# refs

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


id: PMID:21905090
data:
  {"abstract":"The construction of diploid cells eases genetic analysis in haploid genetic systems because diploid cells allow for the characterization of essential genes. Here, we report the construction of diploid cells using ade6 point mutants that suppress each other via interallelic complementation in the fission yeast Schizosaccharomyces japonicus var japonicus (Sz. japonicus). We constructed an ade6-domK mutant in addition to the previously described ade6-domE. Phenotypes of both mutants exhibited adenine auxotrophy and red colonies. The mutations complemented the phenotypes in a mutually dependent manner. Diploid zygotes, in which the two mutations were introduced simultaneously into the same cells, were isolated by selecting for adenine independence. Such diploid cells are apparently larger in size than haploid cells, yet have a similar nuclear/cytoplasmic ratio, and thus the nuclear size control that has been reported in Sz. pombe is also present in Sz. japonicus.","alleles_by_uniquename":{"SJAG_01081:allele-1":{"allele_type":"nonsense_mutation","description":"S427>stop","gene_uniquename":"SJAG_01081","name":"ade6-domE","uniquename":"SJAG_01081:allele-1"},"SJAG_01081:allele-2":{"allele_type":"amino_acid_mutation","description":"Q262A","gene_uniquename":"SJAG_01081","name":"ade6-domK","uniquename":"SJAG_01081:allele-2"},"SJAG_01081:allele-3":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01081","name":"ade6delta","uniquename":"SJAG_01081:allele-3"}},"annotation_curators":[{"annotation_count":3,"community_curator":true,"file_name":null,"file_type":null,"name":"Sho Okamoto","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2022-11-23","authors":"Furuya K, Niki H","authors_abbrev":"Furuya K et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2022-11-23 13:21:47","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Sho Okamoto","canto_curator_role":"community","canto_first_approved_date":"2022-11-23 13:21:47","canto_session_key":"7c1c894d4ee8d8d3","canto_session_submitted_date":"2022-11-23 13:21:40","canto_triage_status":"Curatable","citation":"Yeast 2011 Oct;28(10):747-54","cv_annotations":{"single_locus_phenotype":[{"annotations":[115340,115341,115342],"is_not":false,"summary":null,"term":"FYPO:0000747"}]},"doi":"10.1002/yea.1898","gene_count":1,"genes_by_uniquename":{"SJAG_01081":null},"genotypes_by_uniquename":{"ade6-domE-S427>stop-nonsense_mutation-expression-not_assayed_or_wild_type":{"display_name":"ade6-domE(S427>stop)","display_uniquename":"ade6-domE-S427>stop-nonsense_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01081:allele-1","expression":"Not assayed or wild type"}]}]},"ade6-domK-Q262A-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"ade6-domK(Q262A aa)","display_uniquename":"ade6-domK-Q262A-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01081:allele-2","expression":"Not assayed or wild type"}]}]},"ade6delta":{"display_name":"ade6delta","display_uniquename":"ade6delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01081:allele-3","expression":"Null"}]}]}},"ltp_gene_count":1,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2011","pubmed_entrez_date":"2011-09-10","pubmed_publication_date":"Oct 2011","terms_by_termid":{"FYPO:0000747":null},"title":"Construction of diploid zygotes by interallelic complementation of ade6 in Schizosaccharomyces japonicus.","uniquename":"PMID:21905090"}


id: PMID:23090706
data:
  {"abstract":"DNA damage response includes DNA repair, nucleotide metabolism and even a control of cell fates including differentiation, cell death pathway or some combination of these. The responses to DNA damage differ from species to species. Here we aim to delineate the checkpoint pathway in the dimorphic fission yeast Schizosaccharomyces japonicus, where DNA damage can trigger a differentiation pathway that is a switch from a bidirectional yeast growth mode to an apical hyphal growth mode, and the switching is regulated via a checkpoint kinase, Chk1. This Chk1-dependent switch to hyphal growth is activated with even low doses of agents that damage DNA; therefore, we reasoned that this switch may depend on other genes orthologous to the components of the classical Sz. pombe Chk1-dependent DNA checkpoint pathway. As an initial test of this hypothesis, we assessed the effects of mutations in Sz. japonicus orthologs of Sz. pombe checkpoint genes on this switch from bidirectional to hyphal growth. The same set of DNA checkpoint genes was confirmed in Sz. japonicus. We tested the effect of each DNA checkpoint mutants on hyphal differentiation by DNA damage. We found that the Sz. japonicus hyphal differentiation pathway was dependent on Sz. japonicus orthologs of Sz. pombe checkpoint genes-(SP)rad3, (SP)rad26, (SP)rad9, (SP)rad1, (SP)rad24, (SP)rad25, (SP)crb2, and (SP)chk1-that function in the DNA damage checkpoint pathway, but was not dependent on orthologs of two Sz. pombe genes-(SP)cds1 or (SP)mrc1-that function in the DNA replication checkpoint pathway. These findings indicated that although the role of each component of the DNA damage checkpoint and DNA replication checkpoint is mostly same between the two fission yeasts, the DNA damage checkpoint was the only pathway that governed DNA damage-dependent hyphal growth. We also examined whether DNA damage checkpoint signaling engaged in functional crosstalk with other hyphal differentiation pathways because hyphal differentiation can also be triggered by nutritional stress. Here, we discovered genetic interactions that indicated that the cAMP pathway engaged in crosstalk with Chk1-dependent signaling.","alleles_by_uniquename":{"SJAG_00364:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00364","name":"rad3delta","uniquename":"SJAG_00364:allele-1"},"SJAG_00429:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00429","name":"rad26delta","uniquename":"SJAG_00429:allele-1"},"SJAG_01205:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01205","name":"crb2delta","uniquename":"SJAG_01205:allele-1"},"SJAG_01605:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01605","name":"rad9delta","uniquename":"SJAG_01605:allele-1"},"SJAG_01680:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01680","name":"chk1delta","uniquename":"SJAG_01680:allele-1"},"SJAG_01680:allele-2":{"allele_type":"amino_acid_mutation","description":"P470L","gene_uniquename":"SJAG_01680","name":"chk1-P470L","synonyms":[{"name":"chk1- hyperactive (chk1-hyp)","reference":"PMID:23090706","type":"exact"},{"name":"chk1-hyperactive (chk1-hyp)","reference":"PMID:20368354","type":"exact"}],"uniquename":"SJAG_01680:allele-2"},"SJAG_02266:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02266","name":"rad24delta","uniquename":"SJAG_02266:allele-1"},"SJAG_02576:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02576","name":"rad25delta","uniquename":"SJAG_02576:allele-1"},"SJAG_02771:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02771","name":"rad1delta","uniquename":"SJAG_02771:allele-1"},"SJAG_03720:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03720","name":"tel1delta","uniquename":"SJAG_03720:allele-1"},"SJAG_04287:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04287","name":"cds1delta","uniquename":"SJAG_04287:allele-1"},"SJAG_04671:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04671","name":"mrc1delta","uniquename":"SJAG_04671:allele-1"}},"annotation_curators":[{"annotation_count":28,"community_curator":true,"file_name":null,"file_type":null,"name":"Sho Okamoto","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2022-11-21","authors":"Furuya K, Niki H","authors_abbrev":"Furuya K et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2022-11-21 17:21:20","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Sho Okamoto","canto_curator_role":"community","canto_first_approved_date":"2022-11-21 17:21:20","canto_session_key":"5f68f94ee65a99b7","canto_session_submitted_date":"2022-11-21 17:21:13","canto_triage_status":"Curatable","citation":"Curr Genet 2012 Dec;58(5-6):291-303","cv_annotations":{"multi_locus_phenotype":[{"annotations":[115484],"is_not":false,"summary":null,"term":"FYPO:0007790"},{"annotations":[115490],"is_not":false,"summary":null,"term":"FYPO:0000085"},{"annotations":[115487],"is_not":false,"summary":null,"term":"FYPO:0000088"}],"single_locus_phenotype":[{"annotations":[115475,115476,115477,115478,115479,115480,115482,115483],"is_not":false,"summary":null,"term":"FYPO:0007782"},{"annotations":[115501],"is_not":false,"summary":null,"term":"FYPO:0007774"},{"annotations":[115500],"is_not":false,"summary":null,"term":"FYPO:0001690"},{"annotations":[115474,115481],"is_not":false,"summary":null,"term":"FYPO:0007790"},{"annotations":[115499],"is_not":false,"summary":null,"term":"FYPO:0004693"},{"annotations":[115488,115489,115494,115495,115496],"is_not":false,"summary":null,"term":"FYPO:0000085"},{"annotations":[115485,115486,115491,115492,115493],"is_not":false,"summary":null,"term":"FYPO:0000088"},{"annotations":[115497,115498],"is_not":false,"summary":null,"term":"FYPO:0001234"}]},"doi":"10.1007/s00294-012-0384-4","gene_count":11,"genes_by_uniquename":{"SJAG_00364":null,"SJAG_00429":null,"SJAG_01205":null,"SJAG_01605":null,"SJAG_01680":null,"SJAG_02266":null,"SJAG_02576":null,"SJAG_02771":null,"SJAG_03720":null,"SJAG_04287":null,"SJAG_04671":null},"genotypes_by_uniquename":{"cds1delta":{"display_name":"cds1delta","display_uniquename":"cds1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04287:allele-1","expression":"Null"}]}]},"chk1-P470L-P470L-amino_acid_mutation-expression-not_assayed_or_wild_type__rad24delta":{"display_name":"chk1-P470L(aa) rad24delta","display_uniquename":"chk1-P470L-P470L-amino_acid_mutation-expression-not_assayed_or_wild_type__rad24delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01680:allele-2","expression":"Not assayed or wild type"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_02266:allele-1","expression":"Null"}]}]},"chk1delta":{"display_name":"chk1delta","display_uniquename":"chk1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01680:allele-1","expression":"Null"}]}]},"chk1delta__crb2delta":{"display_name":"chk1delta crb2delta","display_uniquename":"chk1delta__crb2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01680:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_01205:allele-1","expression":"Null"}]}]},"crb2delta":{"display_name":"crb2delta","display_uniquename":"crb2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01205:allele-1","expression":"Null"}]}]},"mrc1delta":{"display_name":"mrc1delta","display_uniquename":"mrc1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04671:allele-1","expression":"Null"}]}]},"rad1delta":{"display_name":"rad1delta","display_uniquename":"rad1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02771:allele-1","expression":"Null"}]}]},"rad24delta":{"display_name":"rad24delta","display_uniquename":"rad24delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02266:allele-1","expression":"Null"}]}]},"rad25delta":{"display_name":"rad25delta","display_uniquename":"rad25delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02576:allele-1","expression":"Null"}]}]},"rad26delta":{"display_name":"rad26delta","display_uniquename":"rad26delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00429:allele-1","expression":"Null"}]}]},"rad3delta":{"display_name":"rad3delta","display_uniquename":"rad3delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00364:allele-1","expression":"Null"}]}]},"rad9delta":{"display_name":"rad9delta","display_uniquename":"rad9delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01605:allele-1","expression":"Null"}]}]},"tel1delta":{"display_name":"tel1delta","display_uniquename":"tel1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03720:allele-1","expression":"Null"}]}]}},"ltp_gene_count":11,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2012","pubmed_entrez_date":"2012-10-24","pubmed_publication_date":"Dec 2012","terms_by_termid":{"FYECO:0000005":null,"FYECO:0000137":null,"FYECO:0000314":null,"FYPO:0000085":null,"FYPO:0000088":null,"FYPO:0001234":null,"FYPO:0001690":null,"FYPO:0004693":null,"FYPO:0007774":null,"FYPO:0007782":null,"FYPO:0007790":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null,"FYPO_EXT:0000003":null},"title":"Hyphal differentiation induced via a DNA damage checkpoint-dependent pathway engaged in crosstalk with nutrient stress signaling in Schizosaccharomyces japonicus.","uniquename":"PMID:23090706"}


id: 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:23145069
data:
  {"abstract":"The ERH gene encodes a highly conserved small nuclear protein with a unique amino acid sequence and three-dimensional structure but unknown function. The gene is present in animals, plants, and protists but to date has only been found in few fungi. Here we report that ERH homologs are also present in all four species from the genus Schizosaccharomyces, S. pombe, S. octosporus, S. cryophilus, and S. japonicus, which, however, are an exception in this respect among Ascomycota and Basidiomycota. The ERH protein sequence is moderately conserved within the genus (58% identity between S. pombe and S.japonicus), but the intron-rich genes have almost identical intron-exon organizations in all four species. In S. pombe, erh1(+) is expressed at a roughly constant level during vegetative growth and adaptation to unfavorable conditions such as nutrient limitation and hyperosmotic stress caused by sorbitol. Erh1p localizes preferentially to the nucleus with the exception of the nucleolus, but is also present in the cytoplasm. Cells lacking erh1(+) have an aberrant cell morphology and a comma-like shape when cultured to the stationary phase, and exhibit a delayed recovery from this phase followed by slower growth. Loss of erh1(+) in an auxotrophic background results in enhanced arrest in the G1 phase following nutritional stress, and also leads to hypersensitivity to agents inducing hyperosmotic stress (sorbitol), inhibiting DNA replication (hydroxyurea), and destabilizing the plasma membrane (SDS); this hypersensitivity can be abolished by expression of S. pombe erh1(+) and, to a lesser extent, S. japonicus erh1(+) or human ERH. Erh1p fails to interact with the human Ciz1 and PDIP46/SKAR proteins, known molecular partners of human ERH. Our data suggest that in Schizosaccharomyces sp. erh1(+) is non-essential for normal growth and Erh1p could play a role in response to adverse environmental conditions and in cell cycle regulation.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Krzyzanowski MK, Kozlowska E, Kozlowski P","authors_abbrev":"Krzyzanowski MK et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Sequence feature or region","citation":"PLoS One 2012;7(11):e49059","cv_annotations":{},"doi":"10.1371/journal.pone.0049059","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2012","pubmed_entrez_date":"2012-11-13","pubmed_publication_date":"2012","terms_by_termid":{},"title":"Identification and functional analysis of the erh1(+) gene encoding enhancer of rudimentary homolog from the fission yeast Schizosaccharomyces pombe.","uniquename":"PMID:23145069"}


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


id: PMID:33791858
data:
  {"abstract":"Mitogen-activated protein kinase (MAPK) signalling pathways regulate multiple cellular functions in eukaryotic organisms in response to environmental cues, including the dynamic remodeling of the actin cytoskeleton. The fission yeast S. pombe is an optimal model to investigate the conserved regulatory mechanisms of cytokinesis, which relies in an actomyosin-based contractile ring (CAR) that prompts the physical separation of daughter cells during cellular division. Our group has recently shown that p38 MAPK ortholog Sty1, the core component of the stress-activated pathway (SAPK), negatively modulates CAR assembly and integrity in S. pombe during actin cytoskeletal damage induced with Latrunculin A and in response to environmental stress. This response involves downregulation of protein levels of the formin For3, which assembles actin filaments for cables and the CAR, likely through an ubiquitin-mediated degradation mechanism. Contrariwise, Sty1 function positively reinforces CAR assembly during stress in the close relative dimorphic fission yeast S. japonicus. The opposite effect of SAPK signaling on CAR integrity may represent an evolutionary refined adaptation to cope with the marked differences in cytokinesis onset in both fission yeast species.","alleles_by_uniquename":{"SJAG_00266:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00266","name":"atf1delta","uniquename":"SJAG_00266:allele-1"},"SJAG_02592:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02592","name":"sty1delta","uniquename":"SJAG_02592:allele-1"}},"annotation_curators":[{"annotation_count":4,"community_curator":true,"file_name":null,"file_type":null,"name":"Elisa Gómez Gil","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-09-14","authors":"Madrid M, Gómez-Gil E, Cansado J","authors_abbrev":"Madrid M et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-09-14 21:24:28","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Elisa Gómez Gil","canto_curator_role":"community","canto_first_approved_date":"2021-09-14 21:24:28","canto_session_key":"84ac20b0ff20a3cd","canto_session_submitted_date":"2021-09-14 16:45:32","canto_triage_status":"Curatable","citation":"Curr Genet 2021 Oct;67(5):715-721","cv_annotations":{"PSI-MOD":[{"annotations":[115642],"is_not":false,"summary":null,"term":"MOD:00696"}],"single_locus_phenotype":[{"annotations":[115641],"is_not":false,"summary":null,"term":"FYPO:0002998"},{"annotations":[115639,115640],"is_not":false,"summary":null,"term":"FYPO:0000107"}]},"doi":"10.1007/s00294-021-01155-6","gene_count":2,"genes_by_uniquename":{"SJAG_00266":null,"SJAG_02592":null},"genotypes_by_uniquename":{"atf1delta":{"display_name":"atf1delta","display_uniquename":"atf1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00266:allele-1","expression":"Null"}]}]},"sty1delta":{"display_name":"sty1delta","display_uniquename":"sty1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02592:allele-1","expression":"Null"}]}]}},"ltp_gene_count":2,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2021","pubmed_entrez_date":"2021-04-01","pubmed_publication_date":"Oct 2021","terms_by_termid":{"FYECO:0000248":null,"FYPO:0000107":null,"FYPO:0002998":null,"FYPO_EXT:0000001":null,"GO:0120306":null,"MOD:00696":null},"title":"Negative control of cytokinesis by stress-activated MAPK signaling.","uniquename":"PMID:33791858"}


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


id: 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":[115318],"is_not":false,"summary":null,"term":"GO:0005730"}],"multi_locus_phenotype":[{"annotations":[115332,115333,115334,115336],"is_not":false,"summary":null,"term":"FYPO:0000674"}],"single_locus_phenotype":[{"annotations":[115319,115320,115321,115335],"is_not":false,"summary":null,"term":"FYPO:0000080"},{"annotations":[115328,115329,115330],"is_not":false,"summary":null,"term":"FYPO:0000618"},{"annotations":[115337,115338,115339],"is_not":false,"summary":null,"term":"FYPO:0001327"},{"annotations":[115325,115326,115327],"is_not":false,"summary":null,"term":"FYPO:0001387"},{"annotations":[115322,115323,115324],"is_not":false,"summary":null,"term":"FYPO:0000324"},{"annotations":[115331],"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:37233261
data:
  {"abstract":"Gene targeting is a commonly used method to reveal the function of genes. Although it is an attractive tool for molecular studies, it can frequently be a challenge because its efficiency can be low and it requires the screening of a large number of transformants. Generally, these problems originate from the elevated level of ectopic integration caused by non-homologous DNA end joining (NHEJ). To eliminate this problem, NHEJ-related genes are frequently deleted or disrupted. Although these manipulations can improve gene targeting, the phenotype of the mutant strains raised the question of whether mutations have side effects. The aim of this study was to disrupt the  lig4  gene in the dimorphic fission yeast,  S. japonicus , and investigate the phenotypic changes of the mutant strain. The mutant cells have shown various phenotypic changes, such as increased sporulation on complete medium, decreased hyphal growth, faster chronological aging, and higher sensitivity to heat shock, UV light, and caffeine. In addition, higher flocculation capacity has been observed, especially at lower sugar concentrations. These changes were supported by transcriptional profiling. Many genes belonging to metabolic and transport processes, cell division, or signaling had altered mRNA levels compared to the control strain. Although the disruption improved the gene targeting, we assume that the  lig4  inactivation can cause unexpected physiological side effects, and we have to be very careful with the manipulations of the NHEJ-related genes. To reveal the exact mechanisms behind these changes, further investigations are required.","alleles_by_uniquename":{"SJAG_02527:allele-1":{"allele_type":"disruption","description":"RNA sequencing revealed that only the 5' end of the disrupted allele showed low RNA expression and coverage","gene_uniquename":"SJAG_02527","name":"lig4::KanMX6","uniquename":"SJAG_02527:allele-1"}},"annotation_curators":[{"annotation_count":7,"community_curator":true,"file_name":null,"file_type":null,"name":"Ida Miklos","orcid":"0000-0002-7074-4019"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2023-08-08","authors":"Acs-Szabo L, Papp LA, Takacs S, Miklos I","authors_abbrev":"Acs-Szabo L et al.","canto_added_date":"2023-05-27 00:40:04","canto_annotation_status":"APPROVED","canto_approved_date":"2023-08-08 20:07:33","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Ida Miklos","canto_curator_role":"community","canto_first_approved_date":"2023-08-08 20:07:33","canto_session_key":"c74bdd0a67b132f8","canto_session_submitted_date":"2023-08-08 20:07:15","canto_triage_status":"Curatable","citation":"J Fungi (Basel) 2023 May 10;9(5)","cv_annotations":{"single_locus_phenotype":[{"annotations":[115466],"is_not":false,"summary":null,"term":"FYPO:0007776"},{"annotations":[115468],"is_not":false,"summary":null,"term":"FYPO:0009111"},{"annotations":[115465],"is_not":false,"summary":null,"term":"FYPO:0000588"},{"annotations":[115471],"is_not":false,"summary":null,"term":"FYPO:0005705"},{"annotations":[115469],"is_not":false,"summary":null,"term":"FYPO:0005231"},{"annotations":[115467],"is_not":false,"summary":null,"term":"FYPO:0000097"},{"annotations":[115470],"is_not":false,"summary":null,"term":"FYPO:0001408"}]},"doi":"10.3390/jof9050550","gene_count":1,"genes_by_uniquename":{"SJAG_02527":null},"genotypes_by_uniquename":{"lig4::KanMX6-RNA_sequencing_revealed_that_only_the_5'_end_of_the_disrupted_allele_showed_low_RNA_expression_and_coverage-disruption-expression-knockdown":{"display_name":"lig4::KanMX6(RNA sequencing revealed that only the 5' end of the disrupted allele showed low RNA expression and coverage)[Knockdown]","display_uniquename":"lig4::KanMX6-RNA_sequencing_revealed_that_only_the_5'_end_of_the_disrupted_allele_showed_low_RNA_expression_and_coverage-disruption-expression-knockdown","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02527:allele-1","expression":"Knockdown"}]}]}},"ltp_gene_count":1,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2023","pubmed_entrez_date":"2023-05-26","pubmed_publication_date":"10 May 2023","terms_by_termid":{"FYECO:0000005":null,"FYECO:0000081":null,"FYECO:0000117":null,"FYECO:0000126":null,"FYECO:0000137":null,"FYECO:0000315":null,"FYPO:0000097":null,"FYPO:0000588":null,"FYPO:0001408":null,"FYPO:0005231":null,"FYPO:0005705":null,"FYPO:0007776":null,"FYPO:0009111":null},"title":"Disruption of the  Schizosaccharomyces japonicus lig4  Disturbs Several Cellular Processes and Leads to a Pleiotropic Phenotype.","uniquename":"PMID:37233261"}


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


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


id: 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:0000091
data:
  {"abstract":"We have created a standard template for classes describing the cell migration process for a cell type as a biological process. The underlying equivalence axiom template is \"'cell migration' and 'alters_location_of' some C\", where C is a native cell (CL:0000004).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of cell migration as biological processes in the Gene Ontology","uniquename":"GO_REF:0000091"}


id: GO_REF:0000002
data:
  {"abstract":"Transitive assignment of GO terms based on InterPro classification. For any database entry (representing a protein or protein-coding gene) that has been annotated with one or more InterPro domains, the corresponding GO terms are obtained from a translation table of InterPro entries to GO terms (interpro2go) generated manually by the InterPro team at EBI. The mapping file is available at http://www.geneontology.org/external2go/interpro2go.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"DDB, FB, MGI, GOA, ZFIN 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id: PMID:23873862
data:
  {"abstract":"Many fungi respond to light and regulate fungal development and behavior. A blue light-activated complex has been identified in Neurospora crassa as the product of the wc-1 and wc-2 genes. Orthologs of WC-1 and WC-2 have hitherto been found only in filamentous fungi and not in yeast, with the exception of the basidiomycete pathogenic yeast Cryptococcus. Here, we report that the fission yeast Schizosaccharomyces japonicus responds to blue light depending on Wcs1 and Wcs2, orthologs of components of the WC complex. Surprisingly, those of ascomycete S. japonicus are more closely related to those of the basidiomycete. S. japonicus reversibly changes from yeast to hyphae in response to environmental stresses. After incubation at 30°C, a colony of yeast was formed, and then hyphal cells extended from the periphery of the colony. When light cycles were applied, distinct dark- and bright-colored hyphal cell stripes were formed because the growing hyphal cells had synchronously activated cytokinesis. In addition, temperature cycles of 30°C for 12 h and 35°C for 12 h or of 25°C for 12 h and 30°C for 12 h during incubation in the dark induced a response in the hyphal cells similar to that of light. The stripe formation of the temperature cycles was independent of the wcs genes. Both light and temperature, which are daily external cues, have the same effect on growing hyphal cells. A dual sensing mechanism of external cues allows organisms to adapt to daily changes of environmental alteration. ","alleles_by_uniquename":{"SJAG_02860:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02860","name":"wcs1delta","uniquename":"SJAG_02860:allele-1"},"SJAG_05242:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_05242","name":"wcs2delta","uniquename":"SJAG_05242:allele-1"}},"annotation_curators":[{"annotation_count":7,"community_curator":true,"file_name":null,"file_type":null,"name":"Sho Okamoto","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2022-12-01","authors":"Okamoto S, Furuya K, Nozaki S, Aoki K, Niki H","authors_abbrev":"Okamoto S et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2022-12-01 10:29:08","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Sho Okamoto","canto_curator_role":"community","canto_first_approved_date":"2022-12-01 10:29:08","canto_session_key":"0e71b7054e7d7754","canto_session_submitted_date":"2022-12-01 10:28:58","canto_triage_status":"Curatable","citation":"Eukaryot Cell 2013 Sep;12(9):1235-43","cv_annotations":{"biological_process":[{"annotations":[115212,115213],"is_not":false,"summary":null,"term":"GO:0071483"}],"molecular_function":[{"annotations":[115211],"is_not":false,"summary":null,"term":"GO:0009882"}],"single_locus_phenotype":[{"annotations":[115214,115215],"is_not":false,"summary":null,"term":"FYPO:0008031"},{"annotations":[115216,115217],"is_not":false,"summary":null,"term":"FYPO:0008046"}]},"doi":"10.1128/EC.00109-13","gene_count":2,"genes_by_uniquename":{"SJAG_02860":null,"SJAG_05242":null},"genotypes_by_uniquename":{"wcs1delta":{"display_name":"wcs1delta","display_uniquename":"wcs1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02860:allele-1","expression":"Null"}]}]},"wcs2delta":{"display_name":"wcs2delta","display_uniquename":"wcs2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_05242:allele-1","expression":"Null"}]}]}},"ltp_gene_count":2,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2013","pubmed_entrez_date":"2013-07-23","pubmed_publication_date":"Sep 2013","terms_by_termid":{"FYECO:0000005":null,"FYECO:0000126":null,"FYPO:0008031":null,"FYPO:0008046":null,"FYPO_EXT:0000001":null,"GO:0009882":null,"GO:0071483":null},"title":"Synchronous activation of cell division by light or temperature stimuli in the dimorphic yeast Schizosaccharomyces japonicus.","uniquename":"PMID:23873862"}


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


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


id: PMID:37164017
data:
  {"abstract":"Most eukaryotes respire oxygen, using it to generate biomass and energy. However, a few organisms have lost the capacity to respire. Understanding how they manage biomass and energy production may illuminate the critical points at which respiration feeds into central carbon metabolism and explain possible routes to its optimization. Here, we use two related fission yeasts, Schizosaccharomyces pombe and Schizosaccharomyces japonicus, as a comparative model system. We show that although S. japonicus does not respire oxygen, unlike S. pombe, it is capable of efficient NADH oxidation, amino acid synthesis, and ATP generation. We probe possible optimization strategies through the use of stable isotope tracing metabolomics, mass isotopologue distribution analysis, genetics, and physiological experiments. S. japonicus appears to have optimized cytosolic NADH oxidation via glycerol-3-phosphate synthesis. It runs a fully bifurcated TCA pathway, sustaining amino acid production. Finally, we propose that it has optimized glycolysis to maintain high ATP/ADP ratio, in part by using the pentose phosphate pathway as a glycolytic shunt, reducing allosteric inhibition of glycolysis and supporting biomass generation. By comparing two related organisms with vastly different metabolic strategies, our work highlights the versatility and plasticity of central carbon metabolism in eukaryotes, illuminating critical adaptations supporting the preferential use of glycolysis over oxidative phosphorylation.","alleles_by_uniquename":{"SJAG_00409:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00409","name":"gpd1delta","uniquename":"SJAG_00409:allele-1"},"SJAG_00601:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00601","name":"rip1delta","uniquename":"SJAG_00601:allele-1"},"SJAG_01355:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01355","name":"cox6delta","uniquename":"SJAG_01355:allele-1"},"SJAG_01753:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01753","name":"mdh1delta","uniquename":"SJAG_01753:allele-1"},"SJAG_02796:allele-1":{"allele_type":"amino_acid_mutation","description":"A343T","gene_uniquename":"SJAG_02796","name":"pyk1-A343T","uniquename":"SJAG_02796:allele-1"},"SJAG_03920:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03920","name":"sdh3delta","uniquename":"SJAG_03920:allele-1"},"SJAG_04843:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04843","name":"fum1delta","uniquename":"SJAG_04843:allele-1"}},"annotation_curators":[{"annotation_count":20,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2023-05-18","authors":"Alam S, Gu Y, Reichert P, Bähler J, Oliferenko S","authors_abbrev":"Alam S et al.","canto_added_date":"2023-05-12 00:40:04","canto_annotation_status":"APPROVED","canto_approved_date":"2024-07-03 11:37:10","canto_approver_orcid":"0000-0001-6330-7526","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2023-05-18 12:11:54","canto_session_key":"94bcbfb72cf94809","canto_session_submitted_date":"2023-05-18 12:11:43","canto_triage_status":"Curatable","citation":"Curr Biol 2023 Apr 30;","cv_annotations":{"single_locus_phenotype":[{"annotations":[115634],"is_not":false,"summary":null,"term":"FYPO:0007363"},{"annotations":[115632],"is_not":false,"summary":null,"term":"FYPO:0000026"},{"annotations":[115631],"is_not":false,"summary":null,"term":"FYPO:0001355"},{"annotations":[115633],"is_not":false,"summary":null,"term":"FYPO:0001489"},{"annotations":[115635],"is_not":false,"summary":null,"term":"FYPO:0004165"},{"annotations":[115629,115630],"is_not":false,"summary":null,"term":"FYPO:0007790"},{"annotations":[115623,115626],"is_not":false,"summary":null,"term":"FYPO:0000760"},{"annotations":[115625,115628],"is_not":false,"summary":null,"term":"FYPO:0000579"},{"annotations":[115624,115627],"is_not":false,"summary":null,"term":"FYPO:0000590"},{"annotations":[115620,115621,115622],"is_not":false,"summary":null,"term":"FYPO:0001357"},{"annotations":[115619],"is_not":false,"summary":null,"term":"FYPO:0001234"},{"annotations":[115636,115637,115638],"is_not":false,"summary":null,"term":"FYPO:0002058"}]},"doi":"10.1016/j.cub.2023.04.046","gene_count":7,"genes_by_uniquename":{"SJAG_00409":null,"SJAG_00601":null,"SJAG_01355":null,"SJAG_01753":null,"SJAG_02796":null,"SJAG_03920":null,"SJAG_04843":null},"genotypes_by_uniquename":{"cox6delta":{"display_name":"cox6delta","display_uniquename":"cox6delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01355:allele-1","expression":"Null"}]}]},"fum1delta":{"display_name":"fum1delta","display_uniquename":"fum1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04843:allele-1","expression":"Null"}]}]},"gpd1delta":{"display_name":"gpd1delta","display_uniquename":"gpd1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00409:allele-1","expression":"Null"}]}]},"mdh1delta":{"display_name":"mdh1delta","display_uniquename":"mdh1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01753:allele-1","expression":"Null"}]}]},"pyk1-A343T-A343T-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"pyk1-A343T(aa)","display_uniquename":"pyk1-A343T-A343T-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02796:allele-1","expression":"Not assayed or wild type"}]}]},"rip1delta":{"display_name":"rip1delta","display_uniquename":"rip1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00601:allele-1","expression":"Null"}]}]},"sdh3delta":{"display_name":"sdh3delta","display_uniquename":"sdh3delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03920:allele-1","expression":"Null"}]}]}},"ltp_gene_count":7,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2023","pubmed_entrez_date":"2023-05-10","pubmed_publication_date":"30 Apr 2023","terms_by_termid":{"FYECO:0000005":null,"FYECO:0000015":null,"FYECO:0000126":null,"FYECO:0000137":null,"FYPO:0000026":null,"FYPO:0000579":null,"FYPO:0000590":null,"FYPO:0000760":null,"FYPO:0001234":null,"FYPO:0001355":null,"FYPO:0001357":null,"FYPO:0001489":null,"FYPO:0002058":null,"FYPO:0004165":null,"FYPO:0007363":null,"FYPO:0007790":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null,"FYPO_EXT:0000003":null},"title":"Optimization of energy production and central carbon metabolism in a non-respiring eukaryote.","uniquename":"PMID:37164017"}


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


id: PMID:12236685
data:
  {"abstract":"Dimethyl dicarbonate (DMDC) was added to grape must and to synthetic media and results showed that, at 20 degrees C, 150 mg.L(-)(1) DMDC completely inhibited the fermentation of a grape must that was previously inoculated with 10(6) cells.mL(-)(1) Saccharomyces bayanus and Saccharomyces uvarum. Brettanomyces intermedius, Candida guilliermondii, Hansenula jadinii, Hansenula petersonii, Kloeckera apiculata, Pichia membranaefaciens, and Saccharomyces cerevisiae were inhibited by 250 mg.L(-)(1). Candida valida was inhibited in the presence of 350 mg.L(-)(1), whereas Hanseniaspora osmophila, Saccharomycodes ludwigii, Schizosaccharomyces pombe, and Zygosaccharomyces bailii required 400 mg.L(-)(1). Delay of fermentation (but not inhibition) was noted in the presence of 400 mg.L(-)(1) for the following cultures: Brettanomyces anomalus, Hanseniaspora uvarum, Metschnikowia pulcherrima, Schizosaccharomyces japonicus, Torulaspora delbrueckii, and Zygosaccharomyces florentinus. Acetobacter aceti and Lactobacillus sp. were completely inhibited using 1000 and 500 mg.L(-)(1) DMDC, respectively. The fermentation of a grape must inoculated with 10(6) cells.mL(-)(1) of different wine yeasts was delayed for 4 days after the prior addition of 200 mg.L(-)(1) of DMDC; 200 mg.L(-)(1) DMDC did not show any residual inhibitory effect after 12 h, nor did 300 mg.L(-)(1) 24 h after the addition. In cellar experiments, indigenously contaminated grape musts (with and without skins) showed a delay in fermentation of 48 h after the addition of only 50 mg.L(-)(1) DMDC. The possibility of using DMDC (as pure grade as commercially available) in grape must as a disinfectant for the decontamination of musts indigenously contaminated with wild yeast should be considered seriously, despite its apparent low solubility in water.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Delfini C, Gaia P, Schellino R, Strano M, Pagliara A, Ambrò S","authors_abbrev":"Delfini C et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Biotech","citation":"J Agric Food Chem 2002 Sep 25;50(20):5605-11","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2002","pubmed_entrez_date":"2002-09-19","pubmed_publication_date":"25 Sep 2002","terms_by_termid":{},"title":"Fermentability of grape must after inhibition with dimethyl dicarbonate (DMDC).","uniquename":"PMID:12236685"}


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


id: PMID:23150598
data:
  {"abstract":"A key question in developmental biology addresses the mechanism of asymmetric cell division. Asymmetry is crucial for generating cellular diversity required for development in multicellular organisms. As one of the potential mechanisms, chromosomally borne epigenetic difference between sister cells that changes mating/cell type has been demonstrated only in the Schizosaccharomyces pombe fission yeast. For technical reasons, it is nearly impossible to determine the existence of such a mechanism operating during embryonic development of multicellular organisms. Our work addresses whether such an epigenetic mechanism causes asymmetric cell division in the recently sequenced fission yeast, S. japonicus (with 36% GC content), which is highly diverged from the well-studied S. pombe species (with 44% GC content). We find that the genomic location and DNA sequences of the mating-type loci of S. japonicus differ vastly from those of the S. pombe species. Remarkably however, similar to S. pombe, the S. japonicus cells switch cell/mating type after undergoing two consecutive cycles of asymmetric cell divisions: only one among four \"granddaughter\" cells switches. The DNA-strand-specific epigenetic imprint at the mating-type locus1 initiates the recombination event, which is required for cellular differentiation. Therefore the S. pombe and S. japonicus mating systems provide the first two examples in which the intrinsic chirality of double helical structure of DNA forms the primary determinant of asymmetric cell division. Our results show that this unique strand-specific imprinting/segregation epigenetic mechanism for asymmetric cell division is evolutionary conserved. Motivated by these findings, we speculate that DNA-strand-specific epigenetic mechanisms might have evolved to dictate asymmetric cell division in diploid, higher eukaryotes as well.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Yu C, Bonaduce MJ, Klar AJ","authors_abbrev":"Yu C et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"Genetics 2013 Jan;193(1):85-94","cv_annotations":{},"doi":"10.1534/genetics.112.146233","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2013","pubmed_entrez_date":"2012-11-15","pubmed_publication_date":"Jan 2013","terms_by_termid":{},"title":"Defining the epigenetic mechanism of asymmetric cell division of Schizosaccharomyces japonicus yeast.","uniquename":"PMID:23150598"}


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


id: PMID:7612397
data:
  {"abstract":"The ultrastructure of isolated cell walls of Schizosaccharomyces pombe was studied by electron microscopy after treatment with the following purified enzymes: endo-beta-(1-->3)-glucanase, endo-beta-(-->6)-glucanase, and endo-alpha-(1-->3)-glucanase produced by Bacillus circulans; exo-beta-(1-->3)-glucanase and endo-beta-(1-->3)-glucanase produced by Schizosaccharomyces japonicus var. versatilis. The exo-beta-(1-->3)-glucanase had no detectable effect on the walls, but amorphous wall material was removed by action of the endo-beta-(1-->3)- and endo-beta-(1-->6)-glucanases of B. circulans to reveal a wall component consisting of densely interwoven microfibrils. The fibrils were hydrolyzed by treatment with the Schiz. japonicus endo-beta-(1-->3)-glucanase followed by B. circulans endo-alpha-(1-->3)-glucanase--suggesting that they were composed of -beta-(1-->3)-linked glucan and alpha-(1-->3)-linked glucan. The presence of a fibrillar component in untreated walls was evident after negative staining.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Kopecká M, Fleet GH, Phaff HJ","authors_abbrev":"Kopecká 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":"J Struct Biol 1995 Mar;114(2):140-52","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1995","pubmed_entrez_date":"1995-03-01","pubmed_publication_date":"Mar 1995","terms_by_termid":{},"title":"Ultrastructure of the cell wall of Schizosaccharomyces pombe following treatment with various glucanases.","uniquename":"PMID:7612397"}


id: PMID:26343758
data:
  {"abstract":"CENP-A is a centromere-specific histone H3 variant that is required for kinetochore assembly and accurate chromosome segregation. For it to function properly, CENP-A must be specifically localized to centromeres. In fission yeast, Scm3sp and the Mis18 complex, composed of Mis16, Eic1, and Mis18, function as a CENP-A(Cnp1)-specific chaperone and a recruiting factor, respectively, and together ensure accurate delivery of CENP-A(Cnp1) to centromeres. Although how Scm3sp specifically recognizes CENP-A(Cnp1) has been revealed recently, the recruiting mechanism of CENP-A(Cnp1) via the Mis18 complex remains unknown. In this study, we have determined crystal structures of Schizosaccharomyces japonicus Mis16 alone and in complex with the helix 1 of histone H4 (H4α1). Crystal structures followed by mutant analysis and affinity pull-downs have revealed that Mis16 recognizes both H4α1 and Scm3sp independently within the CENP-A(Cnp1)/H4:Scm3sp complex. This observation suggests that Mis16 gains CENP-A(Cnp1) specificity by recognizing both Scm3sp and histone H4. Our studies provide insights into the molecular mechanisms underlying specific recruitment of CENP-A(Cnp1)/H4:Scm3sp into centromeres. ","alleles_by_uniquename":{},"annotation_curators":[{"annotation_count":4,"community_curator":false,"file_name":null,"file_type":null,"name":"Val Wood","orcid":"0000-0001-6330-7526"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-05-13","authors":"An S, Kim H, Cho US","authors_abbrev":"An S et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-05-13 14:11:41","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Val Wood","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-05-13 14:11:41","canto_session_key":"fb189c5ef542852c","canto_session_submitted_date":"2021-05-12 16:00:22","canto_triage_status":"Curatable","citation":"J Mol Biol 2015 Oct 09;427(20):3230-3240","cv_annotations":{"molecular_function":[{"annotations":[115197,115198,115199,115200],"is_not":false,"summary":null,"term":"GO:0042393"}]},"doi":"10.1016/j.jmb.2015.08.022","gene_count":4,"genes_by_uniquename":{"SJAG_00303":null,"SJAG_02513":null,"SJAG_03542":null,"SJAG_03867":null},"genotypes_by_uniquename":{},"ltp_gene_count":3,"ortholog_annotations":[],"paralog_annotations":[],"pdb_entries":[{"entry_authors":"An S,Kim H,Cho U-S","entry_authors_abbrev":"An S et al.","experimental_method":"X-ray","gene_chains":[{"chain":"A","gene_uniquename":"SJAG_03867","position":"1-427"}],"pdb_id":"4xyh","reference_uniquename":"PMID:26343758","resolution":"2.3","title":"Wild-type full length Mis16 in Schizosaccharomyces japonicus"},{"entry_authors":"An S,Kim H,Cho U-S","entry_authors_abbrev":"An S et al.","experimental_method":"X-ray","gene_chains":[{"chain":"B","gene_uniquename":"SJAG_03542","position":"1-103"},{"chain":"A","gene_uniquename":"SJAG_03867","position":"1-427"}],"pdb_id":"4xyi","reference_uniquename":"PMID:26343758","resolution":"3.0","title":"Mis16 with H4 peptide"}],"physical_interactions":[],"publication_year":"2015","pubmed_entrez_date":"2015-09-08","pubmed_publication_date":"09 Oct 2015","terms_by_termid":{"GO:0042393":null},"title":"Mis16 Independently Recognizes Histone H4 and the CENP-ACnp1-Specific Chaperone Scm3sp.","uniquename":"PMID:26343758"}


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


id: PMID: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: 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":[115444],"is_not":false,"summary":null,"term":"GO:0005801"},{"annotations":[115446],"is_not":false,"summary":null,"term":"GO:0005829"}],"single_locus_phenotype":[{"annotations":[115445],"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:0000043
data:
  {"abstract":"Transitive assignments using UniProtKB/Swiss-Prot keywords. The UniProtKB keyword controlled vocabulary contains 10 different categories of information to UniProtKB entries. Further information on the UniProtKB keyword resource can be found at https://www.uniprot.org/keywords/.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"UniProt-GOA","canto_curator_role":"JaponicusDB","cv_annotations":{"biological_process":[{"annotations":[66143],"is_not":false,"summary":null,"term":"GO:0000272"},{"annotations":[64899],"is_not":false,"summary":null,"term":"GO:0075523"}],"molecular_function":[{"annotations":[68566],"is_not":false,"summary":null,"term":"GO:0004812"},{"annotations":[57605],"is_not":false,"summary":null,"term":"GO:0005524"},{"annotations":[66142],"is_not":false,"summary":null,"term":"GO:0008061"},{"annotations":[57970,66525],"is_not":false,"summary":null,"term":"GO:0008483"}]},"gene_count":6,"genes_by_uniquename":{"SJAG_00620":null,"SJAG_00691":null,"SJAG_01595":null,"SJAG_02263":null,"SJAG_03856":null,"SJAG_04546":null},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{"GO:0000272":null,"GO:0004812":null,"GO:0005524":null,"GO:0008061":null,"GO:0008483":null,"GO:0075523":null},"title":"Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping","uniquename":"GO_REF:0000043"}


id: PMID:34427722
data:
  {"abstract":"Fungal pathogens, from phytopathogenic fungus to human pathogens, are able to alternate between the yeast-like form and filamentous forms. This morphological transition (dimorphism) is in close connection with their pathogenic lifestyles and with their responses to changing environmental conditions. The mechanisms governing these morphogenetic conversions are still not fully understood. Therefore, we studied the filamentous growth of the less-known, non-pathogenic dimorphic fission yeast, S. japonicus, which belongs to an ancient and early evolved branch of the Ascomycota. Its RNA sequencing revealed that several hundred genes were up- or down-regulated in the hyphae compared to the yeast-phase cells. These genes belonged to different GO categories, confirming that mycelial growth is a rather complex process. The genes of transport- and metabolic processes appeared especially in high numbers among them. High expression of genes involved in glycolysis and ethanol production was found in the hyphae, while other results pointed to the regulatory role of the protein kinase A (PKA) pathway. The homologues of 49 S. japonicus filament-associated genes were found by sequence alignments also in seven distantly related dimorphic and filamentous species. The comparative genomic analyses between S. japonicus and the closely related but non-dimorphic S. pombe shed some light on the differences in their genomes. All these data can contribute to a better understanding of hyphal growth and those genomic rearrangements that underlie it.","alleles_by_uniquename":{},"annotation_curators":[{"annotation_count":2,"community_curator":true,"file_name":null,"file_type":null,"name":"Ida Miklos","orcid":"0000-0002-7074-4019"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-10-06","authors":"Papp LA, Ács-Szabó L, Batta G, Miklós I","authors_abbrev":"Papp LA et al.","canto_added_date":"2021-09-29 13:11:40","canto_annotation_status":"APPROVED","canto_approved_date":"2021-10-06 13:34:09","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Ida Miklos","canto_curator_role":"community","canto_first_approved_date":"2021-10-06 13:34:09","canto_session_key":"acb5c82405799ef1","canto_session_submitted_date":"2021-09-29 13:38:18","canto_triage_status":"Curatable","citation":"Curr Genet 2021 Dec;67(6):953-968","cv_annotations":{"biological_process":[{"annotations":[115472,115473],"is_not":false,"summary":null,"term":"GO:0030448"}]},"doi":"10.1007/s00294-021-01206-y","gene_count":2,"genes_by_uniquename":{"SJAG_00124":null,"SJAG_04312":null},"genotypes_by_uniquename":{},"ltp_gene_count":2,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2021","pubmed_entrez_date":"2021-08-24","pubmed_publication_date":"Dec 2021","terms_by_termid":{"GO:0030448":null},"title":"Molecular and comparative genomic analyses reveal evolutionarily conserved and unique features of the Schizosaccharomyces japonicus mycelial growth and the underlying genomic changes.","uniquename":"PMID:34427722"}


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


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


id: GO_REF:0000012
data:
  {"abstract":"Pairwise alignments are generated by taking two sequences and aligning them so that the maximum number of amino acids in each protein match, or are similar to, each other. Tools such as BLAST work by comparing a protein-of-interest individually with every protein in a database of known protein sequences and retaining only those matches with a high probability of being significant. Basic BLAST generates local alignments between proteins for regions of high similarity. Other pairwise alignment tools attempt to generate global (full-length) protein alignments. A tool called Blast_Extend_repraze (BER, http://ber.sourceforge.net) has some benefits over basic BLAST. Input into the BER tool includes the underlying DNA sequence for each protein as well as 300 nucleotides upstream and downstream of the predicted boundaries of the protein coding sequence. This allows annotators to see the DNA sequence that underlies the query protein as part of the alignment. In addition, the BER tool is able to look for continuation of regions of similarity through frameshifts and in-frame stop codons.  If such regions are found the alignment is continued. BER searches are done in a two-step process: step one is a BLAST search against a non-redundant protein database, significant BLAST hits are stored in a mini-database for each query protein; step two is a modified Smith-Waterman alignment between the query and the proteins in its mini-database. In order to assess whether a given BER alignment is good enough to assert that the query shares the function of the match protein, one must look at a several factors. First of all, the match protein must itself be experimentally characterized in order to avoid transitive annotation errors. In addition, any residues or secondary structures known to be important for function in the match protein must be conserved in the query. The alignment should be visually inspected to look for any areas of lesser quality that might indicate the two proteins do not share the same function. Although it is impossible to set cutoff values for percent identity and length of match that will apply for every alignment, there are some guidelines. In general at least 40% identity that extends over the full lengths of both proteins is required in order to even consider functional equivalence. However, this percentage is highly dependent on the length and complexity of the proteins. 40% identity between two proteins 500 amino acids long is much more significant that 40% identity between two proteins that are only 100 amino acids long. Therefore, the annotator's experience and knowledge of what is considered significant for the organism and protein family in question is very important. Some sets of proteins are much more highly conserved than others and therefore tolerances for percent identity may have to be adjusted. Finally, the alignment must be considered in the context of what else is known about the query protein and the organism as a whole.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Michelle Gwinn, TIGR 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":"Pairwise alignment (TIGR)","uniquename":"GO_REF:0000012"}


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


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


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


id: GO_REF:0000109
data:
  {"abstract":"Trypanosomes are exquisitely structured cells in which protein localisation can be extremely informative for likely function. TrypTag is a project using expression of N- and C-terminal mNeonGreen fusion proteins from the endogenous loci to determine the subcellular localisation of every gene in the Trypanosoma brucei genome. GO Cellular Component terms are manually assigned by curators studying fluorescence microscope images of the resulting cells labelled with mNeonGreen fusion proteins. As trypanosomes are a pathogenic basal eukaryote, this will indicate likely function of both highly conserved eukaryote genes and parasite-specific genes. Resource URL: http://www.tryptag.org Protein subcellular localisation images can be viewed on the Tryptag website, e.g. http://www.tryptag.org?id=Tb927.8.1550","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"TrypTag","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Gene Ontology annotation based on curation of genome-wide subcellular localisation of proteins using fluorescent protein tagging in Trypanosoma brucei","uniquename":"GO_REF:0000109"}


id: PMID:27734801
data:
  {"abstract":"Many eukaryotes assemble a ring-shaped actomyosin network that contracts to drive cytokinesis. Unlike actomyosin in sarcomeres, which cycles through contraction and relaxation, the cytokinetic ring disassembles during contraction through an unknown mechanism. Here we find in  Schizosaccharomyces japonicus  and  Schizosaccharomyces pombe  that, during actomyosin ring contraction, actin filaments associated with actomyosin rings are expelled as micron-scale bundles containing multiple actomyosin ring proteins. Using functional isolated actomyosin rings we show that expulsion of actin bundles does not require continuous presence of cytoplasm. Strikingly, mechanical compression of actomyosin rings results in expulsion of bundles predominantly at regions of high curvature. Our work unprecedentedly reveals that the increased curvature of the ring itself promotes its disassembly. It is likely that such a curvature-induced mechanism may operate in disassembly of other contractile networks.","alleles_by_uniquename":{},"annotation_curators":[{"annotation_count":2,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-07-09","authors":"Huang J, Chew TG, Gu Y, Palani S, Kamnev A, Martin DS, Carter NJ, Cross RA, Oliferenko S, Balasubramanian MK","authors_abbrev":"Huang J et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-07-09 15:10:46","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-07-09 15:10:46","canto_session_key":"f47401f00ac444e0","canto_session_submitted_date":"2021-07-09 15:10:39","canto_triage_status":"Curatable","citation":"Elife 2016 10 13;5","cv_annotations":{"cellular_component":[{"annotations":[115210],"is_not":false,"summary":null,"term":"GO:0032432"},{"annotations":[115209],"is_not":false,"summary":null,"term":"GO:0005826"}]},"doi":"10.7554/eLife.21383","gene_count":1,"genes_by_uniquename":{"SJAG_04887":null},"genotypes_by_uniquename":{},"ltp_gene_count":1,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2016","pubmed_entrez_date":"2016-10-14","pubmed_publication_date":"13 10 2016","terms_by_termid":{"GO:0005826":null,"GO:0032432":null},"title":"Curvature-induced expulsion of actomyosin bundles during cytokinetic ring contraction.","uniquename":"PMID:27734801"}


id: PMID: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:20618870
data:
  {"abstract":"The genus Schizosaccharomyces is presently comprised of three species, namely Schizosaccharomyces pombe, Schizosaccharomyces octosporus and Schizosaccharomyces japonicus. Here, we describe a hitherto unknown species, Schizosaccharomyces cryophilus, named for its preference for growth at lower temperatures than the other fission yeast species. Although morphologically similar to S. octosporus, analysis of several rapidly evolving sequences, including the D1/D2 divergent domain of the large subunit (LSU) rRNA gene, the RNA subunit of RNAse P and the internal transcribed spacer elements, revealed significant divergence from any previously characterized Schizosaccharomyces strain. Based on phylogenetic analysis of the D1/D2 domain of the LSU rRNA gene, S. octosporus is the closest known relative of S. cryophilus, with the sequences of the two species differing by 25 nucleotide substitutions (>4%). Sequencing of the S. cryophilus genome and phylogenetic analysis of all 1 : 1 protein orthologs confirmed this observation, and together with morphological and physiological characterization, supports the assignment of S. cryophilus as a new species within the genus Schizosaccharomyces. The type strain of the new species is NRRL Y-48691(T) (=NBRC 106824(T)=CBS 11777(T)).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Helston RM, Box JA, Tang W, Baumann P","authors_abbrev":"Helston RM et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Phylogeny and evolutionary studies","citation":"FEMS Yeast Res 2010 Sep;10(6):779-86","cv_annotations":{},"doi":"10.1111/j.1567-1364.2010.00657.x","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2010","pubmed_entrez_date":"2010-07-13","pubmed_publication_date":"Sep 2010","terms_by_termid":{},"title":"Schizosaccharomyces cryophilus sp. nov., a new species of fission yeast.","uniquename":"PMID:20618870"}


id: PMID: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:27697163
data:
  {"abstract":"The present work demonstrates that yeasts belonging to the Schizosaccharomyces genus release a high quantity of polysaccharides of cell wall origin starting from the onset of the alcoholic fermentation. By the end of the alcoholic fermentation, all of the Schizosaccharomyces yeast strains released a quantity of polysaccharides approximately 3-7 times higher than that released by a commercial Saccharomyces cerevisiae yeast strain under the same fermentative conditions of synthetic juice. A higher content of polysaccharide was found in media fermented by Schizosaccharomyces japonicus with respect to that of Schizosaccharomyces pombe. Some of the strains evaluated were also able to produce high levels of pyruvic acid, which has been shown to be an important compound for color stability of wine. The presence of strains with different malic acid consumption patterns along with high polysaccharide release would enable production of naturally modified wines with enhanced mouth feel and reduced acidity. The chemical analysis of the released polysaccharides demonstrated divergence between the two yeast species S. pombe and S. japonicus. A different mannose/galactose ratio and a different percentage of proteins was observed on the polysaccharides released by S. pombe as compared to S. japonicus. Analysis of the proteins released in the media revealed the presence of a glycoprotein with a molecular size around 32-33 kDa only for the species S. japonicus. Mass spectrometry analysis of carbohydrate moieties showed similar proportions among the N-glycan chains released in the media by both yeast species but differences between the two species were also observed. These observations suggest a possible role of rapid MALDI-TOF screening of N-glycans compositional fingerprint as a taxonomic tool for this genus. Polysaccharides release in the media, in particular galactomannoproteins in significant amounts, could make these yeasts particularly interesting also for the industrial production of exogenous polysaccharide preparations.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Domizio P, Liu Y, Bisson LF, Barile D","authors_abbrev":"Domizio P et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"Food Microbiol 2017 Feb;61:136-149","cv_annotations":{},"doi":"10.1016/j.fm.2016.08.010","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2017","pubmed_entrez_date":"2016-10-05","pubmed_publication_date":"Feb 2017","terms_by_termid":{},"title":"Cell wall polysaccharides released during the alcoholic fermentation by Schizosaccharomyces pombe and S. japonicus: quantification and characterization.","uniquename":"PMID:27697163"}


id: PMID:26896847
data:
  {"abstract":"Evolution provides the unifying framework with which to understand biology. The coherent investigation of genic and genomic data often requires comparative genomics analyses based on whole-genome alignments, sets of homologous genes and other relevant datasets in order to evaluate and answer evolutionary-related questions. However, the complexity and computational requirements of producing such data are substantial: this has led to only a small number of reference resources that are used for most comparative analyses. The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained elements are obtained. Gene alignments are used to define Ensembl Protein Families, GeneTrees and homologies for both protein-coding and non-coding RNA genes. These resources are updated frequently and have a consistent informatics infrastructure and data presentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views. The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here is relevant to these projects. The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. We use robust software and pipelines to produce reference comparative data and make it freely available. Database URL: http://www.ensembl.org.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Herrero J, Muffato M, Beal K, Fitzgerald S, Gordon L, Pignatelli M, Vilella AJ, Searle SM, Amode R, Brent S, Spooner W, Kulesha E, Yates A, Flicek P","authors_abbrev":"Herrero J et al.","canto_curator_role":"JaponicusDB","citation":"Database (Oxford) 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id: GO_REF:0000088
data:
  {"abstract":"We have created a standard template for classes defining a protein complex by a molecular function as a cellular component. The underlying equivalence axiom template is \"GO:0043234 and 'capable_of' some ?A\", where A is a molecular function.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of protein complex by molecular function in the Gene Ontology","uniquename":"GO_REF:0000088"}


id: 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":[115222,115223],"is_not":false,"summary":null,"term":"GO:0006744"},{"annotations":[115221],"is_not":false,"summary":null,"term":"GO:0006743"}],"molecular_function":[{"annotations":[115220],"is_not":false,"summary":null,"term":"GO:0002083"},{"annotations":[115218,115219],"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: GO_REF:0000047
data:
  {"abstract":"This describes a method for supplying a NOT-qualified, IKR-evidenced GO annotation to a gene product, when general sequence homology considerations would suggest a function or location, or a role in a biological process, but where a curator has determined that the absence of key sequence residues, known to be required for an expected activity or location, indicating the gene product is unlikely to be able to carry out the implied activity, involvement in a process or cellular component location. This reference should only be used used when an IKR-evidenced annotation is made based on curator judgement from manually reviewing the sequence of the gene product and where no publication can be found to support the curators conclusion. It is preferable to cite a peer-reviewed publication (such as a PubMed identifier) for IKR-evidenced annotations whenever possible. Curators will have carefully reviewed the sequence of the annotated protein, and established that the key residues known to be required for an expected activity or location are not present. Inclusion of an identifier in the 'with/from' field, that highlights to the user the lacking residues(e.g. an alignment, domain or rule identifier) is absolutely required when annotating to IKR with this GO_REF. Documentation on the GOC website provides more details on the <a href = \"http://www.geneontology.org/GO.evidence.shtml#ikr\">correct use of the IKR evidence code</a>.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO curators","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Gene Ontology annotation based on absence of key sequence residues.","uniquename":"GO_REF:0000047"}


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


id: 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":[115573],"is_not":false,"summary":null,"term":"GO:0070762"},{"annotations":[115574],"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:2226803
data:
  {"abstract":"In the fission yeast Schizosaccharomyces pombe, the enzyme RNAse P copurifies with two RNAs, K1- and K2-RNA, which are identical except for their termini [1] and which are encoded by a single gene [2]. We have undertaken the cloning of the K-RNA genes in related organisms in order to gain comparative structural information. Because the K-RNA sequence is poorly conserved across species, we have cloned the K-RNA genes in the Schizosaccharomyces species S. malidevorans, S. japonicus, S. versatilis, and S. octosporus. Of the 4 species, only S. octosporus contains a K-RNA gene different from that in S. pombe; the gene diverges by 20%. Based on the two sequences, nuclease protection data and computer analysis, we have proposed a secondary structure model for the K-RNA. Northern analysis shows the K-RNA genes in all four Schizosaccharomyces species to be expressed as two RNAs, as in S. pombe.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Zimmerly S, Gamulin V, Burkard U, Söll D","authors_abbrev":"Zimmerly S et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Sequence feature or region","citation":"FEBS Lett 1990 Oct 01;271(1-2):189-93","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1990","pubmed_entrez_date":"1990-10-01","pubmed_publication_date":"01 Oct 1990","terms_by_termid":{},"title":"The RNA component of RNase P in Schizosaccharomyces species.","uniquename":"PMID:2226803"}


id: PMID:27678009
data:
  {"abstract":"The cAMP cascade plays an important role in several biological processes. Thus, study of its molecular details can contribute to a better understanding of these processes, treatment of diseases, or even finding antifungal drug targets. To gain further information about the PKA pathway, and its evolutionarily conserved and species-specific features, the central regulator pka1 gene, which encodes the cAMP-dependent protein kinase catalytic subunit, was studied in the less known haplontic, dimorphic fission yeast Schizosaccharomyces japonicus. Namely, this species belongs to a highly divergent phylogenetic branch of fungi. Furthermore, S. japonicus had only a single copy pka1 gene in contrast to the budding yeasts. Therefore, the pka1 deleted mutant was created, whose RNA sequencing and phenotypic studies revealed that the Pka1 regulated at least 373 genes, among them further kinases, phosphatases and transcriptional regulators. It regulated elongation of hyphae, cell size, aging and stress response. Furthermore, half of the pka1 target genes seemed to be conserved in Schizosaccharomyces pombe and S. japonicus. However, there were oppositely regulated genes in the two closely related species. The target genes suggest that this single gene must be able to fulfill all the functions of TPK1-3 of Saccharomyces cerevisiae. Thus, our results shed light on certain similarities and differences of the PKA pathway of S. japonicus compared to the budding yeasts and confirmed the multifunctionality of the pka1 gene, but further experiments are needed to prove its involvement in the metabolic processes and transport.","alleles_by_uniquename":{"SJAG_04312:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04312","name":"pka1delta","uniquename":"SJAG_04312:allele-1"}},"annotation_curators":[{"annotation_count":6,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-07-07","authors":"Papp L, Sipiczki M, Miklós I","authors_abbrev":"Papp L et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-07-07 12:57:27","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-07-07 12:57:27","canto_session_key":"9dc3302039d46818","canto_session_submitted_date":"2021-07-07 12:56:39","canto_triage_status":"Curatable","citation":"Curr Genet 2017 Jun;63(3):487-497","cv_annotations":{"single_locus_phenotype":[{"annotations":[115371],"is_not":false,"summary":null,"term":"FYPO:0007773"},{"annotations":[115370],"is_not":false,"summary":null,"term":"FYPO:0001122"},{"annotations":[115372],"is_not":false,"summary":null,"term":"FYPO:0000245"},{"annotations":[115374],"is_not":false,"summary":null,"term":"FYPO:0000097"},{"annotations":[115373],"is_not":false,"summary":null,"term":"FYPO:0000087"},{"annotations":[115375],"is_not":false,"summary":null,"term":"FYPO:0001214"}]},"doi":"10.1007/s00294-016-0651-x","gene_count":1,"genes_by_uniquename":{"SJAG_04312":null},"genotypes_by_uniquename":{"pka1delta":{"display_name":"pka1delta","display_uniquename":"pka1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04312:allele-1","expression":"Null"}]}]}},"ltp_gene_count":1,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2017","pubmed_entrez_date":"2016-09-29","pubmed_publication_date":"Jun 2017","terms_by_termid":{"FYECO:0000004":null,"FYECO:0000005":null,"FYECO:0000102":null,"FYECO:0000137":null,"FYPO:0000087":null,"FYPO:0000097":null,"FYPO:0000245":null,"FYPO:0001122":null,"FYPO:0001214":null,"FYPO:0007773":null,"FYPO_EXT:0000002":null,"FYPO_EXT:0000003":null},"title":"Expression pattern and phenotypic characterization of the mutant strain reveals target genes and processes regulated by pka1 in the dimorphic fission yeast Schizosaccharomyces japonicus.","uniquename":"PMID:27678009"}


id: PMID:11504450
data:
  {"abstract":"We compared the effects of four quaternary benzo[c]phenanthridine alkaloids--chelerythrine, chelilutine, sanguinarine, and sanguilutine--and two quaternary protoberberine alkaloids-berberine and coptisine--on the human cell line HeLa (cervix carcinoma cells) and the yeasts Saccharomyces cerevisiae and Schizosaccharomyces japonicus var. versatilis. The ability of alkaloids to display primary fluorescence, allowed us to record their dynamics and localization in cells. Cytotoxic, anti-microtubular, and anti-actin effects in living cells were studied. In the yeasts, neither microtubules nor cell growth was seriously affected even at the alkaloid concentration of 100 microg/ml. The HeLa cells, however, responded to the toxic effect of alkaloids at concentrations ranging from 1 to 50 microg/ml. IC50 values for individual alkaloids were: sanguinarine IC50 = 0.8 microg/ml, sanguilutine IC50 = 8.3 microg/ml, chelerythrine IC50 = 6.2 microg/ml, chelilutine IC50 = 5.2 microg/ml, coptisine IC50 = 2.6 microg/ml and berberine IC50 > 10.0 microg/ml. In living cells, sanguinarine produced a decrease in microtubule numbers, particularly at the cell periphery, at a concentration of 0.1 microg/ml. The other alkaloids showed a similar effect but at higher concentrations (5-50 microg/ml). The strongest effects of sanguinarine were explained as a consequence of its easy penetration through the cell membrane owing to nonpolar pseudobase formation and to a high degree of molecular planarity.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Slaninová I, Táborská E, Bochoráková H, Slanina J","authors_abbrev":"Slaninová I et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Cell composition or WT feature","citation":"Cell Biol Toxicol 2001;17(1):51-63","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2001","pubmed_entrez_date":"2001-08-16","pubmed_publication_date":"2001","terms_by_termid":{},"title":"Interaction of benzo[c]phenanthridine and protoberberine alkaloids with animal and yeast cells.","uniquename":"PMID:11504450"}


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":[115511,115512],"is_not":false,"summary":null,"term":"MOD:00046"}],"biological_process":[{"annotations":[115523],"is_not":false,"summary":null,"term":"GO:0090158"},{"annotations":[115525],"is_not":false,"summary":null,"term":"GO:0019915"},{"annotations":[115524],"is_not":false,"summary":null,"term":"GO:0071763"}],"cellular_component":[{"annotations":[115508],"is_not":false,"summary":null,"term":"GO:0005654"}],"single_locus_phenotype":[{"annotations":[115517,115520],"is_not":false,"summary":null,"term":"FYPO:0006054"},{"annotations":[115522],"is_not":false,"summary":null,"term":"FYPO:0005957"},{"annotations":[115504,115505,115507,115516,115519],"is_not":false,"summary":null,"term":"FYPO:0001784"},{"annotations":[115502,115503,115506,115510,115515,115518],"is_not":false,"summary":null,"term":"FYPO:0001556"},{"annotations":[115514,115521],"is_not":false,"summary":null,"term":"FYPO:0006945"},{"annotations":[115513],"is_not":false,"summary":null,"term":"FYPO:0003751"},{"annotations":[115509],"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: GO_REF:0000081
data:
  {"abstract":"We have created a standard template for classes describing the formation of a plant structure as a biological process. The underlying equivalence axiom template is \"'anatomical structure formation involved in morphogenesis' and 'results in formation of' some P\", where P is a plant anatomical entity (PO:0025131).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of plant formation as biological process in the Gene Ontology","uniquename":"GO_REF:0000081"}


id: PMID:12527786
data:
  {"abstract":"The fission yeasts are members of the fungal order Schizosaccharomycetales, a candidate deep-diverging group within Ascomycota. Although a great deal of molecular information is available from Schizosaccharomyces pombe, a model eukaryote, very little is available from other members of this group. In order to better characterize mitochondrial genome evolution in this fungal lineage, the mitochondrial DNA (mtDNA) of two additional fission yeasts, Schizosaccharomyces octosporus and Schizosaccharomyces japonicus var. japonicus, was sequenced. Whereas the mtDNA of S.pombe is only 19 431 bp, the mtDNA of S.octosporus is 44 227 bp, and that of S.japonicus var. japonicus is over 80 kb. The size variation of these mtDNAs is due largely to non-coding regions. The gene content in the latter two mtDNAs is almost identical to that of the completely sequenced S.pombe mtDNA, which encodes 25 tRNA species, the large and small mitochondrial ribosomal RNAs (rnl and rns), the RNA component of mitochondrial RNaseP (rnpB), mitochondrial small subunit ribosomal protein 3 (rps3), cytochrome oxidase subunits 1, 2 and 3 (cox1, cox2 and cox3) and ATP-synthase subunits 6, 8 and 9 (atp6, atp8 and atp9). However, trnI2(cau) (C modified to lysidine) is absent in the S.octosporus mtDNA, as are corresponding ATA codons in its protein-coding genes, and rps3 and rnpB are not found in the mtDNA of S.japonicus var. japonicus. The mtDNA of S.octosporus contains five double hairpin elements, the first report of these elements in an ascomycete. This study provides further evidence in favor of the mobility of these elements, and supports their role in mitochondrial genome rearrangement. The results of our phylogenetic analysis support the monophyly of the Schizosaccharomycetales, but question their grouping within the Archiascomycota.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Bullerwell CE, Leigh J, Forget L, Lang BF","authors_abbrev":"Bullerwell CE et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Sequence feature or region","citation":"Nucleic Acids Res 2003 Jan 15;31(2):759-68","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2003","pubmed_entrez_date":"2003-01-16","pubmed_publication_date":"15 Jan 2003","terms_by_termid":{},"title":"A comparison of three fission yeast mitochondrial genomes.","uniquename":"PMID:12527786"}


id: PMID:25866389
data:
  {"abstract":"Strategies to position the division apparatus exhibit a bewildering diversity [1], but how these mechanisms evolve remains virtually unknown. Here, we explore the plasticity of division site positioning in fission yeasts Schizosaccharomyces pombe and Schizosaccharomyces japonicus. We demonstrate that, whereas both species divide in the middle, only S. pombe uses the anillin Mid1 as a primary nucleus-derived cue to assemble the actomyosin ring at the equatorial cortex. We trace this variance to the divergence in subcellular targeting of Mid1 and show that duplication of an ancestral anillin early in the Schizosaccharomyces lineage may have led to subfunctionalization of the Mid1 orthologs. In contrast to S. pombe, medial assembly of the actomyosin ring in mitotic S. japonicus relies on the cortical anchor protein Cdc15 regulated by the tip-localized kinase Pom1. Our data suggest that division site placement is determined by cortical positioning of the actomyosin-plasma membrane linkers and that both identity of the linker and control of its subcellular targeting are highly modular.","alleles_by_uniquename":{"SJAG_00118:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00118","name":"mid2delta","uniquename":"SJAG_00118:allele-1"},"SJAG_01143:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01143","name":"mid1delta","uniquename":"SJAG_01143:allele-1"},"SJAG_01143:allele-2":{"allele_type":"partial_amino_acid_deletion","description":"711-723","gene_uniquename":"SJAG_01143","name":"mid1-delta(711-723 a.a.)","uniquename":"SJAG_01143:allele-2"},"SJAG_02392:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02392","name":"pom1delta","uniquename":"SJAG_02392:allele-1"},"SJAG_03596:allele-1":{"allele_type":"amino_acid_mutation","description":"L264P,P442T","gene_uniquename":"SJAG_03596","name":"cdc15-A","uniquename":"SJAG_03596:allele-1"},"SJAG_04332:allele-1":{"allele_type":"amino_acid_mutation","description":"I30T,T572P","gene_uniquename":"SJAG_04332","name":"cdc25-D9","uniquename":"SJAG_04332:allele-1"}},"annotation_curators":[{"annotation_count":3,"community_curator":false,"file_name":null,"file_type":null,"name":"Val Wood","orcid":"0000-0001-6330-7526"},{"annotation_count":34,"community_curator":true,"file_name":null,"file_type":null,"name":"Ying Gu","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-05-12","authors":"Gu Y, Yam C, Oliferenko S","authors_abbrev":"Gu Y et al.","canto_added_date":"2021-05-10 02:37:54","canto_annotation_status":"APPROVED","canto_approved_date":"2021-05-16 08:31:49","canto_approver_orcid":"0000-0001-6330-7526","canto_curator_name":"Ying Gu","canto_curator_role":"community","canto_first_approved_date":"2021-05-12 14:24:14","canto_session_key":"bc986e831d627df1","canto_session_submitted_date":"2021-05-14 13:43:22","canto_triage_status":"Curatable","citation":"Curr Biol 2015 May 04;25(9):1187-94","cv_annotations":{"biological_process":[{"annotations":[115254],"is_not":false,"summary":null,"term":"GO:1902408"},{"annotations":[115255],"is_not":false,"summary":null,"term":"GO:1903617"},{"annotations":[115253],"is_not":true,"summary":null,"term":"GO:1902408"}],"cellular_component":[{"annotations":[115261,115262],"is_not":false,"summary":null,"term":"GO:0051286"},{"annotations":[115257,115259,115264,115266],"is_not":false,"summary":null,"term":"GO:1990753"},{"annotations":[115258,115260,115263,115265,115267],"is_not":false,"summary":null,"term":"GO:0110085"}],"multi_locus_phenotype":[{"annotations":[115245],"is_not":false,"summary":null,"term":"FYPO:0000231"},{"annotations":[115249],"is_not":false,"summary":null,"term":"FYPO:0005503"},{"annotations":[115251],"is_not":false,"summary":null,"term":"FYPO:0007177"},{"annotations":[115250],"is_not":false,"summary":null,"term":"FYPO:0000729"},{"annotations":[115247],"is_not":false,"summary":null,"term":"FYPO:0003946"},{"annotations":[115246],"is_not":false,"summary":null,"term":"FYPO:0000118"}],"qualitative_gene_expression":[{"annotations":[115237,115256],"is_not":false,"summary":null,"term":"PomGeneEx:0000011"}],"single_locus_phenotype":[{"annotations":[115238],"is_not":false,"summary":null,"term":"FYPO:0000231"},{"annotations":[115269,115270],"is_not":false,"summary":null,"term":"FYPO:0000731"},{"annotations":[115243],"is_not":false,"summary":null,"term":"FYPO:0005503"},{"annotations":[115240,115241,115248,115252],"is_not":false,"summary":null,"term":"FYPO:0007177"},{"annotations":[115271],"is_not":false,"summary":null,"term":"FYPO:0002026"},{"annotations":[115268],"is_not":false,"summary":null,"term":"FYPO:0003535"},{"annotations":[115239],"is_not":false,"summary":null,"term":"FYPO:0000729"},{"annotations":[115242],"is_not":false,"summary":null,"term":"FYPO:0007701"},{"annotations":[115235,115236],"is_not":false,"summary":null,"term":"FYPO:0000118"},{"annotations":[115244],"is_not":false,"summary":null,"term":"FYPO:0000644"}]},"doi":"10.1016/j.cub.2015.02.056","gene_count":8,"genes_by_uniquename":{"SJAG_00118":null,"SJAG_01143":null,"SJAG_01665":null,"SJAG_02392":null,"SJAG_03596":null,"SJAG_03703":null,"SJAG_04332":null,"SJAG_04498":null},"genotypes_by_uniquename":{"cdc15-A-L264P,P442T-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"cdc15-A(L264P,P442T aa)","display_uniquename":"cdc15-A-L264P,P442T-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03596:allele-1","expression":"Not assayed or wild type"}]}]},"cdc15-A-L264P,P442T-amino_acid_mutation-expression-not_assayed_or_wild_type__mid1delta":{"display_name":"cdc15-A(L264P,P442T aa) mid1delta","display_uniquename":"cdc15-A-L264P,P442T-amino_acid_mutation-expression-not_assayed_or_wild_type__mid1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03596:allele-1","expression":"Not assayed or wild type"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_01143:allele-1","expression":"Null"}]}]},"cdc25-D9-I30T,T572P-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"cdc25-D9(I30T,T572P aa)","display_uniquename":"cdc25-D9-I30T,T572P-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04332:allele-1","expression":"Not assayed or wild type"}]}]},"mid1-delta(711-723_a.a.)-711-723-partial_amino_acid_deletion-expression-not_assayed_or_wild_type":{"display_name":"mid1-delta(711-723 a.a.)(aa)","display_uniquename":"mid1-delta(711-723_a.a.)-711-723-partial_amino_acid_deletion-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01143:allele-2","expression":"Not assayed or wild type"}]}]},"mid1delta":{"display_name":"mid1delta","display_uniquename":"mid1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01143:allele-1","expression":"Null"}]}]},"mid1delta__mid2delta":{"display_name":"mid1delta mid2delta","display_uniquename":"mid1delta__mid2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01143:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_00118:allele-1","expression":"Null"}]}]},"mid1delta__pom1delta":{"display_name":"mid1delta pom1delta","display_uniquename":"mid1delta__pom1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01143:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_02392:allele-1","expression":"Null"}]}]},"mid2delta":{"display_name":"mid2delta","display_uniquename":"mid2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00118:allele-1","expression":"Null"}]}]},"pom1delta":{"display_name":"pom1delta","display_uniquename":"pom1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02392:allele-1","expression":"Null"}]}]}},"ltp_gene_count":8,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2015","pubmed_entrez_date":"2015-04-14","pubmed_publication_date":"04 May 2015","terms_by_termid":{"FYECO:0000004":null,"FYECO:0000005":null,"FYECO:0000137":null,"FYECO:0000162":null,"FYPO:0000118":null,"FYPO:0000231":null,"FYPO:0000644":null,"FYPO:0000729":null,"FYPO:0000731":null,"FYPO:0002026":null,"FYPO:0003535":null,"FYPO:0003946":null,"FYPO:0005503":null,"FYPO:0007177":null,"FYPO:0007701":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null,"GO:0000085":null,"GO:0000087":null,"GO:0051286":null,"GO:0051325":null,"GO:0051329":null,"GO:0110085":null,"GO:1902408":null,"GO:1903617":null,"GO:1990753":null,"PomGeneEx:0000011":null},"title":"Rewiring of cellular division site selection in evolution of fission yeasts.","uniquename":"PMID:25866389"}


id: PMID:33947067
data:
  {"abstract":"The fission yeast  Schizosaccharomyces japonicus , comprising  S. japonicus  var.  japonicus  and  S. japonicus  var.  versatilis  varieties, has unique characteristics such as striking hyphal growth not seen in other  Schizosaccharomyces  species; however, information on its diversity and evolution, in particular mating and sporulation, remains limited. Here we compared the growth and mating phenotypes of 17 wild strains of  S. japonicus , including eight  S. japonicus  var.  japonicus  strains newly isolated from an insect ( Drosophila ). Unlike existing wild strains isolated from fruits/plants, the strains isolated from  Drosophila  sporulated at high frequency even under nitrogen-abundant conditions. In addition, one of the strains from  Drosophila  was stained by iodine vapor, although the type strain of  S. japonicus  var.  japonicus  is not stained. Sequence analysis further showed that the nucleotide and amino acid sequences of pheromone-related genes have diversified among the eight strains from  Drosophila , suggesting crossing between  S. japonicus  cells of different genetic backgrounds occurs frequently in this insect. Much of yeast ecology remains unclear, but our findings suggest that insects such as  Drosophila  might be a good niche for mating and sporulation, and will provide a basis for the understanding of sporulation mechanisms via signal transduction, as well as the ecology and evolution of yeast.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Seike T, Sakata N, Matsuda F, Furusawa C","authors_abbrev":"Seike 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 Fungi (Basel) 2021 Apr 29;7(5)","cv_annotations":{},"doi":"10.3390/jof7050350","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":"2021-05-05","pubmed_publication_date":"29 Apr 2021","terms_by_termid":{},"title":"Elevated Sporulation Efficiency in Fission Yeast  Schizosaccharomyces japonicus  Strains Isolated from  Drosophila .","uniquename":"PMID:33947067"}


id: PMID:30726171
data:
  {"abstract":"Many fungal species are dimorphic, exhibiting both unicellular yeast-like and filamentous forms. Schizosaccharomyces japonicus, a member of the fission yeast clade, is one such dimorphic fungus. Here, we first identify fruit extracts as natural, stress-free, starvation-independent inducers of filamentation, which we use to describe the properties of the dimorphic switch. During the yeast-to-hypha transition, the cell evolves from a bipolar to a unipolar system with 10-fold accelerated polarized growth but constant width, vacuoles segregated to the nongrowing half of the cell, and hyper-lengthening of the cell. We demonstrate unusual features of S. japonicus hyphae: these cells lack a Spitzenkörper, a vesicle distribution center at the hyphal tip, but display more rapid cytoskeleton-based transport than the yeast form, with actin cables being essential for the transition. S. japonicus hyphae also remain mononuclear and undergo complete cell divisions, which are highly asymmetric: one daughter cell inherits the vacuole, the other the growing tip. We show that these elongated cells scale their nuclear size, spindle length, and elongation rates, but display altered division size controls. This establishes S. japonicus as a unique system that switches between symmetric and asymmetric modes of growth and division.","alleles_by_uniquename":{"SJAG_02392:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02392","name":"pom1delta","uniquename":"SJAG_02392:allele-1"},"SJAG_02695:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02695","name":"tip1delta","uniquename":"SJAG_02695:allele-1"},"SJAG_04703:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04703","name":"for3delta","uniquename":"SJAG_04703:allele-1"}},"annotation_curators":[{"annotation_count":21,"community_curator":true,"file_name":null,"file_type":null,"name":"Sophie Martin","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-06-16","authors":"Kinnaer C, Dudin O, Martin SG","authors_abbrev":"Kinnaer C et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-06-16 18:49:31","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Sophie Martin","canto_curator_role":"community","canto_first_approved_date":"2021-06-16 18:49:31","canto_session_key":"bf05a60cb09b4cdb","canto_session_submitted_date":"2021-06-04 10:25:08","canto_triage_status":"Curatable","citation":"Mol Biol Cell 2019 04 01;30(8):975-991","cv_annotations":{"cellular_component":[{"annotations":[115169],"is_not":false,"summary":null,"term":"GO:0051286"},{"annotations":[115151,115153,115155,115157,115159,115161],"is_not":false,"summary":null,"term":"GO:0035838"},{"annotations":[115170],"is_not":false,"summary":null,"term":"GO:0085039"},{"annotations":[115152,115154,115156,115158,115160,115162],"is_not":false,"summary":null,"term":"GO:0001411"},{"annotations":[115163],"is_not":false,"summary":null,"term":"GO:0035371"},{"annotations":[115164],"is_not":false,"summary":null,"term":"GO:0030133"}],"single_locus_phenotype":[{"annotations":[115166],"is_not":false,"summary":null,"term":"FYPO:0003315"},{"annotations":[115167],"is_not":false,"summary":null,"term":"FYPO:0001355"},{"annotations":[115171],"is_not":false,"summary":null,"term":"FYPO:0007801"},{"annotations":[115168],"is_not":false,"summary":null,"term":"FYPO:0004293"},{"annotations":[115165],"is_not":false,"summary":null,"term":"FYPO:0001956"}]},"doi":"10.1091/mbc.E18-12-0774","gene_count":9,"genes_by_uniquename":{"SJAG_01196":null,"SJAG_02392":null,"SJAG_02695":null,"SJAG_03011":null,"SJAG_03625":null,"SJAG_03915":null,"SJAG_04624":null,"SJAG_04703":null,"SJAG_04960":null},"genotypes_by_uniquename":{"for3delta":{"display_name":"for3delta","display_uniquename":"for3delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04703:allele-1","expression":"Null"}]}]},"pom1delta":{"display_name":"pom1delta","display_uniquename":"pom1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02392:allele-1","expression":"Null"}]}]},"tip1delta":{"display_name":"tip1delta","display_uniquename":"tip1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02695:allele-1","expression":"Null"}]}]}},"ltp_gene_count":9,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2019","pubmed_entrez_date":"2019-02-07","pubmed_publication_date":"01 04 2019","terms_by_termid":{"FYPO:0001355":null,"FYPO:0001956":null,"FYPO:0003315":null,"FYPO:0004293":null,"FYPO:0007801":null,"GO:0001411":null,"GO:0030133":null,"GO:0035371":null,"GO:0035838":null,"GO:0051286":null,"GO:0085039":null},"title":"Yeast-to-hypha transition of Schizosaccharomyces japonicus in response to environmental stimuli.","uniquename":"PMID:30726171"}


id: PMID:30664646
data:
  {"abstract":"Cells of a specific cell type may divide within a certain size range. Yet, functionally optimal cellular organization is typically maintained across different cell sizes, a phenomenon known as scaling. The mechanisms underlying scaling and its physiological significance remain elusive. Here we approach this problem by interfering with scaling in the rod-shaped fission yeast Schizosaccharomyces japonicus that relies on cellular geometry cues to position the division site. We show that S. japonicus uses the Cdc42 polarity module to adjust its geometry to changes in the cell size. When scaling is prevented resulting in abnormal cellular length-to-width aspect ratio, cells exhibit severe division site placement defects. We further show that despite the generally accepted view, a similar scaling phenomenon can occur in the sister species, Schizosaccharomyces pombe. Our results demonstrate that scaling is required for normal cell function and delineate possible rules for cellular geometry maintenance in populations of proliferating cells.","alleles_by_uniquename":{"SJAG_00028:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00028","name":"rga6delta","uniquename":"SJAG_00028:allele-1"},"SJAG_00514:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00514","name":"scd1delta","uniquename":"SJAG_00514:allele-1"},"SJAG_03048:allele-1":{"allele_type":"amino_acid_mutation","description":"G146D","gene_uniquename":"SJAG_03048","name":"cdc2-1w","uniquename":"SJAG_03048:allele-1"},"SJAG_03581:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03581","name":"gef1delta","uniquename":"SJAG_03581:allele-1"},"SJAG_04280:allele-1":{"allele_type":"amino_acid_mutation","description":"T582G","gene_uniquename":"SJAG_04280","name":"wee1-as8","uniquename":"SJAG_04280:allele-1"},"SJAG_04280:allele-2":{"allele_type":"amino_acid_mutation","description":"G788E","gene_uniquename":"SJAG_04280","name":"wee1-G788E","uniquename":"SJAG_04280:allele-2"},"SJAG_04522:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04522","name":"rga4delta","uniquename":"SJAG_04522:allele-1"}},"annotation_curators":[{"annotation_count":3,"community_curator":false,"file_name":null,"file_type":null,"name":"Val Wood","orcid":"0000-0001-6330-7526"},{"annotation_count":22,"community_curator":true,"file_name":null,"file_type":null,"name":"Ying Gu","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-07-02","authors":"Gu Y, Oliferenko S","authors_abbrev":"Gu Y et al.","canto_added_date":"2021-05-10 02:37:31","canto_annotation_status":"APPROVED","canto_approved_date":"2021-09-01 07:53:28","canto_approver_orcid":"0000-0001-6330-7526","canto_curator_name":"Ying Gu","canto_curator_role":"community","canto_first_approved_date":"2021-07-02 12:32:27","canto_session_key":"0922e2a5229110bd","canto_session_submitted_date":"2021-06-30 22:18:13","canto_triage_status":"Curatable","citation":"Nat Commun 2019 01 21;10(1):268","cv_annotations":{"biological_process":[{"annotations":[115194],"is_not":false,"summary":null,"term":"GO:0061171"},{"annotations":[115195,115196],"is_not":false,"summary":null,"term":"GO:0008360"}],"multi_locus_phenotype":[{"annotations":[115182,115187],"is_not":false,"summary":null,"term":"FYPO:0007783"},{"annotations":[115193],"is_not":false,"summary":null,"term":"FYPO:0004105"},{"annotations":[115184],"is_not":false,"summary":null,"term":"FYPO:0001369"},{"annotations":[115186],"is_not":false,"summary":null,"term":"FYPO:0004293"}],"single_locus_phenotype":[{"annotations":[115188],"is_not":false,"summary":null,"term":"FYPO:0000198"},{"annotations":[115189,115190,115192],"is_not":false,"summary":null,"term":"FYPO:0005503"},{"annotations":[115183],"is_not":false,"summary":null,"term":"FYPO:0007783"},{"annotations":[115177],"is_not":false,"summary":null,"term":"FYPO:0004105"},{"annotations":[115191],"is_not":false,"summary":null,"term":"FYPO:0002870"},{"annotations":[115185],"is_not":false,"summary":null,"term":"FYPO:0001369"},{"annotations":[115178],"is_not":false,"summary":null,"term":"FYPO:0001234"},{"annotations":[115172,115173,115176],"is_not":false,"summary":null,"term":"FYPO:0000648"},{"annotations":[115174,115175,115181],"is_not":false,"summary":null,"term":"FYPO:0001877"},{"annotations":[115179,115180],"is_not":false,"summary":null,"term":"FYPO:0006616"}]},"doi":"10.1038/s41467-018-08218-2","gene_count":8,"genes_by_uniquename":{"SJAG_00028":null,"SJAG_00030":null,"SJAG_00514":null,"SJAG_01794":null,"SJAG_03048":null,"SJAG_03581":null,"SJAG_04280":null,"SJAG_04522":null},"genotypes_by_uniquename":{"cdc2-1w-G146D-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"cdc2-1w(G146D aa)","display_uniquename":"cdc2-1w-G146D-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03048:allele-1","expression":"Not assayed or wild type"}]}]},"gef1delta":{"display_name":"gef1delta","display_uniquename":"gef1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03581:allele-1","expression":"Null"}]}]},"rga4delta":{"display_name":"rga4delta","display_uniquename":"rga4delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04522:allele-1","expression":"Null"}]}]},"rga4delta__rga6delta":{"display_name":"rga4delta rga6delta","display_uniquename":"rga4delta__rga6delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04522:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_00028:allele-1","expression":"Null"}]}]},"rga4delta__wee1-G788E-G788E-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"rga4delta wee1-G788E(aa)","display_uniquename":"rga4delta__wee1-G788E-G788E-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04522:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_04280:allele-2","expression":"Not assayed or wild type"}]}]},"rga4delta__wee1-as8-T582G-amino_acid_mutation-expression-not_assayed_or_wild_type":{"display_name":"rga4delta wee1-as8(T582G aa)","display_uniquename":"rga4delta__wee1-as8-T582G-amino_acid_mutation-expression-not_assayed_or_wild_type","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04522:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_04280:allele-1","expression":"Not assayed or wild 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id: GO_REF:0000113
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id: GO_REF:0000028
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id: GO_REF:0000033
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id: PMID:25361970
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  {"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:9884240
data:
  {"abstract":"Fission yeast cells grow by extension at the ends (poles) and divide by transverse fission. It has previously been reported that Schizosaccharomyces japonicus var. japonicus can switch to unipolar, filamentous growth. Here it is shown that the yeast-to-mycelium transition is a gradual process involving a changeover to unipolar growth associated with asymmetric divisions, the development of large polarly located vacuoles, the modifications of the actin and microtubular cytoskeleton and the repression of cell separation after division. High concentrations of glucose in the medium or supplementation of the medium with caffeine or cAMP support the bipolar yeast phase, inhibit the transition to the mycelial phase and induce the conversion of hyphae to yeasts. These effects suggest that cAMP may be involved in the regulation of dimorphism. Temperatures below 18 degrees C or over 35 degrees C are restrictive for the mycelial phase and provoke a return to yeast phase.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-10-07","authors":"Sipiczki M, Takeo K, Grallert A","authors_abbrev":"Sipiczki M et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-10-07 12:31:51","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-10-07 12:31:51","canto_session_key":"5ac54d09f220d215","canto_session_submitted_date":"2021-09-30 09:01:47","canto_triage_status":"Curatable","citation":"Microbiology (Reading) 1998 Dec;144 ( Pt 12):3475-3485","cv_annotations":{},"doi":"10.1099/00221287-144-12-3475","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"1998","pubmed_entrez_date":"1999-01-12","pubmed_publication_date":"Dec 1998","terms_by_termid":{},"title":"Growth polarity transitions in a dimorphic fission yeast.","uniquename":"PMID:9884240"}


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


id: 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: 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: GO_REF:0000036
data:
  {"abstract":"The Gene Ontology Consortium uses the IC (Inferred by Curator) evidence code when an annotation cannot be supported by any direct evidence, but can be inferred by GO annotations that have been annotated to the same gene/gene product identifier in conjunction with the curator's knowledge of biology (supporting GO annotations must not be IC-evidenced). In many cases an IC-evidenced annotation simply applies the same reference that was used in the supporting GO annotation.  The use of IC evidence code in an annotation with reference GO_REF:0000036 signifies a curator inferred the GO term based on evidence from multiple sources of evidence/GO annotations. The 'with/from' field in these annotations will therefore supply more than one GO identifier, obtained from the set of supporting GO annotations assigned to the same gene/gene product identifier which cite publicly-available references.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO Annotation working group","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Manual annotations that require more than one source of functional data to support the assignment of the associated GO term","uniquename":"GO_REF:0000036"}


id: PMID:36695178
data:
  {"abstract":"Nuclear envelope (NE) expansion must be controlled to maintain nuclear shape and function. The nuclear membrane expands massively during closed mitosis, enabling chromosome segregation within an intact NE. Phosphatidic acid (PA) and diacylglycerol (DG) can both serve as biosynthetic precursors for membrane lipid synthesis. How they are regulated in time and space and what the implications are of changes in their flux for mitotic fidelity are largely unknown. Using genetically encoded PA and DG probes, we show that DG is depleted from the inner nuclear membrane during mitosis in the fission yeast Schizosaccharomyces pombe, but PA does not accumulate, indicating that it is rerouted to membrane synthesis. We demonstrate that DG-to-PA conversion catalyzed by the diacylglycerol kinase Dgk1 (also known as Ptp4) and direct glycerophospholipid synthesis from DG by diacylglycerol cholinephosphotransferase/ethanolaminephosphotransferase Ept1 reinforce NE expansion. We conclude that DG consumption through both the de novo pathway and the Kennedy pathway fuels a spike in glycerophospholipid biosynthesis, controlling NE expansion and, ultimately, mitotic fidelity.","alleles_by_uniquename":{"SJAG_04883:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04883","name":"ptp4delta","uniquename":"SJAG_04883:allele-1"}},"annotation_curators":[{"annotation_count":1,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2023-03-02","authors":"Foo S, Cazenave-Gassiot A, Wenk MR, Oliferenko S","authors_abbrev":"Foo S et al.","canto_added_date":"2023-03-02 10:54:59","canto_annotation_status":"APPROVED","canto_approved_date":"2023-03-02 10:59:33","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2023-03-02 10:59:33","canto_session_key":"d8cda300a89f71aa","canto_session_submitted_date":"2023-03-02 10:59:20","canto_triage_status":"Curatable","citation":"J Cell Sci 2023 Feb 01;136(3)","cv_annotations":{"single_locus_phenotype":[{"annotations":[115343],"is_not":false,"summary":null,"term":"FYPO:0001007"}]},"doi":"10.1242/jcs.260568","gene_count":1,"genes_by_uniquename":{"SJAG_04883":null},"genotypes_by_uniquename":{"ptp4delta":{"display_name":"ptp4delta","display_uniquename":"ptp4delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04883:allele-1","expression":"Null"}]}]}},"ltp_gene_count":1,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2023","pubmed_entrez_date":"2023-01-25","pubmed_publication_date":"01 Feb 2023","terms_by_termid":{"FYECO:0000005":null,"FYECO:0000137":null,"FYPO:0001007":null},"title":"Diacylglycerol at the inner nuclear membrane fuels nuclear envelope expansion in closed mitosis.","uniquename":"PMID:36695178"}


id: PMID:32243490
data:
  {"abstract":"The nuclear envelope (NE) undergoes dynamic remodeling to maintain NE integrity, a process involving the inner nuclear membrane protein LEM2 recruiting CHMP7/Cmp7 and then ESCRT-III. However, prior work has hinted at CHMP7/ESCRT-independent mechanisms. To identify such mechanisms, we studied NE assembly in Schizosaccharomyces japonicus, a fission yeast that undergoes partial mitotic NE breakdown and reassembly. S. japonicus cells lacking Cmp7 have compromised NE sealing after mitosis but are viable. A genetic screen identified mutations that promote NE integrity in cmp7Δ cells. Unexpectedly, loss of Lem2 or its interacting partner Nur1 suppressed cmp7Δ defects. In the absence of Cmp7, Lem2 formed aggregates that appear to interfere with ESCRT-independent NE sealing. A gain-of-function mutation implicated a membrane and ESCRT-III regulator, Alx1, in this alternate pathway. Additional results suggest a potentially general role for unsaturated fatty acids in NE integrity. These findings establish the existence of mechanisms for NE sealing independent of the canonical ESCRT pathway.","alleles_by_uniquename":{"SJAG_01242:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01242","name":"vps32delta","uniquename":"SJAG_01242:allele-1"},"SJAG_01745:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_01745","name":"lem2delta","uniquename":"SJAG_01745:allele-1"},"SJAG_03891:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03891","name":"alx1delta","uniquename":"SJAG_03891:allele-1"},"SJAG_05207:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_05207","name":"cmp7delta","uniquename":"SJAG_05207:allele-1"}},"annotation_curators":[{"annotation_count":21,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"},{"annotation_count":4,"community_curator":false,"file_name":null,"file_type":null,"name":"Val Wood","orcid":"0000-0001-6330-7526"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-07-09","authors":"Lee IJ, Stokasimov E, Dempsey N, Varberg JM, Jacob E, Jaspersen SL, Pellman D","authors_abbrev":"Lee IJ et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-07-14 11:10:55","canto_approver_orcid":"0000-0001-6330-7526","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-07-09 15:55:25","canto_session_key":"e134ba05c345c3f5","canto_session_submitted_date":"2021-07-09 15:55:19","canto_triage_status":"Curatable","citation":"J Cell Biol 2020 06 01;219(6)","cv_annotations":{"biological_process":[{"annotations":[115366,115367,115368,115369],"is_not":false,"summary":null,"term":"GO:0007084"}],"cellular_component":[{"annotations":[115365],"is_not":false,"summary":null,"term":"GO:0005783"},{"annotations":[115351,115353,115363],"is_not":false,"summary":null,"term":"GO:0044732"},{"annotations":[115352,115354,115362],"is_not":false,"summary":null,"term":"GO:0005635"}],"single_locus_phenotype":[{"annotations":[115355],"is_not":false,"summary":null,"term":"FYPO:0001375"},{"annotations":[115360],"is_not":false,"summary":null,"term":"FYPO:0000080"},{"annotations":[115356,115357,115364],"is_not":false,"summary":null,"term":"FYPO:0007772"},{"annotations":[115361],"is_not":false,"summary":null,"term":"FYPO:0000714"},{"annotations":[115358,115359],"is_not":false,"summary":null,"term":"FYPO:0001234"}]},"doi":"10.1083/jcb.201908232","gene_count":6,"genes_by_uniquename":{"SJAG_01050":null,"SJAG_01242":null,"SJAG_01745":null,"SJAG_03891":null,"SJAG_03943":null,"SJAG_05207":null},"genetic_interactions":[[{"gene_a_uniquename":"SJAG_01242","gene_b_uniquename":"SJAG_01050","interaction_type":"Phenotypic Suppression"},[{"reference_uniquename":"PMID:32243490","throughput":"low"}]],[{"gene_a_uniquename":"SJAG_05207","gene_b_uniquename":"SJAG_01745","interaction_type":"Phenotypic Suppression"},[{"reference_uniquename":"PMID:32243490","throughput":"low"}]],[{"gene_a_uniquename":"SJAG_01242","gene_b_uniquename":"SJAG_01745","interaction_type":"Phenotypic Suppression"},[{"reference_uniquename":"PMID:32243490","throughput":"low"}]],[{"gene_a_uniquename":"SJAG_01242","gene_b_uniquename":"SJAG_03891","interaction_type":"Phenotypic Enhancement"},[{"reference_uniquename":"PMID:32243490","throughput":"low"}]],[{"gene_a_uniquename":"SJAG_05207","gene_b_uniquename":"SJAG_03943","interaction_type":"Dosage Rescue"},[{"reference_uniquename":"PMID:32243490","throughput":"low"}]],[{"gene_a_uniquename":"SJAG_01745","gene_b_uniquename":"SJAG_01050","interaction_type":"Phenotypic Suppression"},[{"reference_uniquename":"PMID:32243490","throughput":"low"}]]],"genotypes_by_uniquename":{"alx1delta":{"display_name":"alx1delta","display_uniquename":"alx1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03891:allele-1","expression":"Null"}]}]},"cmp7delta":{"display_name":"cmp7delta","display_uniquename":"cmp7delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_05207:allele-1","expression":"Null"}]}]},"lem2delta":{"display_name":"lem2delta","display_uniquename":"lem2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01745:allele-1","expression":"Null"}]}]},"vps32delta":{"display_name":"vps32delta","display_uniquename":"vps32delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_01242:allele-1","expression":"Null"}]}]}},"ltp_gene_count":6,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2020","pubmed_entrez_date":"2020-04-04","pubmed_publication_date":"01 06 2020","terms_by_termid":{"FYECO:0000006":null,"FYPO:0000080":null,"FYPO:0000714":null,"FYPO:0001234":null,"FYPO:0001375":null,"FYPO:0007772":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000003":null,"GO:0005635":null,"GO:0005783":null,"GO:0007084":null,"GO:0044732":null},"title":"Factors promoting nuclear envelope assembly independent of the canonical ESCRT pathway.","uniquename":"PMID:32243490"}


id: GO_REF:0000044
data:
  {"abstract":"Transitive assignment of GO terms based on the UniProtKB/Swiss-Prot Subcellular Location vocabulary. UniProtKB Subcellular Location is a controlled vocabulary used to supply subcellular location information to UniProtKB entries in the SUBCELLULAR LOCATION lines. Terms from this vocabulary are annotated manually to UniProtKB/Swiss-Prot entries but are automatically assigned to UniProtKB/TrEMBL entries from the underlying nucleic acid databases and/or by the UniProt automatic annotation program.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"UniProt-GOA","canto_curator_role":"JaponicusDB","cv_annotations":{"cellular_component":[{"annotations":[65278],"is_not":false,"summary":null,"term":"GO:0001725"}]},"gene_count":1,"genes_by_uniquename":{"SJAG_01739":null},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{"GO:0001725":null},"title":"Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt. ","uniquename":"GO_REF:0000044"}


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


id: PMID:28342076
data:
  {"abstract":"Environmental glucose is an important regulator of biological processes, as it can launch different cell processes depending on its concentration. Thus, low glucose concentration can induce entry into quiescence, which ensures long-term viability for the cells or in other cases mycelial growth in the dimorphic species, which, in turn, provides the cells with fresh nutrients. Several genes, such as the genes of cAMP cascade, are involved in glucose sensing and response. Since this signal transduction pathway seemed to be an evolutionarily conserved process, we assumed that its genes were also conserved and preserved their functional homology. To obtain evidence, Schizosaccharomyces pombe rsv1 and its orthologous genes were investigated using in silico and experimental approaches. Our results supported that the Rsv1 zinc-finger transcription factors of Schizosaccharomyces japonicus and Schizosaccharomyces octosporus and the Candida albicans cas5p were really functional homologues of the S. pombe Rsv1. Namely, the homologous proteins were able to restore mutant phenotype of the S. pombe rsv1-deleted cells. Bioinformatic anaysis revealed that the most conserved parts of the proteins always contained the C2H2 domains and the complementation abilities of the counterpart genes were not uniform regarding the investigated features, which can be in connection with the conserved regions outside C2H2.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Pataki E, Sipiczki M, Miklos I","authors_abbrev":"Pataki E et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Sequence feature or region","citation":"Curr Microbiol 2017 Jun;74(6):710-717","cv_annotations":{},"doi":"10.1007/s00284-017-1227-9","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2017","pubmed_entrez_date":"2017-03-26","pubmed_publication_date":"Jun 2017","terms_by_termid":{},"title":"Schizosaccharomyces pombe rsv1 Transcription Factor and its Putative Homologues Preserved their Functional Homology and are Evolutionarily Conserved.","uniquename":"PMID:28342076"}


id: PMID:22586155
data:
  {"abstract":"tRNA genes are interspersed throughout eukaryotic DNA, contributing to genome architecture and evolution in addition to translation of the transcriptome. Codon use correlates with tRNA gene copy number in noncomplex organisms including yeasts. Synonymous codons impact translation with various outcomes, dependent on relative tRNA abundances. Availability of whole-genome sequences allowed us to examine tRNA gene copy number variation (tgCNV) and codon use in four Schizosaccharomyces species and Saccharomyces cerevisiae. tRNA gene numbers vary from 171 to 322 in the four Schizosaccharomyces despite very high similarity in other features of their genomes. In addition, we performed whole-genome sequencing of several related laboratory strains of Schizosaccharomyces pombe and found tgCNV at a cluster of tRNA genes. We examined for the first time effects of wobble rules on correlation of tRNA gene number and codon use and showed improvement for S. cerevisiae and three of the Schizosaccharomyces species. In contrast, correlation in Schizosaccharomyces japonicus is poor due to markedly divergent tRNA gene content, and much worsened by the wobble rules. In japonicus, some tRNA iso-acceptor genes are absent and others are greatly reduced relative to the other yeasts, while genes for synonymous wobble iso-acceptors are amplified, indicating wobble use not apparent in any other eukaryote. We identified a subset of japonicus-specific wobbles that improves correlation of codon use and tRNA gene content in japonicus. We conclude that tgCNV is high among Schizo species and occurs in related laboratory strains of S. pombe (and expectedly other species), and tRNAome-codon analyses can provide insight into species-specific wobble decoding.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Iben JR, Maraia RJ","authors_abbrev":"Iben JR et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Sequence feature or region","citation":"RNA 2012 Jul;18(7):1358-72","cv_annotations":{},"doi":"10.1261/rna.032151.111","gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2012","pubmed_entrez_date":"2012-05-16","pubmed_publication_date":"Jul 2012","terms_by_termid":{},"title":"tRNAomics: tRNA gene copy number variation and codon use provide bioinformatic evidence of a new anticodon:codon wobble pair in a eukaryote.","uniquename":"PMID:22586155"}


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


id: 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: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":[68240],"is_not":false,"summary":null,"term":"GO:0003925"},{"annotations":[58966],"is_not":false,"summary":null,"term":"GO:0043864"},{"annotations":[65159],"is_not":false,"summary":null,"term":"GO:0052832"},{"annotations":[65160],"is_not":false,"summary":null,"term":"GO:0052833"},{"annotations":[68010],"is_not":false,"summary":null,"term":"GO:1990817"}]},"gene_count":4,"genes_by_uniquename":{"SJAG_02383":null,"SJAG_02721":null,"SJAG_03739":null,"SJAG_04509":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:1990817":null},"title":"Gene Ontology annotation based on Enzyme Commission mapping","uniquename":"GO_REF:0000003"}


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


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


id: PMID:24699070
data:
  {"abstract":"The post-cytokinetic separation of cells in cell-walled organisms involves enzymic processes that degrade a specific layer of the division septum and the region of the mother cell wall that edges the septum. In the fission yeast Schizosaccharomyces pombe, the 1,3-α-glucanase Agn1p, originally identified as a mutanase-like glycoside hydrolase family 71 (GH71) enzyme, dissolves the mother cell wall around the septum edge. Our search in the genomes of completely sequenced fungi identified GH71 hydrolases in Basidiomycota, Taphrinomycotina and Pezizomycotina, but not in Saccharomycotina. The most likely Agn1p orthologues in Pezizomycotina species are not mutanases having mutanase-binding domains, but experimentally non-characterized hypothetical proteins that have no carbohydrate-binding domains. The analysis of the GH71 domains corroborated the phylogenetic relationships of the Schizosaccharomyces species determined by previous studies, but suggested a closer relationship to the Basidiomycota proteins than to the Ascomycota proteins. In the Schizosaccharomyces genus, the Agn1p proteins are structurally conserved: their GH71 domains are flanked by N-terminal secretion signals and C-terminal sequences containing the conserved block YNFNA(Y)/HTG. The inactivation of the agn1(Sj) gene in Schizosaccharomyces japonicus, the only true dimorphic member of the genus, caused a severe cell-separation defect in its yeast phase, but had no effect on the hyphal growth and yeast-to-mycelium transition. It did not affect the mycelium-to-yeast transition either, only delaying the separation of the yeast cells arising from the fragmenting hyphae. The heterologous expression of agn1(Sj) partially rescued the separation defect of the agn1Δ cells of Schizosaccharomyces pombe. The results presented indicate that the fission yeast Agn1p 1,3-α-glucanases of Schizosaccharomyces japonicus and Schizosaccharomyces pombe share conserved functions in the yeast phase. ","alleles_by_uniquename":{"SJAG_03444:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_03444","name":"agn1delta","uniquename":"SJAG_03444:allele-1"}},"annotation_curators":[{"annotation_count":1,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"},{"annotation_count":1,"community_curator":false,"file_name":null,"file_type":null,"name":"Val Wood","orcid":"0000-0001-6330-7526"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-07-09","authors":"Sipiczki M, Balazs A, Monus A, Papp L, Horvath A, Sveiczer A, Miklos I","authors_abbrev":"Sipiczki M et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-09-01 07:35:20","canto_approver_orcid":"0000-0001-6330-7526","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2021-07-09 13:16:43","canto_session_key":"b8bc1733e6f2c600","canto_session_submitted_date":"2021-07-09 13:16:35","canto_triage_status":"Curatable","citation":"Microbiology (Reading) 2014 Jun;160(Pt 6):1063-1074","cv_annotations":{"biological_process":[{"annotations":[115448],"is_not":false,"summary":null,"term":"GO:0030995"}],"single_locus_phenotype":[{"annotations":[115447],"is_not":false,"summary":null,"term":"FYPO:0001971"}]},"doi":"10.1099/mic.0.077511-0","gene_count":1,"genes_by_uniquename":{"SJAG_03444":null},"genotypes_by_uniquename":{"agn1delta":{"display_name":"agn1delta","display_uniquename":"agn1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_03444:allele-1","expression":"Null"}]}]}},"ltp_gene_count":1,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2014","pubmed_entrez_date":"2014-04-05","pubmed_publication_date":"Jun 2014","terms_by_termid":{"FYPO:0001971":null,"GO:0030995":null},"title":"Phylogenetic and comparative functional analysis of the cell-separation α-glucanase Agn1p in Schizosaccharomyces.","uniquename":"PMID:24699070"}


id: PMID: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:31150379
data:
  {"abstract":"Quorum sensing (QS), a mechanism of microbial communication dependent on cell density, governs developmental decisions in many bacteria and in some pathogenic and non-pathogenic fungi including yeasts. In these simple eukaryotes this response is mediated by the release into the growth medium of quorum-sensing molecules (QSMs) whose concentration increases proportionally to the population density. To date the occurrence of QS is restricted to a few yeast species. We show that a QS mediated by the aromatic alcohols phenylethanol and tryptophol represses the dimorphic yeast to hypha differentiation in the fission yeast S. japonicus in response to an increased population density. In addition, the stress activated MAPK pathway (SAPK), which controls cell cycle progression and adaptation to environmental changes in this organism, constitutively represses yeast to hypha differentiation both at transcriptional and post-translational levels. Moreover, deletion of its main effectors Sty1 MAPK and Atf1 transcription factor partially suppressed the QS-dependent block of hyphal development under inducing conditions. RNAseq analysis showed that the expression of nrg1+, which encodes a putative ortholog of the transcription factor Nrg1 that represses yeast to hypha dimorphism in C. albicans, is downregulated both by QS and the SAPK pathway. Remarkably, Nrg1 may act in S. japonicus as an activator of hyphal differentiation instead of being a repressor. S. japonicus emerges as an attractive and amenable model organism to explore the QS mechanisms that regulate cellular differentiation in fungi.","alleles_by_uniquename":{"SJAG_00124:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00124","name":"SJAG_00124delta","uniquename":"SJAG_00124:allele-1"},"SJAG_00266:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_00266","name":"atf1delta","uniquename":"SJAG_00266:allele-1"},"SJAG_02013:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02013","name":"pyp1delta","uniquename":"SJAG_02013:allele-1"},"SJAG_02592:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_02592","name":"sty1delta","uniquename":"SJAG_02592:allele-1"}},"annotation_curators":[{"annotation_count":37,"community_curator":true,"file_name":null,"file_type":null,"name":"Elisa Gómez Gil","orcid":null}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-08-04","authors":"Gómez-Gil E, Franco A, Madrid M, Vázquez-Marín B, Gacto M, Fernández-Breis J, Vicente-Soler J, Soto T, Cansado J","authors_abbrev":"Gómez-Gil E et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-08-04 11:11:18","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Elisa Gómez Gil","canto_curator_role":"community","canto_first_approved_date":"2021-08-04 11:11:18","canto_session_key":"0da7a90b15f75d86","canto_session_submitted_date":"2021-08-03 17:26:10","canto_triage_status":"Curatable","citation":"PLoS Genet 2019 05;15(5):e1008192","cv_annotations":{"PSI-MOD":[{"annotations":[115649,115650,115651,115652],"is_not":false,"summary":null,"term":"MOD:00046"}],"multi_locus_phenotype":[{"annotations":[115677],"is_not":false,"summary":null,"term":"FYPO:0007779"}],"single_locus_phenotype":[{"annotations":[115645,115657],"is_not":false,"summary":null,"term":"FYPO:0004481"},{"annotations":[115673],"is_not":false,"summary":null,"term":"FYPO:0007778"},{"annotations":[115672,115675],"is_not":false,"summary":null,"term":"FYPO:0007776"},{"annotations":[115656],"is_not":false,"summary":null,"term":"FYPO:0000708"},{"annotations":[115674,115676],"is_not":false,"summary":null,"term":"FYPO:0007780"},{"annotations":[115678,115679],"is_not":false,"summary":null,"term":"FYPO:0007824"},{"annotations":[115643,115655],"is_not":false,"summary":null,"term":"FYPO:0001122"},{"annotations":[115667,115671],"is_not":false,"summary":null,"term":"FYPO:0007777"},{"annotations":[115666,115670],"is_not":false,"summary":null,"term":"FYPO:0007775"},{"annotations":[115665,115669],"is_not":false,"summary":null,"term":"FYPO:0007774"},{"annotations":[115668],"is_not":false,"summary":null,"term":"FYPO:0007779"},{"annotations":[115648,115660],"is_not":false,"summary":null,"term":"FYPO:0000097"},{"annotations":[115647,115659],"is_not":false,"summary":null,"term":"FYPO:0000726"},{"annotations":[115646,115658],"is_not":false,"summary":null,"term":"FYPO:0000271"},{"annotations":[115661],"is_not":false,"summary":null,"term":"FYPO:0000841"},{"annotations":[115644],"is_not":false,"summary":null,"term":"FYPO:0000280"},{"annotations":[115664],"is_not":false,"summary":null,"term":"FYPO:0000648"}]},"doi":"10.1371/journal.pgen.1008192","gene_count":4,"genes_by_uniquename":{"SJAG_00124":null,"SJAG_00266":null,"SJAG_02013":null,"SJAG_02592":null},"genotypes_by_uniquename":{"SJAG_00124delta":{"display_name":"SJAG_00124delta","display_uniquename":"SJAG_00124delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00124:allele-1","expression":"Null"}]}]},"SJAG_00124delta__sty1delta":{"display_name":"SJAG_00124delta sty1delta","display_uniquename":"SJAG_00124delta__sty1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00124:allele-1","expression":"Null"}]},{"expressed_alleles":[{"allele_uniquename":"SJAG_02592:allele-1","expression":"Null"}]}]},"atf1delta":{"display_name":"atf1delta","display_uniquename":"atf1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_00266:allele-1","expression":"Null"}]}]},"pyp1delta":{"display_name":"pyp1delta","display_uniquename":"pyp1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02013:allele-1","expression":"Null"}]}]},"sty1delta":{"display_name":"sty1delta","display_uniquename":"sty1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02592:allele-1","expression":"Null"}]}]}},"ltp_gene_count":4,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2019","pubmed_entrez_date":"2019-06-01","pubmed_publication_date":"05 2019","terms_by_termid":{"FYECO:0000004":null,"FYECO:0000078":null,"FYECO:0000137":null,"FYECO:0000207":null,"FYECO:0000272":null,"FYECO:0000314":null,"FYPO:0000097":null,"FYPO:0000271":null,"FYPO:0000280":null,"FYPO:0000648":null,"FYPO:0000708":null,"FYPO:0000726":null,"FYPO:0000841":null,"FYPO:0001122":null,"FYPO:0004481":null,"FYPO:0007774":null,"FYPO:0007775":null,"FYPO:0007776":null,"FYPO:0007777":null,"FYPO:0007778":null,"FYPO:0007779":null,"FYPO:0007780":null,"FYPO:0007824":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null,"FYPO_EXT:0000003":null,"GO:0034599":null,"GO:0034605":null,"GO:0071475":null,"GO:1904547":null,"MOD:00046":null},"title":"Quorum sensing and stress-activated MAPK signaling repress yeast to hypha transition in the fission yeast Schizosaccharomyces japonicus.","uniquename":"PMID:31150379"}


id: 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":[65161],"is_not":false,"summary":null,"term":"GO:0006021"},{"annotations":[66653],"is_not":false,"summary":null,"term":"GO:0006782"},{"annotations":[57570],"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:0000065
data:
  {"abstract":"We have created a standard template for classes describing transport of a chemical entity (ChEBI) as a biological process. The underlying equivalence axiom template is \"GO:0006810 and 'transports or maintains localization of' some X\", where X is a chemical entity (CHEBI:24431). The approach to combine GO and ChEBI has been described in the following publication: PMID:23895341.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of transport of a chemical entity as a biological process in the Gene Ontology","uniquename":"GO_REF:0000065"}


id: 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":[115225],"is_not":false,"summary":null,"term":"GO:0101024"},{"annotations":[115230],"is_not":false,"summary":null,"term":"GO:0006998"}],"cellular_component":[{"annotations":[115229],"is_not":false,"summary":null,"term":"GO:0120321"}],"multi_locus_phenotype":[{"annotations":[115232],"is_not":false,"summary":null,"term":"FYPO:0000619"},{"annotations":[115231],"is_not":false,"summary":null,"term":"FYPO:0001489"}],"single_locus_phenotype":[{"annotations":[115233],"is_not":false,"summary":null,"term":"FYPO:0000619"},{"annotations":[115227],"is_not":false,"summary":null,"term":"FYPO:0003738"},{"annotations":[115234],"is_not":false,"summary":null,"term":"FYPO:0000815"},{"annotations":[115226],"is_not":false,"summary":null,"term":"FYPO:0000082"},{"annotations":[115228],"is_not":false,"summary":null,"term":"FYPO:0003976"},{"annotations":[115224],"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:37849458
data:
  {"abstract":"We previously demonstrated that we could hijack the fungal pheromone signaling pathway to provide a living yeast biosensor where peptide biomarkers were recognized by G-protein-coupled receptors and engineered to transcribe a readout. Here, we demonstrated that the protease could be reintroduced to the biosensor to provide a simple mechanism for distinguishing single-amino-acid changes in peptide ligands that, otherwise, would likely be difficult to detect using binding-based assays. We characterized the dose-response curves for five fungal pheromone G-protein-coupled receptors, peptides, and proteases -Saccharomyces cerevisiae ,  Candida albicans ,  Schizosaccharomyces pombe ,  Schizosaccharomyces octosporus , and  Schizosaccharomyces japonicus . Alanine scanning was carried out for the most selective of these- S. cerevisiae  and  C. albicans -with and without the protease. Two peptide variants were discovered, which showed diminished cleavage by the protease (CaPep2A and CaPep2A13A). Those peptides were then distinguished by utilizing the biosensor strains with and without the protease, which selectively cleaved and altered the apparent concentration of peptide required for half-maximal activation for 2 peptides-CaPep and CaPep13A, respectively-by more than one order of magnitude. These results support the hypothesis that the living yeast biosensor with a sequence-specific protease can translate single-amino-acid changes into more than one order of magnitude apparent shift in the concentration of peptide required for half-maximal activation. With further engineering by computational modeling and directed evolution, the biosensor could likely distinguish a wide variety of peptide sequences beyond the alanine scanning carried out here. In the future, we envision incorporating proteases into our living yeast biosensor for use as a point of care diagnostic, a scalable communication language, and other applications.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Crnković T, Bokor BJ, Lockwood ME, Cornish VW","authors_abbrev":"Crnković T et al.","canto_added_date":"2023-10-19 00:40:03","canto_curator_role":"JaponicusDB","canto_triage_status":"Method or reagent","citation":"Biodes Res 2023;5:0003","cv_annotations":{},"doi":"10.34133/bdr.0003","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":"2023-10-18","pubmed_publication_date":"2023","terms_by_termid":{},"title":"Peptide Variant Detection by a Living Yeast Biosensor via an Epitope-Selective Protease.","uniquename":"PMID:37849458"}


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"}


