632],"is_not":false,"summary":null,"term":"FYPO:0001234"},{"annotations":[115639],"is_not":false,"summary":null,"term":"FYPO:0004683"}]},"doi":"10.1016/j.cub.2013.09.057","gene_count":5,"genes_by_uniquename":{"SJAG_00302":null,"SJAG_01777":null,"SJAG_01834":null,"SJAG_03449":null,"SJAG_03603":null},"genotypes_by_uniquename":{"Man1DHEH-man1DHEH-partial_amino_acid_deletion-expression-not_assayed_or_wild_type":{"display_name":"Man1DHEH(man1DHEH)","display_uniquename":"Man1DHEH-man1DHEH-partial_amino_acid_deletion-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03449:allele-2","expression":"Not assayed or wild type"}]}]},"man1-1-488-man1-1-488-amino_acid_insertion_and_deletion-expression-not_assayed_or_wild_type":{"display_name":"man1-1-488(aa)","display_uniquename":"man1-1-488-man1-1-488-amino_acid_insertion_and_deletion-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03449:allele-3","expression":"Not assayed or wild type"}]}]},"man1delta":{"display_name":"man1delta","display_uniquename":"man1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03449:allele-1","expression":"Null"}]}]},"pom152delta":{"display_name":"pom152delta","display_uniquename":"pom152delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01834:allele-1","expression":"Null"}]}]}},"ltp_gene_count":5,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2013","pubmed_entrez_date":"2013-11-05","pubmed_publication_date":"18 Nov 2013","terms_by_termid":{"FYECO:0000005":null,"FYECO:0000162":null,"FYPO:0000671":null,"FYPO:0001234":null,"FYPO:0003779":null,"FYPO:0004683":null,"FYPO:0004890":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null,"FYPO_EXT:0000003":null,"GO:0000781":null,"GO:0005643":null,"GO:0030875":null,"GO:0062239":null,"GO:0101024":null,"GO:0140573":null},"title":"Partitioning and remodeling of the Schizosaccharomyces japonicus mitotic nucleus require chromosome tethers.","uniquename":"PMID:24184107"}


id: GO_REF:0000070
data:
  {"abstract":"We have created a standard template for classes describing the transmembrane transporter activity a chemical entity (ChEBI) as molecular function. This includes variants for secondary active transmembrane transporter activity (GO:0015291), uptake transmembrane transporter activity (GO:0015563), and ATPase activity, coupled to transmembrane movement of substances (GO:0042626). The underlying equivalence axiom template is \"G and 'transports or maintains localization of' some X\",  where the genus G is either GO:0022857 (transmembrane transporter activity), GO:0015291, GO:0015563, or GO:0042626 depending on the variant. The variable 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 transmembrane transporter activity as molecular function in the Gene Ontology","uniquename":"GO_REF:0000070"}


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: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_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":[115588,115589],"is_not":false,"summary":null,"term":"GO:0031507"},{"annotations":[115586,115587],"is_not":false,"summary":null,"term":"GO:0016441"}],"multi_locus_phenotype":[{"annotations":[115582,115584],"is_not":false,"summary":null,"term":"FYPO:0004982"},{"annotations":[115583,115585],"is_not":false,"summary":null,"term":"FYPO:0004573"},{"annotations":[115579],"is_not":false,"summary":null,"term":"FYPO:0002061"},{"annotations":[115580,115581],"is_not":false,"summary":null,"term":"FYPO:0006989"},{"annotations":[115574,115575,115576,115577],"is_not":false,"summary":null,"term":"FYPO:0002058"}],"single_locus_phenotype":[{"annotations":[115568],"is_not":false,"summary":null,"term":"FYPO:0004205"},{"annotations":[115570],"is_not":false,"summary":null,"term":"FYPO:0004982"},{"annotations":[115572],"is_not":false,"summary":null,"term":"FYPO:0000595"},{"annotations":[115569],"is_not":false,"summary":null,"term":"FYPO:0004574"},{"annotations":[115561,115562,115563,115564,115565,115566,115567,115578],"is_not":false,"summary":null,"term":"FYPO:0002061"},{"annotations":[115573],"is_not":false,"summary":null,"term":"FYPO:0006989"},{"annotations":[115571],"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 Suppression"},[{"reference_uniquename":"PMID:35226668","throughput":"low"}]],[{"gene_a_uniquename":"SJAG_03689","gene_b_uniquename":"SJAG_02668","interaction_type":"Phenotypic Suppression"},[{"reference_uniquename":"PMID:35226668","throughput":"low"}]]],"genotypes_by_uniquename":{"ago1delta":{"display_name":"ago1delta","display_uniquename":"ago1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02621:allele-1","expression":"Null"}]}]},"ago1delta__leo1delta":{"display_name":"ago1delta leo1delta","display_uniquename":"ago1delta__leo1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02621:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_03118:allele-1","expression":"Null"}]}]},"arb1delta":{"display_name":"arb1delta","display_uniquename":"arb1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02594:allele-1","expression":"Null"}]}]},"arb2delta":{"display_name":"arb2delta","display_uniquename":"arb2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04061:allele-1","expression":"Null"}]}]},"chp1delta":{"display_name":"chp1delta","display_uniquename":"chp1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03916:allele-1","expression":"Null"}]}]},"clr4delta":{"display_name":"clr4delta","display_uniquename":"clr4delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04574:allele-1","expression":"Null"}]}]},"clr4delta__leo1delta":{"display_name":"clr4delta 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: 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: 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_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":[115399,115400,115401],"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: 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: PMID:7166567
data:
  {"abstract":"The fine structure of ascospore formation in the fission yeasts Schizosaccharomyces pombe and Schizosaccharomyces japonicus var. japonicus was studied by serial thin-sectioning and electron microscopy. The morphogenetic events were almost the same in both species. Ascospore development was initiated by the formation of the forespore membrane on the cytoplasmic side of the differentiated nucleus-associated organelle (NAO) in the interval between meiosis I and II in S. pombe, or during the post-meiotic nuclear division in S. japonicus, and the process proceeded almost synchronously through the two or four nuclei in the ascus. The forespore membrane developed by fusion of the cytoplasmic vesicles and this was clearly demonstrated in S. japonicus where the behaviour of vesicles involved in the forespore membrane development could be traced as they were marked by the presence of electron-dense granules. The staining technique, by phosphotungustic acid--chromic acid (PTA-CA) after treatment with periodic acid, was used to attempt to elucidate the origin and the nature of the forespore membrane. The method specific to plasmalemma-type membranes stained both ascus and ascospore plasmalemmas; the forespore membrane was not stained at first but developed the same affinity for stain as the plasma membrane in the course of ascospore development. The results suggest that the forespore membrane did not come directly from the ascus plasma membrane, but from another membrane system such as the endoplasmic reticulum. Spore wall material was deposited in the space between the inner and outer leaflets of the forespore membrane.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Tanaka K, Hirata A","authors_abbrev":"Tanaka K et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"J Cell Sci 1982 Aug;56:263-79","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1982","pubmed_entrez_date":"1982-08-01","pubmed_publication_date":"Aug 1982","terms_by_termid":{},"title":"Ascospore development in the fission yeasts Schizosaccharomyces pombe and S. japonicus.","uniquename":"PMID:7166567"}


id: 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:0000104
data:
  {"abstract":"GO terms are manually assigned to each rule in UniRule. These rules are prepared manually by UniProt curators based on the annotations present in reviewed UniProtKB/Swiss-Prot records that share sequence features, sequence similarity and taxonomy. The assigned GO terms are then transferred to all unreviewed UniProtKB/TrEMBL proteins that meet the conditions given in the UniRule rule. GO annotations using this technique receive the evidence code Inferred from Electronic Annotation (IEA; ECO:0000501). These annotations are updated regularly by UniProt and are available for download on both the GO and GOA EBI ftp sites. To report an annotation error or inconsistency, or for further information, please contact the UniProt Automated Annotation team at automated_annotation@ebi.ac.uk. UniRule is a collaboration between the European Bioinformatics Institute (EMBL-EBI), the Swiss Institute of Bioinformatics (SIB), and the Protein Information Resource at Georgetown University (PIR). For further information, please see UniProt: a hub for protein information Nucleic Acids Res. 2015, 43, D204, doi: 10.1093/nar/gku989 or www.uniprot.org.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"UniProt 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id: PMID:37279666
data:
  {"abstract":"A new study finds that Schizosaccharomyces japonicus, a eukaryote that lost the ability to respire, modified its central carbon metabolism to maintain efficient ATP production, cofactor regeneration, and amino-acid production. This remarkable metabolic flexibility opens new avenues towards applications.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Cool L, Hanon S, Verstrepen KJ","authors_abbrev":"Cool L et al.","canto_added_date":"2023-06-08 00:40:04","canto_curator_role":"JaponicusDB","canto_triage_status":"Review or comment","citation":"Curr Biol 2023 Jun 05;33(11):R444-R447","cv_annotations":{},"doi":"10.1016/j.cub.2023.05.002","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":"2023-06-06","pubmed_publication_date":"05 Jun 2023","terms_by_termid":{},"title":"Metabolism: How a eukaryote adapted to life without respiration.","uniquename":"PMID:37279666"}


id: GO_REF:0000118
data:
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