# refs

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: GO_REF:0000108
data:
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id: PMID:20737410
data:
  {"abstract":"Schizosaccharomyces japonicus is a fission yeast for which new genetic tools have recently been developed. Here, we report novel plasmid vectors with high transformation efficiency and an electroporation method for Sz. japonicus. We isolated 44 replicating segments from 12 166 transformants of Sz. japonicus genomic fragments and found a chromosomal fragment, RS1, as a new replicating sequence that conferred high transformation activity to Sz. japonicus cells. This sequence was cloned into a pUC19 vector with ura4(+) of Sz. pombe (pSJU11) or the kan gene on the kanMX6 module (pSJK11) as selection markers. These plasmids transformed Sz. japonicus cells in the early-log phase by electroporation at a frequency of 123 cfu/µg for pSJK11 and 301 cfu/µg for pSJU11, which were higher than previously reported autonomously replicating sequences. Although a portion of plasmids remained in host cells by integration into the chromosome via RS1 segment, the plasmids could be recovered from transformants. The plasmid copy number was estimated to be 1.88 copies per cell by Southern blot analysis using a Sz. pombe ura4(+) probe. The plasmid containing ade6(+) suppressed the auxotrophic growth of the ade6-domE mutant, indicating that the plasmid would be useful for suppressor screening and complementation assays in Sz. japonicus. Furthermore, pSJU11 transformed Sz. pombe cells with the same frequency as the pREP2 plasmid. This study is a report to demonstrate practical use of episomal plasmid vectors for genetic research in Sz. japonicus.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Aoki K, Nakajima R, Furuya K, Niki H","authors_abbrev":"Aoki K et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Method or reagent","citation":"Yeast 2010 Dec;27(12):1049-60","cv_annotations":{},"doi":"10.1002/yea.1815","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2010","pubmed_entrez_date":"2010-08-26","pubmed_publication_date":"Dec 2010","terms_by_termid":{},"title":"Novel episomal vectors and a highly efficient transformation procedure for the fission yeast Schizosaccharomyces japonicus.","uniquename":"PMID:20737410"}


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


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


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


id: GO_REF: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:23786411
data:
  {"abstract":"Three types of mitosis, which are open, closed or semi-open mitosis, function in eukaryotic cells, respectively. The open mitosis involves breakage of the nuclear envelope before nuclear division, whereas the closed mitosis proceeds with an intact nuclear envelope. To understand the mechanism and significance of three types of mitotic division in eukaryotes, we investigated the process of semi-open mitosis, in which the nuclear envelope is only partially broken, in the fission yeast Schizosaccharomyces japonicus. In anaphase-promoting complex/cyclosome (APC/C) mutants of Sz. japonicus, the nuclear envelope remained relatively intact during anaphase, resulting in impaired semi-open mitosis. As a suppressor of apc2 mutant, a mutation of Oar2, which was a 3-oxoacyl-[acyl carrier protein] reductase, was obtained. The level of the Oar2, which had two destruction-box motifs recognized by APC/C, was increased in APC/C mutants. Furthermore, the defective semi-open mitosis observed in an apc2 mutant was restored by mutated oar2+. Based on these findings, we propose that APC/C regulates the dynamics of the nuclear envelope through degradation of Oar2 dependent on APC/C during the metaphase-to-anaphase transition of semi-open mitosis in Sz. japonicus.","alleles_by_uniquename":{"SJAG_01946:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01946","name":"cem1delta","uniquename":"SJAG_01946:allele-1"},"SJAG_01956:allele-1":{"allele_type":"amino_acid_mutation","description":"E405K ts","gene_uniquename":"SJAG_01956","name":"nuc2-1051","uniquename":"SJAG_01956:allele-1"},"SJAG_03198:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03198","name":"oar2delta","uniquename":"SJAG_03198:allele-1"},"SJAG_03198:allele-2":{"allele_type":"amino_acid_mutation","description":"Y189D cold sensitive","gene_uniquename":"SJAG_03198","name":"oar2-51","uniquename":"SJAG_03198:allele-2"},"SJAG_03198:allele-3":{"allele_type":"amino_acid_mutation","description":"R72A,L75A,R106A,L109A","gene_uniquename":"SJAG_03198","name":"oar2-dm12","synonyms":[{"name":"destruction box mutations","reference":"PMID:23786411","type":"exact"}],"uniquename":"SJAG_03198:allele-3"},"SJAG_03351:allele-1":{"allele_type":"amino_acid_mutation","description":"A186T ts","gene_uniquename":"SJAG_03351","name":"cut23-415","uniquename":"SJAG_03351:allele-1"},"SJAG_03575:allele-1":{"allele_type":"amino_acid_mutation","description":"E548K ts","gene_uniquename":"SJAG_03575","name":"apc2-361","uniquename":"SJAG_03575:allele-1"}},"annotation_curators":[{"annotation_count":22,"community_curator":true,"file_name":null,"file_type":null,"name":"Sho Okamoto","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2022-11-21","authors":"Aoki K, Shiwa Y, Takada H, Yoshikawa H, Niki H","authors_abbrev":"Aoki K et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2022-11-21 18:57:14","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Sho Okamoto","canto_curator_role":"community","canto_first_approved_date":"2022-11-21 18:57:14","canto_session_key":"a0c3e1394f326db9","canto_session_submitted_date":"2022-11-21 18:57:00","canto_triage_status":"Curatable","citation":"Genes Cells 2013 Sep;18(9):733-52","cv_annotations":{"cellular_component":[{"annotations":[115564],"is_not":false,"summary":null,"term":"GO:0005730"}],"multi_locus_phenotype":[{"annotations":[115578,115579,115580,115582],"is_not":false,"summary":null,"term":"FYPO:0000674"}],"single_locus_phenotype":[{"annotations":[115565,115566,115567,115581],"is_not":false,"summary":null,"term":"FYPO:0000080"},{"annotations":[115574,115575,115576],"is_not":false,"summary":null,"term":"FYPO:0000618"},{"annotations":[115583,115584,115585],"is_not":false,"summary":null,"term":"FYPO:0001327"},{"annotations":[115571,115572,115573],"is_not":false,"summary":null,"term":"FYPO:0001387"},{"annotations":[115568,115569,115570],"is_not":false,"summary":null,"term":"FYPO:0000324"},{"annotations":[115577],"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","terms_by_termid":{"FYECO:0000004":null,"FYECO:0000006":null,"FYECO:0000137":null,"FYPO:0000080":null,"FYPO:0000324":null,"FYPO:0000618":null,"FYPO:0000674":null,"FYPO:0001327":null,"FYPO:0001387":null,"FYPO:0004683":null,"FYPO_EXT:0000001":null,"GO:0005730":null},"title":"Regulation of nuclear envelope dynamics via APC/C is necessary for the progression of semi-open mitosis in Schizosaccharomyces japonicus.","uniquename":"PMID:23786411"}


id: PMID:25361970
data:
  {"abstract":"PomBase (http://www.pombase.org) is the model organism database for the fission yeast Schizosaccharomyces pombe. PomBase provides a central hub for the fission yeast community, supporting both exploratory and hypothesis-driven research. It provides users easy access to data ranging from the sequence level, to molecular and phenotypic annotations, through to the display of genome-wide high-throughput studies. Recent improvements to the site extend annotation specificity, improve usability and allow for monthly data updates. Both in-house curators and community researchers provide manually curated data to PomBase. The genome browser provides access to published high-throughput data sets and the genomes of three additional Schizosaccharomyces species (Schizosaccharomyces cryophilus, Schizosaccharomyces japonicus and Schizosaccharomyces octosporus). ","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"McDowall MD, Harris MA, Lock A, Rutherford K, Staines DM, Bähler J, Kersey PJ, Oliver SG, Wood V","authors_abbrev":"McDowall MD et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Database","citation":"Nucleic Acids Res 2015 Jan;43(Database issue):D656-61","cv_annotations":{},"doi":"10.1093/nar/gku1040","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2015","pubmed_entrez_date":"2014-11-02","pubmed_publication_date":"Jan 2015","terms_by_termid":{},"title":"PomBase 2015: updates to the fission yeast database.","uniquename":"PMID:25361970"}


id: PMID:35380656
data:
  {"abstract":"The fission yeast Schizosaccharomyces japonicus has recently emerged as a powerful system for studying the evolution of essential cellular processes, drawing on similarities as well as key differences between S. japonicus and the related, well-established model Schizosaccharomyces pombe. We have deployed the open-source, modular code and tools originally developed for PomBase, the S. pombe model organism database (MOD), to create JaponicusDB (www.japonicusdb.org), a new MOD dedicated to S. japonicus. By providing a central resource with ready access to a growing body of experimental data, ontology-based curation, seamless browsing and querying, and the ability to integrate new data with existing knowledge, JaponicusDB supports fission yeast biologists to a far greater extent than any other source of S. japonicus data. JaponicusDB thus enables S. japonicus researchers to realize the full potential of studying a newly emerging model species and illustrates the widely applicable power and utility of harnessing reusable PomBase code to build a comprehensive, community-maintainable repository of species-relevant knowledge.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Rutherford KM, Harris MA, Oliferenko S, Wood V","authors_abbrev":"Rutherford KM et al.","canto_added_date":"2023-05-04 00:40:03","canto_curator_role":"JaponicusDB","canto_triage_status":"Database","citation":"Genetics 2022 Apr 04;220(4)","cv_annotations":{},"doi":"10.1093/genetics/iyab223","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2022","pubmed_entrez_date":"2022-04-05","pubmed_publication_date":"04 Apr 2022","terms_by_termid":{},"title":"JaponicusDB: rapid deployment of a model organism database for an emerging model species.","uniquename":"PMID:35380656"}


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


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


id: GO_REF:0000028
data:
  {"abstract":"This GO reference describes the criteria used in assigning the evidence codes of IDA (ECO:0000314), IEP (ECO:0000270), ISS (ECO:0000250), IGC (ECO_0000317), RCA (ECO:0000245) and IEA (ECO:0000501) to annotate gene products from PAMGO_MGG. Standard BLASTP from NCBI was used (http://www.ncbi.nih.gov/blast) to iteratively search reciprocal best hits and thus identify orthologs between predicted proteins of Magnaporthe grisea and GO proteins from multiple organisms with published association to GO terms. The alignments were manually reviewed for those hits with e-value equal to zero and with 80% or better coverage of both query and subject sequences, and for those hits with e<=10^-20, pid >=35 and sequence coverage >=80%. Furthermore, experimental or reviewed data from literature and other sources were incorporated into the GO annotation. IDA was assigned to an annotation if normal function of its gene was determined through transfections into a cell line and overexpression. IEP was assigned to an annotation if according to microarray experiments, its gene was upregulated in a biological process and the fold change was equal to or bigger than 10, or if according to Massively Parallel Signature Sequencing (MPSS), its gene was upregulated only in a certain biological process and the fold change was equal to or bigger than 10. ISS was assigned to an annotation if the entry at the With_column was experimentally characterized and the pairwise alignments were manually reviewed. IGC was assigned to an annotation if it based on comparison and analysis of gene location and structure, clustering of genes, and phylogenetic reconstruction of these genes. RCA was assigned to an annotation if it based on integrated computational analysis of whole genome microarray data, and matches to InterPro, pfam, and COG etc. IEA was assigned to an annotation if its function assignment based on computational work, and no manual review was done.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"PAMGO_MGG 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":"Criteria for IDA, IEP, ISS, IGC, RCA, and IEA assignment in PAMGO_MGG","uniquename":"GO_REF:0000028"}


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


id: PMID:26774782
data:
  {"abstract":"Eukaryotes remodel the nucleus during mitosis using a variety of mechanisms that differ in the timing and the extent of nuclear envelope (NE) breakdown. Here, we probe the principles enabling this functional diversity by exploiting the natural divergence in NE management strategies between the related fission yeasts Schizosaccharomyces pombe and Schizosaccharomyces japonicus [1-3]. We show that inactivation of Ned1, the phosphatidic acid phosphatase of the lipin family, by CDK phosphorylation is both necessary and sufficient to promote NE expansion required for \"closed\" mitosis in S. pombe. In contrast, Ned1 is not regulated during division in S. japonicus, thus limiting membrane availability and necessitating NE breakage. Interspecies gene swaps result in phenotypically normal divisions with the S. japonicus lipin acquiring an S. pombe-like mitotic phosphorylation pattern. Our results provide experimental evidence for the mitotic regulation of phosphatidic acid flux and suggest that the regulatory networks governing lipin activity diverged in evolution to give rise to strikingly dissimilar mitotic programs. ","alleles_by_uniquename":{"SJAG_01906:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01906","name":"nem1delta","uniquename":"SJAG_01906:allele-1"},"SJAG_02763:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02763","name":"ned1delta","uniquename":"SJAG_02763:allele-1"},"SJAG_02763:allele-2":{"allele_type":"amino_acid_mutation","description":"D422E,D424E","gene_uniquename":"SJAG_02763","name":"ned1cat","synonyms":[{"name":"Catalytic mutant","reference":"PMID:26774782","type":"exact"}],"uniquename":"SJAG_02763:allele-2"},"SJAG_02763:allele-3":{"allele_type":"amino_acid_mutation","description":"S235A; S651","gene_uniquename":"SJAG_02763","name":"ned1S235A/S651","synonyms":[{"name":"refractory to phosphorylation","reference":"PMID:26774782","type":"exact"}],"uniquename":"SJAG_02763:allele-3"},"SJAG_02763:allele-4":{"allele_type":"amino_acid_mutation","description":"S235E; S651E","gene_uniquename":"SJAG_02763","name":"ned1S235E/S651E","synonyms":[{"name":"phosphomimetic","reference":"PMID:26774782","type":"exact"}],"uniquename":"SJAG_02763:allele-4"},"SJAG_02763:allele-5":{"allele_type":"amino_acid_mutation","description":"S499E; S538E; T620E; T638E; S651E","gene_uniquename":"SJAG_02763","name":"ned1-5E","uniquename":"SJAG_02763:allele-5"},"SJAG_02763:allele-6":{"allele_type":"amino_acid_mutation","description":"S499A; S538A; T620A; T638A; S651A","gene_uniquename":"SJAG_02763","name":"ned1-5A","synonyms":[{"name":"refractory to potential proline-directed kinase phosphorylation","reference":"PMID:26774782","type":"exact"}],"uniquename":"SJAG_02763:allele-6"},"SJAG_03940:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03940","name":"nem2delta","uniquename":"SJAG_03940:allele-1"}},"annotation_curators":[{"annotation_count":21,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"},{"annotation_count":3,"community_curator":false,"file_name":null,"file_type":null,"name":"Val Wood","orcid":"0000-0001-6330-7526"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-07-07","authors":"Makarova M, Gu Y, Chen JS, Beckley JR, Gould KL, Oliferenko S","authors_abbrev":"Makarova M et al.","canto_added_date":"2021-05-10 02:37:43","canto_annotation_status":"APPROVED","canto_approved_date":"2021-09-01 07:39:35","canto_approver_orcid":"0000-0001-6330-7526","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-07-07 15:21:04","canto_session_key":"aa811803aa1555a2","canto_session_submitted_date":"2021-07-09 07:42:46","canto_triage_status":"Curatable","citation":"Curr Biol 2016 Jan 25;26(2):237-243","cv_annotations":{"PSI-MOD":[{"annotations":[115255,115256],"is_not":false,"summary":null,"term":"MOD:00046"}],"biological_process":[{"annotations":[115267],"is_not":false,"summary":null,"term":"GO:0090158"},{"annotations":[115269],"is_not":false,"summary":null,"term":"GO:0019915"},{"annotations":[115268],"is_not":false,"summary":null,"term":"GO:0071763"}],"cellular_component":[{"annotations":[115252],"is_not":false,"summary":null,"term":"GO:0005654"}],"single_locus_phenotype":[{"annotations":[115261,115264],"is_not":false,"summary":null,"term":"FYPO:0006054"},{"annotations":[115266],"is_not":false,"summary":null,"term":"FYPO:0005957"},{"annotations":[115248,115249,115251,115260,115263],"is_not":false,"summary":null,"term":"FYPO:0001784"},{"annotations":[115246,115247,115250,115254,115259,115262],"is_not":false,"summary":null,"term":"FYPO:0001556"},{"annotations":[115258,115265],"is_not":false,"summary":null,"term":"FYPO:0006945"},{"annotations":[115257],"is_not":false,"summary":null,"term":"FYPO:0003751"},{"annotations":[115253],"is_not":false,"summary":null,"term":"FYPO:0001234"}]},"doi":"10.1016/j.cub.2015.11.061","gene_count":4,"genes_by_uniquename":{"SJAG_00088":null,"SJAG_01906":null,"SJAG_02763":null,"SJAG_03940":null},"genotypes_by_uniquename":{"ned1-5A-S499A__S538A__T620A__T638A__S651A-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"ned1-5A(S499A; S538A; T620A; T638A; S651A aa)","display_uniquename":"ned1-5A-S499A__S538A__T620A__T638A__S651A-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02763:allele-6","expression":"Not assayed or wild type"}]}]},"ned1-5E-S499E__S538E__T620E__T638E__S651E-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"ned1-5E(S499E; S538E; T620E; T638E; S651E aa)","display_uniquename":"ned1-5E-S499E__S538E__T620E__T638E__S651E-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02763:allele-5","expression":"Not assayed or wild type"}]}]},"ned1S235A_S651-S235A__S651-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"ned1S235A/S651(S235A; S651 aa)","display_uniquename":"ned1S235A_S651-S235A__S651-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02763:allele-3","expression":"Not assayed or wild type"}]}]},"ned1S235E_S651E-S235E__S651E-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"ned1S235E/S651E(S235E; S651E aa)","display_uniquename":"ned1S235E_S651E-S235E__S651E-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02763:allele-4","expression":"Not assayed or wild type"}]}]},"ned1cat-D422E,D424E-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"ned1cat(D422E,D424E aa)","display_uniquename":"ned1cat-D422E,D424E-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02763:allele-2","expression":"Not assayed or wild type"}]}]},"ned1delta":{"display_name":"ned1delta","display_uniquename":"ned1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02763:allele-1","expression":"Null"}]}]},"nem1delta":{"display_name":"nem1delta","display_uniquename":"nem1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01906:allele-1","expression":"Null"}]}]},"nem2delta":{"display_name":"nem2delta","display_uniquename":"nem2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03940:allele-1","expression":"Null"}]}]}},"ltp_gene_count":4,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2016","pubmed_entrez_date":"2016-01-18","pubmed_publication_date":"25 Jan 2016","terms_by_termid":{"FYECO:0000005":null,"FYECO:0000162":null,"FYPO:0001234":null,"FYPO:0001556":null,"FYPO:0001784":null,"FYPO:0003751":null,"FYPO:0005957":null,"FYPO:0006054":null,"FYPO:0006945":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null,"GO:0005654":null,"GO:0019915":null,"GO:0071763":null,"GO:0090158":null,"MOD:00046":null},"title":"Temporal Regulation of Lipin Activity Diverged to Account for Differences in Mitotic Programs.","uniquename":"PMID:26774782"}


id: PMID:26104357
data:
  {"abstract":"Cells of the highly diverged Schizosaccharomyces (S.) pombe and S. japonicus fission yeasts exist in one of two sex/mating types, called P (for plus) or M (for minus), specified by which allele, M or P, resides at mat1. The fission yeasts have evolved an elegant mechanism for switching P or M information at mat1 by a programmed DNA recombination event with a copy of one of the two silent mating-type genes residing nearby in the genome. The switching process is highly cell-cycle and generation dependent such that only one of four grandchildren of a cell switches mating type. Extensive studies of fission yeast established the natural DNA strand chirality at the mat1 locus as the primary basis of asymmetric cell division. The asymmetry results from a unique site- and strand-specific epigenetic \"imprint\" at mat1 installed in one of the two chromatids during DNA replication. The imprint is inherited by one daughter cell, maintained for one cell cycle, and is then used for initiating recombination during mat1 replication in the following cell cycle. This mechanism of cell-type switching is considered to be unique to these two organisms, but determining the operation of such a mechanism in other organisms has not been possible for technical reasons. This review summarizes recent exciting developments in the understanding of mating-type switching in fission yeasts and extends these observations to suggest how such a DNA strand-based epigenetic mechanism of cellular differentiation could also operate in diploid organisms. ","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Klar AJS, Ishikawa K, Moore S","authors_abbrev":"Klar AJS et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Review or comment","citation":"Microbiol Spectr 2014 Oct;2(5)","cv_annotations":{},"doi":"10.1128/microbiolspec.MDNA3-0003-2014","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2014","pubmed_entrez_date":"2015-06-25","pubmed_publication_date":"Oct 2014","terms_by_termid":{},"title":"A Unique DNA Recombination Mechanism of the Mating/Cell-type Switching of Fission Yeasts: a Review.","uniquename":"PMID:26104357"}


id: PMID: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:21733045
data:
  {"abstract":"During open mitosis in higher eukaryotic cells, the nuclear envelope completely breaks down and then mitotic chromosomes are exposed in the cytoplasm. By contrast, mitosis in lower eukaryotes, including fungi, proceeds with the nucleus enclosed in an intact nuclear envelope. The mechanism of mitosis has been studied extensively in yeast, a closed mitosis organism. Here, we describe a form of mitosis in which the nuclear envelope is torn by elongation of the nucleus in the fission yeast Schizosaccharomyces japonicus. The mitotic nucleus of Sz. japonicus adopted a fusiform shape in anaphase, and its following extension caused separation. Finally, a tear in the nuclear envelope occurred in late anaphase. At the same time, a polarized-biased localization of nuclear pores was seen in the fusiform-shaped nuclear envelope, suggesting a compromise in the mechanical integrity of the lipid membrane. It has been known that nuclear membrane remains intact in some metazoan mitosis. We found that a similar tear of the nuclear envelope was also observed in late mitosis of the Caenorhabditis elegans embryo. These findings provide insight into the diversity of mitosis and the biological significance of breakdown of the nuclear envelope.","alleles_by_uniquename":{},"annotation_curators":[{"annotation_count":2,"community_curator":true,"file_name":null,"file_type":null,"name":"Sho Okamoto","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2022-11-21","authors":"Aoki K, Hayashi H, Furuya K, Sato M, Takagi T, Osumi M, Kimura A, Niki H","authors_abbrev":"Aoki K et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2022-11-21 17:28:56","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Sho Okamoto","canto_curator_role":"community","canto_first_approved_date":"2022-11-21 17:28:56","canto_session_key":"6063f08db89b54c7","canto_session_submitted_date":"2022-11-21 17:28:46","canto_triage_status":"Curatable","citation":"Genes Cells 2011 Sep;16(9):911-26","cv_annotations":{"cellular_component":[{"annotations":[115108],"is_not":false,"summary":null,"term":"GO:0070762"},{"annotations":[115109],"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: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: PMID:26457121
data:
  {"abstract":"Transposable elements (TEs) are common constituents of centromeres. However, it is not known what causes this relationship. Schizosaccharomyces japonicus contains 10 families of Long Terminal Repeat (LTR)-retrotransposons and these elements cluster in centromeres and telomeres. In the related yeast, Schizosaccharomyces pombe LTR-retrotransposons Tf1 and Tf2 are distributed in the promoter regions of RNA pol II transcribed genes. Sequence analysis of TEs indicates that Tj1 of S. japonicus is related to Tf1 and Tf2, and uses the same mechanism of self-primed reverse transcription. Thus, we wondered why these related retrotransposons localized in different regions of the genome.\nTo characterize the integration behavior of Tj1 we expressed it in S. pombe. We found Tj1 was active and capable of generating de novo integration in the chromosomes of S. pombe. The expression of Tj1 is similar to Type C retroviruses in that a stop codon at the end of Gag must be present for efficient integration. 17 inserts were sequenced, 13 occurred within 12 bp upstream of tRNA genes and 3 occurred at other RNA pol III transcribed genes. The link between Tj1 integration and RNA pol III transcription is reminiscent of Ty3, an LTR-retrotransposon of Saccharomyces cerevisiae that interacts with TFIIIB and integrates upstream of tRNA genes.\nThe integration of Tj1 upstream of tRNA genes and the centromeric clustering of tRNA genes in S. japonicus demonstrate that the clustering of this TE in centromere sequences is due to a unique pattern of integration.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Guo Y, Singh PK, Levin HL","authors_abbrev":"Guo Y et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Sequence feature or region","citation":"Mob DNA 2015;6:19","cv_annotations":{},"doi":"10.1186/s13100-015-0048-2","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2015","pubmed_entrez_date":"2015-10-13","pubmed_publication_date":"2015","terms_by_termid":{},"title":"A long terminal repeat retrotransposon of Schizosaccharomyces japonicus integrates upstream of RNA pol III transcribed genes.","uniquename":"PMID:26457121"}


id: GO_REF:0000024
data:
  {"abstract":"Method for transferring manual annotations to an entry based on a curator's judgment of its similarity to a putative ortholog that has annotations that are supported with experimental evidence. Annotations are created when a curator judges that the sequence of a protein shows high similarity to another protein that has annotation(s) supported by experimental evidence (and therefore display one of the evidence codes EXP, IDA, IGI, IMP, IPI or IEP). Annotations resulting from the transfer of GO terms display the 'ISS' evidence code and include an accession for the protein from which the annotation was projected in the 'with' field (column 8). This field can contain either a UniProtKB accession or an IPI (International Protein Index) identifier. Only annotations with an experimental evidence code and which do not have the 'NOT' qualifier are transferred. Putative orthologs are chosen using information combined from a variety of complementary sources. Potential orthologs are initially identified using sequence similarity search programs such as BLAST. Orthology relationships are then verified manually using a combination of resources including sequence analysis tools, phylogenetic and comparative genomics databases such as Ensembl Compara, INPARANOID and OrthoMCL, as well as other specialised databases such as species-specific collections (e.g. HGNC's HCOP). In all cases curators check each alignment and use their experience to assess whether similarity is considered to be strong enough to infer that the two proteins have a common function so that they can confidently project an annotation. While there is no fixed cut-off point in percentage sequence similarity, generally proteins which have greater than 30% identity that covers greater than 80% of the length of both proteins are examined further. For mammalian proteins this cut-off tends to be higher, with an average of 80% identity over 90% of the length of both proteins. Strict orthologs are desirable but not essential. In general, when there is evidence of multiple paralogs for a single species, annotations using less specific GO terms are transferred to the paralogs, however, annotations using more specific GO terms may be transferred to the most similar paralog in each species, this decision is taken on a case by case basis and may be influenced by statements by researchers in the field. Further detailed information on this procedure, including how ISS annotations are made to protein isoforms, can be found at: http://www.ebi.ac.uk/GOA/ISS_method.html.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"AgBase, BHF-UCL, Parkinson's UK-UCL, dictyBase, HGNC, Roslin Institute, FlyBase and UniProtKB curators.","canto_curator_role":"JaponicusDB","cv_annotations":{"biological_process":[{"annotations":[79279],"is_not":false,"summary":null,"term":"GO:0000122"}],"cellular_component":[{"annotations":[79276],"is_not":false,"summary":null,"term":"GO:0005869"}],"molecular_function":[{"annotations":[79277],"is_not":false,"summary":null,"term":"GO:0001227"},{"annotations":[79278],"is_not":false,"summary":null,"term":"GO:0000978"}]},"gene_count":2,"genes_by_uniquename":{"SJAG_00124":null,"SJAG_01739":null},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{"GO:0000122":null,"GO:0000978":null,"GO:0001227":null,"GO:0005869":null},"title":"Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity.","uniquename":"GO_REF:0000024"}


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


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


id: PMID:32915139
data:
  {"abstract":"Cytokinesis, which enables the physical separation of daughter cells once mitosis has been completed, is executed in fungal and animal cells by a contractile actin- and myosin-based ring (CAR). In the fission yeast  Schizosaccharomyces pombe,  the formin For3 nucleates actin cables and also co-operates for CAR assembly during cytokinesis. Mitogen-activated protein kinases (MAPKs) regulate essential adaptive responses in eukaryotic organisms to environmental changes. We show that the stress-activated protein kinase pathway (SAPK) and its effector, MAPK Sty1, downregulates CAR assembly in  S. pombe  when its integrity becomes compromised during cytoskeletal damage and stress by reducing For3 levels. Accurate control of For3 levels by the SAPK pathway may thus represent a novel regulatory mechanism of cytokinesis outcome in response to environmental cues. Conversely, SAPK signaling favors CAR assembly and integrity in its close relative  Schizosaccharomyces japonicus,  revealing a remarkable evolutionary divergence of this response within the fission yeast clade.","alleles_by_uniquename":{"SJAG_00266:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00266","name":"atf1delta","uniquename":"SJAG_00266:allele-1"},"SJAG_02592:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02592","name":"sty1delta","uniquename":"SJAG_02592:allele-1"}},"annotation_curators":[{"annotation_count":5,"community_curator":true,"file_name":null,"file_type":null,"name":"Elisa Gómez Gil","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-05-13","authors":"Gómez-Gil E, Martín-García R, Vicente-Soler J, Franco A, Vázquez-Marín B, Prieto-Ruiz F, Soto T, Pérez P, Madrid M, Cansado J","authors_abbrev":"Gómez-Gil E et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2023-06-24 05:18:12","canto_approver_orcid":"0000-0001-6330-7526","canto_curator_name":"Elisa Gómez Gil","canto_curator_role":"community","canto_first_approved_date":"2021-05-13 16:19:42","canto_session_key":"382ba25ae62a1134","canto_session_submitted_date":"2021-05-13 14:28:51","canto_triage_status":"Curatable","citation":"Elife 2020 09 11;9","cv_annotations":{"PSI-MOD":[{"annotations":[115589],"is_not":false,"summary":null,"term":"MOD:00696"}],"biological_process":[{"annotations":[115590],"is_not":false,"summary":null,"term":"GO:1903499"}],"single_locus_phenotype":[{"annotations":[115588],"is_not":false,"summary":null,"term":"FYPO:0002998"},{"annotations":[115586,115587],"is_not":false,"summary":null,"term":"FYPO:0000107"}]},"doi":"10.7554/eLife.57951","gene_count":2,"genes_by_uniquename":{"SJAG_00266":null,"SJAG_02592":null},"genotypes_by_uniquename":{"atf1delta":{"display_name":"atf1delta","display_uniquename":"atf1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00266:allele-1","expression":"Null"}]}]},"sty1delta":{"display_name":"sty1delta","display_uniquename":"sty1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02592:allele-1","expression":"Null"}]}]}},"ltp_gene_count":2,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2020","pubmed_entrez_date":"2020-09-11","pubmed_publication_date":"11 09 2020","terms_by_termid":{"FYECO:0000137":null,"FYECO:0000248":null,"FYPO:0000107":null,"FYPO:0002998":null,"FYPO_EXT:0000001":null,"GO:0120306":null,"GO:1903499":null,"MOD:00696":null},"title":"Stress-activated MAPK signaling controls fission yeast actomyosin ring integrity by modulating formin For3 levels.","uniquename":"PMID:32915139"}


id: GO_REF: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: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:0000027
data:
  {"abstract":"This GO reference describes the criteria used in assigning the evidence code of ISS via BLAST searches to annotate gene products from PAMGO_GAT. Standard BLASTP from NCBI was used (http://www.ncbi.nih.gov/blast) to query the non-redundant (NR) database. Hits are considered to be significant if the E-value is at or less than 10^-4. All other parameters are default according to http://www.ncbi.nih.gov/blast.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"PAMGO_GAT 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":"BLAST search criteria for ISS assignment in PAMGO_GAT","uniquename":"GO_REF:0000027"}


id: PMID:26896847
data:
  {"abstract":"Evolution provides the unifying framework with which to understand biology. The coherent investigation of genic and genomic data often requires comparative genomics analyses based on whole-genome alignments, sets of homologous genes and other relevant datasets in order to evaluate and answer evolutionary-related questions. However, the complexity and computational requirements of producing such data are substantial: this has led to only a small number of reference resources that are used for most comparative analyses. The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained elements are obtained. Gene alignments are used to define Ensembl Protein Families, GeneTrees and homologies for both protein-coding and non-coding RNA genes. These resources are updated frequently and have a consistent informatics infrastructure and data presentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views. The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here is relevant to these projects. The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. We use robust software and pipelines to produce reference comparative data and make it freely available. 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id: GO_REF:0000073
data:
  {"abstract":"We have created a standard template for classes describing the import of a chemical entity (ChEBI) as a biological process. The underlying equivalence axiom template is \"GO:0006810 and 'imports' 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 import of a chemical as biological process in the Gene Ontology","uniquename":"GO_REF:0000073"}


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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Gene Ontology annotations created by transferring manual GO annotations between related proteins based on shared sequence features.","uniquename":"GO_REF:0000104"}


id: PMID:33495454
data:
  {"abstract":"The endoplasmic reticulum (ER) network consists of tubules with high membrane curvature in cross-section, generated by the reticulons and REEPs. These proteins have two pairs of trans-membrane (TM) segments, followed by an amphipathic helix (APH), but how they induce curvature is poorly understood. Here, we show that REEPs form homodimers by interaction within the membrane. When overexpressed or reconstituted at high concentrations with phospholipids, REEPs cause extreme curvature through their TMs, generating lipoprotein particles instead of vesicles. The APH facilitates curvature generation, as its mutation prevents ER network formation of reconstituted proteoliposomes, and synthetic L- or D-amino acid peptides abolish ER network formation in Xenopus egg extracts. In Schizosaccharomyces japonicus, the APH is required for reticulon's exclusive ER-tubule localization and restricted mobility. Thus, the TMs and APH cooperate to generate high membrane curvature. We propose that the formation of splayed REEP/reticulon dimers is responsible for ER tubule formation.","alleles_by_uniquename":{"SJAG_01374:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01374","name":"nup132delta","uniquename":"SJAG_01374:allele-1"}},"annotation_curators":[{"annotation_count":8,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-07-09","authors":"Wang N, Clark LD, Gao Y, Kozlov MM, Shemesh T, Rapoport TA","authors_abbrev":"Wang N et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-07-09 16:24:24","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-07-09 16:24:24","canto_session_key":"23c6ae79d435aba5","canto_session_submitted_date":"2021-07-09 16:24:16","canto_triage_status":"Curatable","citation":"Nat Commun 2021 01 25;12(1):568","cv_annotations":{"biological_process":[{"annotations":[115472,115478],"is_not":false,"summary":null,"term":"GO:0097753"}],"cellular_component":[{"annotations":[115473,115474],"is_not":false,"summary":null,"term":"GO:0032541"},{"annotations":[115475,115476],"is_not":false,"summary":null,"term":"GO:0005643"}],"single_locus_phenotype":[{"annotations":[115477],"is_not":false,"summary":null,"term":"FYPO:0003973"}]},"doi":"10.1038/s41467-020-20625-y","gene_count":4,"genes_by_uniquename":{"SJAG_01374":null,"SJAG_01834":null,"SJAG_01848":null,"SJAG_03795":null},"genotypes_by_uniquename":{"nup132delta":{"display_name":"nup132delta","display_uniquename":"nup132delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01374:allele-1","expression":"Null"}]}]}},"ltp_gene_count":4,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[{"evidence":"Reconstituted Complex","gene_uniquename":"SJAG_03795","interactor_uniquename":"SJAG_03795","reference_uniquename":"PMID:33495454","throughput":"low"}],"publication_year":"2021","pubmed_entrez_date":"2021-01-26","pubmed_publication_date":"25 01 2021","terms_by_termid":{"FYPO:0003973":null,"GO:0005643":null,"GO:0032541":null,"GO:0097753":null},"title":"Mechanism of membrane-curvature generation by ER-tubule shaping proteins.","uniquename":"PMID:33495454"}


id: PMID: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_approver_orcid":"0000-0001-6330-7526","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":[115350],"is_not":false,"summary":null,"term":"GO:0101024"}],"cellular_component":[{"annotations":[115335],"is_not":false,"summary":null,"term":"GO:0000781"},{"annotations":[115334],"is_not":false,"summary":null,"term":"GO:0140573"},{"annotations":[115337],"is_not":false,"summary":null,"term":"GO:0005643"},{"annotations":[115336],"is_not":false,"summary":null,"term":"GO:0030875"}],"molecular_function":[{"annotations":[115351],"is_not":false,"summary":null,"term":"GO:0062239"}],"single_locus_phenotype":[{"annotations":[115338,115343,115345],"is_not":false,"summary":null,"term":"FYPO:0003779"},{"annotations":[115347,115348,115349],"is_not":false,"summary":null,"term":"FYPO:0000671"},{"annotations":[115340,115341,115342,115344],"is_not":false,"summary":null,"term":"FYPO:0004890"},{"annotations":[115339],"is_not":false,"summary":null,"term":"FYPO:0001234"},{"annotations":[115346],"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:0000096
data:
  {"abstract":"Mouse Genome Database (MGD), The HUGO Gene Nomenclature Committee (HGNC), and Rat Genome Database (RGD) have extensive procedures in place, overseen by expert curation, to establish orthology relationships between their genes. The Experimentally based annotations annotated by each group (IDA, IMP IPI, IGI, and EXP) are used to provide annotations  to the respective mouse and rat orthologs, and given the ISO evidence code and an entry in the inferred_from field to indicate the orthologous entity. ","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Mouse Genome Informatics scientific curators","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Automated transfer of experimentally-verified manual GO annotation data to close orthologs.","uniquename":"GO_REF:0000096"}


id: PMID:35226668
data:
  {"abstract":"RNA interference (RNAi) is a conserved mechanism of small RNA-mediated genome regulation commonly involved in suppression of transposable elements (TEs) through both post-transcriptional silencing, and transcriptional repression via heterochromatin assembly. The fission yeast Schizosaccharomyces pombe has been extensively utilised as a model for studying RNAi pathways. However, this species is somewhat atypical in that TEs are not major targets of RNAi, and instead small RNAs correspond primarily to non-coding pericentromeric repeat sequences, reflecting a specialised role for the pathway in promoting heterochromatin assembly in these regions. In contrast, in the related fission yeast Schizosaccharomyces japonicus, sequenced small RNAs correspond primarily to TEs. This suggests there may be fundamental differences in the operation of RNAi pathways in these two related species. To investigate these differences, we probed RNAi function in S. japonicus. Unexpectedly, and in contrast to S. pombe, we found that RNAi is essential in this species. Moreover, viability of RNAi mutants can be rescued by mutations implicated in enhancing RNAi-independent heterochromatin propagation. These rescued strains retain heterochromatic marks on TE sequences, but exhibit derepression of TEs at the post-transcriptional level. Our findings indicate that S. japonicus retains the ancestral role of RNAi in facilitating suppression of TEs via both post-transcriptional silencing and heterochromatin assembly, with specifically the heterochromatin pathway being essential for viability, likely due to a function in genome maintenance. The specialised role of RNAi in heterochromatin assembly in S. pombe appears to be a derived state that emerged after the divergence of S. japonicus.","alleles_by_uniquename":{"SJAG_02409:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02409","name":"stc1delta","uniquename":"SJAG_02409:allele-1"},"SJAG_02594:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02594","name":"arb1delta","uniquename":"SJAG_02594:allele-1"},"SJAG_02621:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02621","name":"ago1delta","uniquename":"SJAG_02621:allele-1"},"SJAG_02668:allele-1":{"allele_type":"amino_acid_mutation","description":"R77W","gene_uniquename":"SJAG_02668","name":"mpe1-R77W","uniquename":"SJAG_02668:allele-1"},"SJAG_03118:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03118","name":"leo1delta","uniquename":"SJAG_03118:allele-1"},"SJAG_03118:allele-2":{"allele_type":"nonsense_mutation","description":"aa61->stop","gene_uniquename":"SJAG_03118","name":"frameshift","uniquename":"SJAG_03118:allele-2"},"SJAG_03356:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03356","name":"rdp1delta","uniquename":"SJAG_03356:allele-1"},"SJAG_03689:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03689","name":"dcr1delta","uniquename":"SJAG_03689:allele-1"},"SJAG_03916:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03916","name":"chp1delta","uniquename":"SJAG_03916:allele-1"},"SJAG_04061:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04061","name":"arb2delta","uniquename":"SJAG_04061:allele-1"},"SJAG_04574:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04574","name":"clr4delta","uniquename":"SJAG_04574:allele-1"}},"annotation_curators":[{"annotation_count":31,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2022-03-07","authors":"Chapman E, Taglini F, Bayne EH","authors_abbrev":"Chapman E et al.","canto_added_date":"2022-03-07 09:13:19","canto_annotation_status":"APPROVED","canto_approved_date":"2022-03-07 12:35:06","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2022-03-07 12:35:06","canto_session_key":"3d6467bf1cb92446","canto_session_submitted_date":"2022-03-07 12:34:56","canto_triage_status":"Curatable","citation":"PLoS Genet 2022 Feb 28;18(2):e1010100","cv_annotations":{"biological_process":[{"annotations":[115470,115471],"is_not":false,"summary":null,"term":"GO:0031507"},{"annotations":[115468,115469],"is_not":false,"summary":null,"term":"GO:0016441"}],"multi_locus_phenotype":[{"annotations":[115464,115466],"is_not":false,"summary":null,"term":"FYPO:0004982"},{"annotations":[115465,115467],"is_not":false,"summary":null,"term":"FYPO:0004573"},{"annotations":[115461],"is_not":false,"summary":null,"term":"FYPO:0002061"},{"annotations":[115462,115463],"is_not":false,"summary":null,"term":"FYPO:0006989"},{"annotations":[115456,115457,115458,115459],"is_not":false,"summary":null,"term":"FYPO:0002058"}],"single_locus_phenotype":[{"annotations":[115450],"is_not":false,"summary":null,"term":"FYPO:0004205"},{"annotations":[115452],"is_not":false,"summary":null,"term":"FYPO:0004982"},{"annotations":[115454],"is_not":false,"summary":null,"term":"FYPO:0000595"},{"annotations":[115451],"is_not":false,"summary":null,"term":"FYPO:0004574"},{"annotations":[115443,115444,115445,115446,115447,115448,115449,115460],"is_not":false,"summary":null,"term":"FYPO:0002061"},{"annotations":[115455],"is_not":false,"summary":null,"term":"FYPO:0006989"},{"annotations":[115453],"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: GO_REF:0000075
data:
  {"abstract":"We have created a standard template for classes describing the transport of a chemical entity (ChEBI) into a cellular component as a biological process. The underlying equivalence axiom template is \"GO:0006810 and 'has_target_end_location' some T and 'imports' some S\", where T is a cellular component and S 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 into a cellular component as biological process in the Gene Ontology","uniquename":"GO_REF:0000075"}


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


id: GO_REF:0000003
data:
  {"abstract":"Transitive assignment using Enzyme Commission identifiers. This method is used for any database entry, such as a protein record in UniProtKB or TrEMBL, that has had an Enzyme Commission number assigned. The corresponding GO term is determined using the EC cross-references in the GO molecular function ontology. Also see Hill et al., Genomics (2001) 74:121-128. The mapping file is available at http://www.geneontology.org/external2go/ec2go.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GOA curators, MGI curators","canto_curator_role":"JaponicusDB","cv_annotations":{"molecular_function":[{"annotations":[68439],"is_not":false,"summary":null,"term":"GO:0003925"},{"annotations":[58965],"is_not":false,"summary":null,"term":"GO:0043864"},{"annotations":[65145],"is_not":false,"summary":null,"term":"GO:0052832"},{"annotations":[65146],"is_not":false,"summary":null,"term":"GO:0052833"},{"annotations":[67985],"is_not":false,"summary":null,"term":"GO:1990817"},{"annotations":[60872],"is_not":false,"summary":null,"term":"GO:0102389"}]},"gene_count":5,"genes_by_uniquename":{"SJAG_02383":null,"SJAG_02721":null,"SJAG_03739":null,"SJAG_04509":null,"SJAG_04954":null},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{"GO:0003925":null,"GO:0043864":null,"GO:0052832":null,"GO:0052833":null,"GO:0102389":null,"GO:1990817":null},"title":"Gene Ontology annotation based on Enzyme Commission mapping","uniquename":"GO_REF:0000003"}


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


id: 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: 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":[65147],"is_not":false,"summary":null,"term":"GO:0006021"},{"annotations":[66612],"is_not":false,"summary":null,"term":"GO:0006782"},{"annotations":[57742],"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: GO_REF:0000066
data:
  {"abstract":"We have created a standard template for classes describing the transport of a chemical entity (ChEBI) as a molecular function. The underlying equivalence axiom template is \"GO:0005215 and 'transports or maintains localization of' some X\", where X is a chemical entity (CHEBI:24431). The approach to combine GO and ChEBI has been described in the following publication: PMID:23895341.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of transport of a chemical entity as molecular function in the Gene Ontology","uniquename":"GO_REF:0000066"}


id: GO_REF: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:34251689
data:
  {"abstract":"The polymerase chain reaction (PCR)-based gene targeting method, which can delete a specific gene or introduce tags, has been widely utilized to study gene function in fission yeast. One of the critical steps in this method is to design primers for amplifying DNA fragments of deletion or tagging modules and for checking the integration of those DNA fragments at designated loci. Although the primer design tool Pombe PCR Primer Program (PPPP) is available for Schizosaccharomyces pombe, there is no such publicly available application for the other three fission yeast species, S. cryophilus, S. japonicus, and S. octosporus. Likewise, no application enabling DNA/protein sequence retrieval for these three fission yeast species is available either. Therefore, access to such functionality would substantially assist in retrieval of gene sequences of interest and primer design in these fission yeast species. In this report, we describe two applications for fission yeast study: Yesprit and Yeaseq. Yesprit is a primer design tool for strain construction using the PCR-based method, and Yeaseq is a sequence viewer that can acquire the DNA/protein sequences of specific genes. Both tools can be run on the Windows, macOS, and Linux platforms. We believe that the Yesprit and Yeaseq will facilitate research using the four fission yeast species.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Wang X, Xu R, Wang Y, Liu Z, Lou R, Sugiyama T","authors_abbrev":"Wang X et al.","canto_added_date":"2023-05-04 00:40:04","canto_curator_role":"JaponicusDB","canto_triage_status":"Method or reagent","citation":"Yeast 2021 Nov;38(11):583-591","cv_annotations":{},"doi":"10.1002/yea.3660","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2021","pubmed_entrez_date":"2021-07-12","pubmed_publication_date":"Nov 2021","terms_by_termid":{},"title":"Yesprit and Yeaseq: Applications for designing primers and browsing sequences for research using the four Schizosaccharomyces species.","uniquename":"PMID:34251689"}


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


id: PMID: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:25308606
data:
  {"abstract":"The non-pathogenic dimorphic fission yeast, Schizosaccharomyces japonicus, could be a suitable model organism for investigation of the genetic background of mycelial growth, as it has a haploid chromosome set and its genome is sequenced. Since earlier results have suggested that its morphological transition required solid substrates, but molecular biological experiments would require hyphae production in a liquid medium, we wanted to find circumstances which would enable hyphae production in liquid media. Several external conditions were investigated, but the strongest inducer was fetal bovine serum (FBS). Its positive effect could be hampered by heat and was dependent on pH, temperature and concentration of the serum. Other protein-containing compounds, such as peptone and bovine serum albumin or amino acids, proved to be ineffective or weak. Generally, the uninduced and induced mycelial growth of Sz. japonicus could be improved by lower external pH and higher temperature.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Papp L, Sipiczki M, Holb IJ, Miklós I","authors_abbrev":"Papp L et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"Yeast 2014 Dec;31(12):475-82","cv_annotations":{},"doi":"10.1002/yea.3048","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":"2014-10-14","pubmed_publication_date":"Dec 2014","terms_by_termid":{},"title":"Optimal conditions for mycelial growth of Schizosaccharomyces japonicus cells in liquid medium: it enables the molecular investigation of dimorphism.","uniquename":"PMID:25308606"}


id: PMID:5315726
data:
  {"abstract":"","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Bulder CJ","authors_abbrev":"Bulder CJ","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"Antonie Van Leeuwenhoek 1971;37(3):353-8","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1971","pubmed_entrez_date":"1971-01-01","pubmed_publication_date":"1971","terms_by_termid":{},"title":"Anaerobic growth, ergosterol content and sensitivity to a polyene antibiotic, of the yeast Schizosaccharomyces japonicus.","uniquename":"PMID:5315726"}


id: PMID:35049972
data:
  {"abstract":"The survival of eukaryotic organisms during environmental changes is largely dependent on the adaptive responses elicited by signal transduction cascades, including those regulated by the Mitogen-Activated Protein Kinase (MAPK) pathways. The Cell Integrity Pathway (CIP), one of the three MAPK pathways found in the simple eukaryote fission of yeast  Schizosaccharomyces pombe , shows strong homology with mammalian Extracellular signal-Regulated Kinases (ERKs). Remarkably, studies over the last few decades have gradually positioned the CIP as a multi-faceted pathway that impacts multiple functional aspects of the fission yeast life cycle during unperturbed growth and in response to stress. They include the control of mRNA-stability through RNA binding proteins, regulation of calcium homeostasis, and modulation of cell wall integrity and cytokinesis. Moreover, distinct evidence has disclosed the existence of sophisticated interplay between the CIP and other environmentally regulated pathways, including Stress-Activated MAP Kinase signaling (SAPK) and the Target of Rapamycin (TOR). In this review we present a current overview of the organization and underlying regulatory mechanisms of the CIP in  S. pombe , describe its most prominent functions, and discuss possible targets of and roles for this pathway. The evolutionary conservation of CIP signaling in the dimorphic fission yeast  S. japonicus  will also be addressed.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Cansado J, Soto T, Franco A, Vicente-Soler J, Madrid M","authors_abbrev":"Cansado J et al.","canto_added_date":"2023-05-04 00:40:04","canto_curator_role":"JaponicusDB","canto_triage_status":"Review or comment","citation":"J Fungi (Basel) 2021 Dec 30;8(1)","cv_annotations":{},"doi":"10.3390/jof8010032","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":"2022-01-20","pubmed_publication_date":"30 Dec 2021","terms_by_termid":{},"title":"The Fission Yeast Cell Integrity Pathway: A Functional Hub for Cell Survival upon Stress and Beyond.","uniquename":"PMID:35049972"}


id: PMID:23337086
data:
  {"abstract":"During meiosis, chromosomes adopt a bouquet arrangement, which is widely conserved among eukaryotes. This arrangement is assumed to play an important role in the normal progression of meiosis, by mediating the proper pairing of homologous chromosomes. In Schizosaccharomyces pombe, the complex of Bqt1 and Bqt2 plays a key role in telomere clustering and the subsequent bouquet arrangement of chromosomes during early meiotic prophase. Bqt1 and Bqt2 are part of a multi-protein complex that mediates the attachment of the telomere to the nuclear membrane. However, the structural details of the complex are needed to clarify the mechanism of telomere clustering. To enable biophysical studies of Bqt1 and Bqt2, we established a purification procedure for the Schizosaccharomyces japonicus Bqt1-Bqt2 complex, which is closely related to the S. pombe Bqt1-Bqt2 complex. A co-expression vector, in which one of the expressed subunits is fused to a removable SUMO tag, yielded high amounts of the proteins in the soluble fraction. The solubility of the Bqt1-Bqt2 complex after the removal of the SUMO tag was maintained by including CHAPS, a nondenaturing, zwitterionic detergent, in the purification buffers. These procedures enabled us to rapidly purify the stable Bqt1-Bqt2 complex. The co-purified Bqt1 and Bqt2 proteins formed a stable heterodimer, consistent with results from in vivo studies showing the requirement of both proteins for the bouquet arrangement. The expression and purification procedures established here will facilitate further biophysical studies of the Bqt1-Bqt2 complex.","alleles_by_uniquename":{},"annotation_curators":[{"annotation_count":2,"community_curator":false,"file_name":null,"file_type":null,"name":"Val Wood","orcid":"0000-0001-6330-7526"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-05-12","authors":"Ichikawa Y, Kagawa W, Saito K, Chikashige Y, Haraguchi T, Hiraoka Y, Kurumizaka H","authors_abbrev":"Ichikawa Y et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-05-12 14:11:00","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Val Wood","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-05-12 14:11:00","canto_session_key":"34571f3accd180c4","canto_session_submitted_date":"2021-05-11 18:50:05","canto_triage_status":"Curatable","citation":"Protein Expr Purif 2013 Apr;88(2):207-13","cv_annotations":{"molecular_function":[{"annotations":[115270,115271],"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: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: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: PMID:31956022
data:
  {"abstract":"Membrane function is fundamental to life. Each species explores membrane lipid diversity within a genetically predefined range of possibilities. How membrane lipid composition in turn defines the functional space available for evolution of membrane-centered processes remains largely unknown. We address this fundamental question using related fission yeasts Schizosaccharomyces pombe and Schizosaccharomyces japonicus. We show that, unlike S. pombe that generates membranes where both glycerophospholipid acyl tails are predominantly 16-18 carbons long, S. japonicus synthesizes unusual \"asymmetrical\" glycerophospholipids where the tails differ in length by 6-8 carbons. This results in stiffer bilayers with distinct lipid packing properties. Retroengineered S. pombe synthesizing the S.-japonicus-type phospholipids exhibits unfolded protein response and downregulates secretion. Importantly, our protein sequence comparisons and domain swap experiments support the hypothesis that transmembrane helices co-evolve with membranes, suggesting that, on the evolutionary scale, changes in membrane lipid composition may necessitate extensive adaptation of the membrane-associated proteome.","alleles_by_uniquename":{"SJAG_01458:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01458","name":"acb1delta","uniquename":"SJAG_01458:allele-1"}},"annotation_curators":[{"annotation_count":4,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-07-09","authors":"Makarova M, Peter M, Balogh G, Glatz A, MacRae JI, Lopez Mora N, Booth P, Makeyev E, Vigh L, Oliferenko S","authors_abbrev":"Makarova M et al.","canto_added_date":"2021-05-10 02:37:19","canto_annotation_status":"APPROVED","canto_approved_date":"2021-07-09 13:38:09","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-07-09 13:38:09","canto_session_key":"801e82954edbb6c1","canto_session_submitted_date":"2021-07-09 13:38:00","canto_triage_status":"Curatable","citation":"Curr Biol 2020 02 03;30(3):367-380.e8","cv_annotations":{"cellular_component":[{"annotations":[115632],"is_not":false,"summary":null,"term":"GO:0005801"},{"annotations":[115634],"is_not":false,"summary":null,"term":"GO:0005829"}],"single_locus_phenotype":[{"annotations":[115633],"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: GO_REF:0000058
data:
  {"abstract":"We have created a standard template for the definition of classes for the regulation of a biological process. This includes the definitions for positive and negative regulation. The equivalence axiom templates are \"GO:0065007 and 'regulates' some X\" (regulation), \"GO:0065007 and 'negatively_regulates' some X\" (negative regulation), and \"GO:0065007 and 'positively_regulates' some X\" (positive regulation), where X is a biological process.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of regulation in the Gene Ontology (biological process) ","uniquename":"GO_REF:0000058"}


id: GO_REF: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:0000060
data:
  {"abstract":"We have created a standard template for classes describing processes involved in other processes. The underlying equivalence axiom template is \"P and 'part_of' some W\", where P and W are 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 processes involved in other process in the Gene Ontology","uniquename":"GO_REF:0000060"}


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


id: GO_REF:0000074
data:
  {"abstract":"We have created a standard template for classes describing the export of a chemical entity (ChEBI) as a biological process. The underlying equivalence axiom template is \"GO:0006810 and 'exports' 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 export of a chemical as biological process in the Gene Ontology","uniquename":"GO_REF:0000074"}


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_approver_orcid":"0000-0002-8138-6851","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":[115379],"is_not":false,"summary":null,"term":"GO:0101024"},{"annotations":[115384],"is_not":false,"summary":null,"term":"GO:0006998"}],"cellular_component":[{"annotations":[115383],"is_not":false,"summary":null,"term":"GO:0120321"}],"multi_locus_phenotype":[{"annotations":[115386],"is_not":false,"summary":null,"term":"FYPO:0000619"},{"annotations":[115385],"is_not":false,"summary":null,"term":"FYPO:0001489"}],"single_locus_phenotype":[{"annotations":[115387],"is_not":false,"summary":null,"term":"FYPO:0000619"},{"annotations":[115381],"is_not":false,"summary":null,"term":"FYPO:0003738"},{"annotations":[115388],"is_not":false,"summary":null,"term":"FYPO:0000815"},{"annotations":[115380],"is_not":false,"summary":null,"term":"FYPO:0000082"},{"annotations":[115382],"is_not":false,"summary":null,"term":"FYPO:0003976"},{"annotations":[115378],"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","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:29191091
data:
  {"abstract":"Coenzyme Q (CoQ) is essential for mitochondrial respiration and as a cofactor for sulfide quinone reductase. Schizosaccharomyces pombe produces a human-type CoQ 10 . Here, we analyzed CoQ in other fission yeast species. S. cryophilus and S. octosporus produce CoQ 9 . S. japonicus produces low levels of CoQ 10 , although all necessary genes for CoQ synthesis have been identified in its genome. We expressed three genes (dps1, dlp1, and ppt1) for CoQ synthesis from S. japonicus in the corresponding S. pombe mutants, and confirmed that they were functional. S. japonicus had very low levels of oxygen consumption and was essentially respiration defective, probably due to mitochondrial dysfunction. S. japonicus grows well on minimal medium during anaerobic culture, indicating that it acquires sufficient energy by fermentation. S. japonicus produces comparable levels of ethanol under both normal and elevated temperature (42 °C) conditions, at which S. pombe is not able to grow.","alleles_by_uniquename":{},"annotation_curators":[{"annotation_count":4,"community_curator":true,"file_name":null,"file_type":null,"name":"Makoto Kawamukai","orcid":null},{"annotation_count":3,"community_curator":false,"file_name":null,"file_type":null,"name":"Val Wood","orcid":"0000-0001-6330-7526"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-07-15","authors":"Kaino T, Tonoko K, Mochizuki S, Takashima Y, Kawamukai M","authors_abbrev":"Kaino T et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-09-01 07:29:31","canto_approver_orcid":"0000-0001-6330-7526","canto_curator_name":"Makoto Kawamukai","canto_curator_role":"community","canto_first_approved_date":"2021-07-15 11:51:14","canto_session_key":"53ebb2b64b3102f9","canto_session_submitted_date":"2021-07-15 08:22:11","canto_triage_status":"Curatable","citation":"Biosci Biotechnol Biochem 2018 Jun;82(6):1031-1042","cv_annotations":{"biological_process":[{"annotations":[115141,115142],"is_not":false,"summary":null,"term":"GO:0006744"},{"annotations":[115140],"is_not":false,"summary":null,"term":"GO:0006743"}],"molecular_function":[{"annotations":[115139],"is_not":false,"summary":null,"term":"GO:0002083"},{"annotations":[115137,115138],"is_not":false,"summary":null,"term":"GO:0097269"}]},"doi":"10.1080/09168451.2017.1401914","gene_count":3,"genes_by_uniquename":{"SJAG_01865":null,"SJAG_04568":null,"SJAG_06603":null},"genetic_interactions":[[{"gene_a_uniquename":"SJAG_01865","gene_b_uniquename":"SJAG_04568","interaction_type":"Synthetic Rescue"},[{"reference_uniquename":"PMID:29191091","throughput":"low"}]]],"genotypes_by_uniquename":{},"ltp_gene_count":3,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2018","pubmed_entrez_date":"2017-12-02","pubmed_publication_date":"Jun 2018","terms_by_termid":{"GO:0002083":null,"GO:0006743":null,"GO:0006744":null,"GO:0097269":null},"title":"Schizosaccharomyces japonicus has low levels of CoQ 10  synthesis, respiration deficiency, and efficient ethanol production.","uniquename":"PMID:29191091"}


id: PMID:9611807
data:
  {"abstract":"The fission yeast Schizosaccharomyces pombe shows bipolar growth and is a convenient model for studying cell polarity and polar growth. This paper shows that the related Schiz. japonicus var. japonicus can switch to unipolar growth and can exist in both yeast and mycelial phases. On solid media, the yeast phase is unstable and prone to switch to the mycelial form, which shows unipolar growth by tip elongation. The hyphae can colonize the body of the substrate (true mycelium) or just its surface (pseudo-mycelium). The yeast-to-mycelium transition and the growth of the mycelium are regulated by a nutritional gradient and are associated with extensive vacuolation. The mycelium can convert into arthroconidia or return to the yeast phase in response to environmental changes. These environmentally controlled morphological transitions make Schiz. japonicus var. japonicus an attractive model for the investigation of cell polarity and morphogenesis.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-10-07","authors":"Sipiczki M, Takeo K, Yamaguchi M, Yoshida S, Miklos I","authors_abbrev":"Sipiczki M et al.","canto_added_date":"2021-09-30 08:50:02","canto_annotation_status":"APPROVED","canto_approved_date":"2021-10-07 12:30:26","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-10-07 12:30:26","canto_session_key":"fced61f1377cd206","canto_session_submitted_date":"2021-09-30 08:52:46","canto_triage_status":"Curatable","citation":"Microbiology (Reading) 1998 May;144 ( Pt 5):1319-1330","cv_annotations":{},"doi":"10.1099/00221287-144-5-1319","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1998","pubmed_entrez_date":"1998-06-05","pubmed_publication_date":"May 1998","terms_by_termid":{},"title":"Environmentally controlled dimorphic cycle in a fission yeast.","uniquename":"PMID:9611807"}


