# refs

id: PMID:27678009
data:
  {"abstract":"The cAMP cascade plays an important role in several biological processes. Thus, study of its molecular details can contribute to a better understanding of these processes, treatment of diseases, or even finding antifungal drug targets. To gain further information about the PKA pathway, and its evolutionarily conserved and species-specific features, the central regulator pka1 gene, which encodes the cAMP-dependent protein kinase catalytic subunit, was studied in the less known haplontic, dimorphic fission yeast Schizosaccharomyces japonicus. Namely, this species belongs to a highly divergent phylogenetic branch of fungi. Furthermore, S. japonicus had only a single copy pka1 gene in contrast to the budding yeasts. Therefore, the pka1 deleted mutant was created, whose RNA sequencing and phenotypic studies revealed that the Pka1 regulated at least 373 genes, among them further kinases, phosphatases and transcriptional regulators. It regulated elongation of hyphae, cell size, aging and stress response. Furthermore, half of the pka1 target genes seemed to be conserved in Schizosaccharomyces pombe and S. japonicus. However, there were oppositely regulated genes in the two closely related species. The target genes suggest that this single gene must be able to fulfill all the functions of TPK1-3 of Saccharomyces cerevisiae. Thus, our results shed light on certain similarities and differences of the PKA pathway of S. japonicus compared to the budding yeasts and confirmed the multifunctionality of the pka1 gene, but further experiments are needed to prove its involvement in the metabolic processes and transport.","alleles_by_uniquename":{"SJAG_04312:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04312","name":"pka1delta","uniquename":"SJAG_04312:allele-1"}},"annotation_curators":[{"annotation_count":6,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2021-07-07","authors":"Papp L, Sipiczki M, Miklós I","authors_abbrev":"Papp L et al.","canto_added_date":"2021-05-10 08:46:37","canto_annotation_status":"APPROVED","canto_approved_date":"2021-07-07 12:57:27","canto_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":[115455],"is_not":false,"summary":null,"term":"FYPO:0007773"},{"annotations":[115454],"is_not":false,"summary":null,"term":"FYPO:0001122"},{"annotations":[115456],"is_not":false,"summary":null,"term":"FYPO:0000245"},{"annotations":[115458],"is_not":false,"summary":null,"term":"FYPO:0000097"},{"annotations":[115457],"is_not":false,"summary":null,"term":"FYPO:0000087"},{"annotations":[115459],"is_not":false,"summary":null,"term":"FYPO:0001214"}]},"doi":"10.1007/s00294-016-0651-x","gene_count":1,"genes_by_uniquename":{"SJAG_04312":null},"genotypes_by_uniquename":{"pka1delta":{"display_name":"pka1delta","display_uniquename":"pka1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04312:allele-1","expression":"Null"}]}]}},"ltp_gene_count":1,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2017","pubmed_entrez_date":"2016-09-29","pubmed_publication_date":"Jun 2017","terms_by_termid":{"FYECO:0000004":null,"FYECO:0000005":null,"FYECO:0000102":null,"FYECO:0000137":null,"FYPO:0000087":null,"FYPO:0000097":null,"FYPO:0000245":null,"FYPO:0001122":null,"FYPO:0001214":null,"FYPO:0007773":null,"FYPO_EXT:0000002":null,"FYPO_EXT:0000003":null},"title":"Expression pattern and phenotypic characterization of the mutant strain reveals target genes and processes regulated by pka1 in the dimorphic fission yeast Schizosaccharomyces japonicus.","uniquename":"PMID:27678009"}


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


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


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


id: PMID:26263485
data:
  {"abstract":"Cytokinesis must be regulated in time and space in order to preserve genome integrity during cell proliferation and to allow daughter cells to adopt distinct fates and geometries during differentiation. The fission yeast Schizosaccharomyces pombe has been a popular model organism for understanding spatiotemporal regulation of cytokinesis in a symmetrically dividing cell. Recent work on another member of the same genus, Schisozaccharomyces japonicus, suggests that S. pombe may have evolved an unusual division site placement mechanism based on a recently duplicated anillin paralog. Here we discuss an extraordinary evolutionary plasticity of cytokinesis within the fission yeast clade and argue that the comparative cell biology approach may provide functional insights beyond those afforded by scrutinizing individual model species.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Gu Y, Oliferenko S","authors_abbrev":"Gu Y et al.","canto_added_date":"2023-05-04 00:40:04","canto_curator_role":"JaponicusDB","canto_triage_status":"Review or comment","citation":"Curr Opin Microbiol 2015 Dec;28:18-25","cv_annotations":{},"doi":"10.1016/j.mib.2015.07.011","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":"2015-08-12","pubmed_publication_date":"Dec 2015","terms_by_termid":{},"title":"Comparative biology of cell division in the fission yeast clade.","uniquename":"PMID:26263485"}


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


id: PMID:36058798
data:
  {"abstract":"Schizosaccharomyces japonicus is a dimorphic yeast, transiting between unicellular and hyphal growth. The glycoproteins of fission yeast contain, in addition to mannose (Man), a large number of galactose (Gal) residues. Previously, we reported that the cell-surface O-glycans of S. japonicus comprise mainly tri-saccharides (Gal-Man-Man) as a main component, in contrast to the tetra-saccharides observed in other Schizosaccharomyces species. Here we have investigated the function of cell-surface Gal residues in S. japonicus. Because disruption of gms1 + , encoding the UDP-Gal transporter required for galactomannan synthesis, abolishes cell-surface galactosylation in Schizosaccharomyces pombe, we constructed a deletion mutant of the homologous gene in S. japonicus gms1Δ [gms1 (S.j)] and determined the N- and O-linked oligosaccharide structures present on the cell surface. Disruption of gms1 (S.j) resulted in a complete lack of Gal on the cell surface, indicating that Gms1 plays an essential role in supplying UDP-Gal from the cytoplasm to the Golgi lumen. Analytical microscopy of gms1Δ demonstrated that the lack of cell-surface Gal did not affect cell growth or morphology during vegetative growth. However, hyphal development was blocked in gms1Δ, even in the presence of the topoisomerase I inhibitor camptothecin, which is known to induce hyphal differentiation in wild-type S. japonicus. Collectively, these findings show that Gal-containing oligosaccharides are required for cell wall integrity during filamentous growth in S. japonicus.","alleles_by_uniquename":{"SJAG_04697:allele-1":{"allele_type":"deletion","description":"deletion","gene_uniquename":"SJAG_04697","name":"gms1delta","uniquename":"SJAG_04697:allele-1"}},"annotation_curators":[{"annotation_count":6,"community_curator":false,"file_name":null,"file_type":null,"name":"Snezhana Oliferenko","orcid":"0000-0002-8138-6851"}],"annotation_details":{},"annotation_file_curators":[],"approved_date":"2022-12-01","authors":"Fukunaga T, Ohashi T, Tanaka Y, Yoshimatsu T, Higuchi Y, Maekawa H, Takegawa K","authors_abbrev":"Fukunaga T et al.","canto_added_date":"2022-11-25 12:12:27","canto_annotation_status":"APPROVED","canto_approved_date":"2022-12-01 10:35:53","canto_approver_orcid":"0000-0002-8138-6851","canto_curator_name":"Snezhana Oliferenko","canto_curator_role":"JaponicusDB","canto_first_approved_date":"2022-12-01 10:35:53","canto_session_key":"465355706dc223a3","canto_session_submitted_date":"2022-11-25 12:49:07","canto_triage_status":"Curatable","citation":"J Biosci Bioeng 2022 Nov;134(5):384-392","cv_annotations":{"single_locus_phenotype":[{"annotations":[115425],"is_not":false,"summary":null,"term":"FYPO:0008029"},{"annotations":[115421],"is_not":false,"summary":null,"term":"FYPO:0000082"},{"annotations":[115424],"is_not":false,"summary":null,"term":"FYPO:0007776"},{"annotations":[115423],"is_not":false,"summary":null,"term":"FYPO:0007780"},{"annotations":[115420],"is_not":false,"summary":null,"term":"FYPO:0003727"},{"annotations":[115422],"is_not":false,"summary":null,"term":"FYPO:0000106"}]},"doi":"10.1016/j.jbiosc.2022.07.014","gene_count":1,"genes_by_uniquename":{"SJAG_04697":null},"genotypes_by_uniquename":{"gms1delta":{"display_name":"gms1delta","display_uniquename":"gms1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_04697:allele-1","expression":"Null"}]}]}},"ltp_gene_count":1,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2022","pubmed_entrez_date":"2022-09-04","pubmed_publication_date":"Nov 2022","terms_by_termid":{"FYECO:0000004":null,"FYECO:0000005":null,"FYECO:0000126":null,"FYECO:0000137":null,"FYECO:0000314":null,"FYPO:0000082":null,"FYPO:0000106":null,"FYPO:0003727":null,"FYPO:0007776":null,"FYPO:0007780":null,"FYPO:0008029":null,"FYPO_EXT:0000001":null,"FYPO_EXT:0000002":null},"title":"Galactosylation of cell-surface glycoprotein required for hyphal growth and cell wall integrity in Schizosaccharomyces japonicus.","uniquename":"PMID:36058798"}


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


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


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


id: GO_REF:0000071
data:
  {"abstract":"We have created a standard template for classes describing the response to and cellular response to a chemical entity (ChEBI) as a biological process. The underlying equivalence axiom templates are \"GO:0050896 and 'has input' some X\" (response to) and \"GO:0070887 and 'has input' some X\" (cellular response to), where X is a chemical entity (CHEBI:24431). The approach to combine GO and ChEBI has been described in the following publication: PMID:23895341.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of response to and cellular response to a chemical as biological process in the Gene Ontology","uniquename":"GO_REF:0000071"}


id: PMID: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":[115461,115462],"is_not":false,"summary":null,"term":"GO:0071483"}],"molecular_function":[{"annotations":[115460],"is_not":false,"summary":null,"term":"GO:0009882"}],"single_locus_phenotype":[{"annotations":[115463,115464],"is_not":false,"summary":null,"term":"FYPO:0008031"},{"annotations":[115465,115466],"is_not":false,"summary":null,"term":"FYPO:0008046"}]},"doi":"10.1128/EC.00109-13","gene_count":2,"genes_by_uniquename":{"SJAG_02860":null,"SJAG_05242":null},"genotypes_by_uniquename":{"wcs1delta":{"display_name":"wcs1delta","display_uniquename":"wcs1delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_02860:allele-1","expression":"Null"}]}]},"wcs2delta":{"display_name":"wcs2delta","display_uniquename":"wcs2delta","loci":[{"expressed_alleles":[{"allele_uniquename":"SJAG_05242:allele-1","expression":"Null"}]}]}},"ltp_gene_count":2,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2013","pubmed_entrez_date":"2013-07-23","pubmed_publication_date":"Sep 2013","terms_by_termid":{"FYECO:0000005":null,"FYECO:0000126":null,"FYPO:0008031":null,"FYPO:0008046":null,"FYPO_EXT:0000001":null,"GO:0009882":null,"GO:0071483":null},"title":"Synchronous activation of cell division by light or temperature stimuli in the dimorphic yeast Schizosaccharomyces japonicus.","uniquename":"PMID:23873862"}


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


id: 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":[115296],"is_not":false,"summary":null,"term":"GO:0051286"},{"annotations":[115278,115280,115282,115284,115286,115288],"is_not":false,"summary":null,"term":"GO:0035838"},{"annotations":[115297],"is_not":false,"summary":null,"term":"GO:0085039"},{"annotations":[115279,115281,115283,115285,115287,115289],"is_not":false,"summary":null,"term":"GO:0001411"},{"annotations":[115290],"is_not":false,"summary":null,"term":"GO:0035371"},{"annotations":[115291],"is_not":false,"summary":null,"term":"GO:0030133"}],"single_locus_phenotype":[{"annotations":[115293],"is_not":false,"summary":null,"term":"FYPO:0003315"},{"annotations":[115294],"is_not":false,"summary":null,"term":"FYPO:0001355"},{"annotations":[115298],"is_not":false,"summary":null,"term":"FYPO:0007801"},{"annotations":[115295],"is_not":false,"summary":null,"term":"FYPO:0004293"},{"annotations":[115292],"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: GO_REF:0000105
data:
  {"abstract":"Gene Ontology annotation based on predicted cytoplasmic tRNAs using tRNAscan-SE analysis (doi: 10.1093/nar/25.5.0955) of the Drosophila melanogaster genome (2002). Annotations have been reviewed by FlyBase (2015) and found to be consistent when compared with the most recent tRNAscan-SE analysis of the genome (http://gtrnadb.ucsc.edu/genomes/eukaryota/Dmela6/).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"FlyBase","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Gene Ontology annotation of transfer RNAs based on tRNAscan-SE analysis of the Drosophila melanogaster genome (2002).","uniquename":"GO_REF:0000105"}


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


id: 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:0000094
data:
  {"abstract":"We have created a standard template for classes describing the development of a metazoan structure as a biological process. The underlying equivalence axiom template is \"'anatomical structure development' and 'results in development of' some E\", where E is a anatomical entity (UBERON:0001062).","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GO ontology editors","canto_curator_role":"JaponicusDB","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"terms_by_termid":{},"title":"Representation of metazoan development as biological process in the Gene Ontology","uniquename":"GO_REF:0000094"}


id: GO_REF:0000033
data:
  {"abstract":"The Phylogenetic ANnotation using Gene Ontology (PAN-GO) method annotates evolutionary trees from the PANTHER database with GO terms describing molecular function, biological process and cellular component. The GO terms are manually selected by a curator and used to annotate ancestral genes in the phylogenetic tree using the evidence code IBA (Inferred from Biological Ancestor). All supporting annotations must be based on experimental data from the scientific literature. The PAN-GO annotations are fully traceable from the data in the 'with/from' column of the annotation, which provides the PANTHER node ID (PTN) from which the annotation is derived, as well as all descendants sequences that support the annotation of the ancestral node. 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  {"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":[115721,115722],"is_not":false,"summary":null,"term":"GO:0006744"},{"annotations":[115720],"is_not":false,"summary":null,"term":"GO:0006743"}],"molecular_function":[{"annotations":[115718,115719],"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:0006743":null,"GO:0006744":null,"GO:0097269":null},"title":"Schizosaccharomyces japonicus has low levels of CoQ 10  synthesis, respiration deficiency, and efficient ethanol production.","uniquename":"PMID:29191091"}


id: PMID: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":[115449],"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:12402243
data:
  {"abstract":"The structure and localization of the microtubule organization centres (MTOCs) of the fission yeast Schizosaccharomyces japonicus var. japonicus were examined by fluorescence microscopy and electron microscopy. Spindle pole bodies (SPBs), which are the fungal equivalent of centrosomes, of Sz. japonicus were visualized by immunofluorescent staining using a monoclonal anti-gamma-tubulin antibody. The behaviour of the SPBs during the cell cycle mostly coincided with previous reports on the most widely used fission yeast Schizosaccharomyces pombe. We cloned the gamma-tubulin gene from Sz. japonicus by PCR using redundant sets of primers corresponding to conserved regions of known gamma-tubulins. The predicted amino acid sequence of Sz. japonicus gamma-tubulin was most similar to the Sz. pombe gamma-tubulin. Under the electron microscope, the SPBs of Sz. japonicus were detected as electron-dense multilayered structures located just outside the nuclear envelope. The SPBs of Sz. japonicus were composed of three electron-dense layers and were surrounded by fuzzy material. Each layer showed structural changes according to the progression of the cell cycle. In mitotic cells, the SPBs were located on the fenestrae of the nuclear envelopes through which the mitotic spindle microtubules ran into the nucleoplasm. Our results show that Sz. japonicus is a very potent and attractive organism for the investigation of the microtubule nucleation system and morphogenesis in yeasts. The Accession No. for the nucleotide sequence of the Sz. japonicus gtb1(+) gene is AF159163.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"Horio T, Kimura N, Basaki A, Tanaka Y, Noguchi T, Akashi T, Tanaka K","authors_abbrev":"Horio T et al.","canto_added_date":"2021-05-10 08:46:37","canto_curator_role":"JaponicusDB","canto_triage_status":"Sequence feature or region","citation":"Yeast 2002 Nov;19(15):1335-50","cv_annotations":{},"gene_count":0,"genes_by_uniquename":{},"genotypes_by_uniquename":{},"ltp_gene_count":0,"ortholog_annotations":[],"paralog_annotations":[],"physical_interactions":[],"publication_year":"2002","pubmed_entrez_date":"2002-10-29","pubmed_publication_date":"Nov 2002","terms_by_termid":{},"title":"Molecular and structural characterization of the spindle pole bodies in the fission yeast Schizosaccharomyces japonicus var japonicus.","uniquename":"PMID:12402243"}


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


id: GO_REF:0000107
data:
  {"abstract":"GO terms from a source species are projected onto one or more target species based on gene orthology obtained from Ensembl Compara. One-to-one, one-to-many and many-to-many orthology relations and anntations are transferred between orthologs that have at least a 40% peptide identity to each other. Only GO annotations with evidence codes ECO:0000314 (IDA), ECO:0000270 (IEP), ECO:0000316 (IGI), ECO:0000315 (IMP), and ECO:0000353 (IPI), or their descendants, are transferred; annotations with a 'NOT' qualifier are not transferred, and neither are annotations to GO:0005515 (protein binding). Annotations that are transferred using this method receive the evidence code ECO:0000265 (sequence orthology evidence used in automatic assertion), which maps up to the GO Inferred from Electronic Annotation (IEA) evidence code.  The model organism database identifier of the annotation source will be indicated in the 'With' column of the GOA association file.","alleles_by_uniquename":{},"annotation_curators":[],"annotation_details":{},"annotation_file_curators":[],"authors":"GOA 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