{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T16:03:16Z","timestamp":1779379396639,"version":"3.53.1"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Ustiloxins A and B are toxic cyclic tetrapeptides, Tyr-Val\/Ala-Ile-Gly (Y-V\/A-I-G), that were originally identified from Ustilaginoidea virens, a pathogenic fungus affecting rice plants. Contrary to our report that ustiloxin B is ribosomally synthesized in Aspergillus flavus, a recent report suggested that ustiloxins are synthesized by a non-ribosomal peptide synthetase in U.virens. Thus, we analyzed the U.virens genome, to identify the responsible gene cluster.<\/jats:p>\n               <jats:p>Results: The biosynthetic gene cluster was identified from the genome of U.virens based on homologies to the ribosomal peptide biosynthetic gene cluster for ustiloxin B identified from A.flavus. It contains a gene encoding precursor protein having five Tyr-Val-Ile-Gly and three Tyr-Ala-Ile-Gly motifs for ustiloxins A and B, respectively, strongly indicating that ustiloxins A and B from U.virens are ribosomally synthesized.<\/jats:p>\n               <jats:p>Availability and implementation: Accession codes of the U.virens and A.flavus gene clusters in NCBI are BR001221 and BR001206, respectively.<\/jats:p>\n               <jats:p>Contact: \u00a0umemura-m@aist.go.jp or asai@k.u-tokyo.ac.jp<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu753","type":"journal-article","created":{"date-parts":[[2014,11,21]],"date-time":"2014-11-21T01:18:58Z","timestamp":1416532738000},"page":"981-985","source":"Crossref","is-referenced-by-count":74,"title":["Ustiloxins, fungal cyclic peptides, are ribosomally synthesized in <i>Ustilaginoidea virens<\/i>"],"prefix":"10.1093","volume":"31","author":[{"given":"Takahiro","family":"Tsukui","sequence":"first","affiliation":[{"name":"1 Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan, 2Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido 062-8517, Japan, 3Fermlab Inc., Tokyo 135-0021, Japan, 4INTEC Inc., Tokyo 136-8637, Japan, and 5Department of Computational Biology, Graduate School of Frontier Sciences, the University of Tokyo, Chiba 277-8561, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nozomi","family":"Nagano","sequence":"additional","affiliation":[{"name":"1 Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan, 2Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido 062-8517, Japan, 3Fermlab Inc., Tokyo 135-0021, Japan, 4INTEC Inc., Tokyo 136-8637, Japan, and 5Department of Computational Biology, Graduate School of Frontier Sciences, the University of Tokyo, Chiba 277-8561, Japan"},{"name":"1 Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan, 2Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido 062-8517, Japan, 3Fermlab Inc., Tokyo 135-0021, Japan, 4INTEC Inc., Tokyo 136-8637, Japan, and 5Department of Computational Biology, Graduate School of Frontier Sciences, the University of Tokyo, Chiba 277-8561, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Myco","family":"Umemura","sequence":"additional","affiliation":[{"name":"1 Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan, 2Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido 062-8517, Japan, 3Fermlab Inc., Tokyo 135-0021, Japan, 4INTEC Inc., Tokyo 136-8637, Japan, and 5Department of Computational Biology, Graduate School of Frontier Sciences, the University of Tokyo, Chiba 277-8561, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Toshitaka","family":"Kumagai","sequence":"additional","affiliation":[{"name":"1 Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan, 2Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido 062-8517, Japan, 3Fermlab Inc., Tokyo 135-0021, Japan, 4INTEC Inc., Tokyo 136-8637, Japan, and 5Department of Computational Biology, Graduate School of Frontier Sciences, the University of Tokyo, Chiba 277-8561, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Goro","family":"Terai","sequence":"additional","affiliation":[{"name":"1 Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan, 2Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido 062-8517, Japan, 3Fermlab Inc., Tokyo 135-0021, Japan, 4INTEC Inc., Tokyo 136-8637, Japan, and 5Department of Computational Biology, Graduate School of Frontier Sciences, the University of Tokyo, Chiba 277-8561, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Masayuki","family":"Machida","sequence":"additional","affiliation":[{"name":"1 Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan, 2Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido 062-8517, Japan, 3Fermlab Inc., Tokyo 135-0021, Japan, 4INTEC Inc., Tokyo 136-8637, Japan, and 5Department of Computational Biology, Graduate School of Frontier Sciences, the University of Tokyo, Chiba 277-8561, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kiyoshi","family":"Asai","sequence":"additional","affiliation":[{"name":"1 Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan, 2Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido 062-8517, Japan, 3Fermlab Inc., Tokyo 135-0021, Japan, 4INTEC Inc., Tokyo 136-8637, Japan, and 5Department of Computational Biology, Graduate School of Frontier Sciences, the University of Tokyo, Chiba 277-8561, Japan"},{"name":"1 Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan, 2Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido 062-8517, Japan, 3Fermlab Inc., Tokyo 135-0021, Japan, 4INTEC Inc., Tokyo 136-8637, Japan, and 5Department of Computational Biology, Graduate School of Frontier Sciences, the University of Tokyo, Chiba 277-8561, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2014,11,19]]},"reference":[{"key":"2023051309143645400_btu753-B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023051309143645400_btu753-B2","doi-asserted-by":"crossref","first-page":"W204","DOI":"10.1093\/nar\/gkt449","article-title":"antiSMASH 2.0\u2014a versatile platform for genome mining of secondary metabolite producers","volume":"41","author":"Blin","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023051309143645400_btu753-B3","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1093\/bioinformatics\/16.3.190","article-title":"Homology-based gene structure prediction: simplified matching algorithm using a translated codon (tron) and improved accuracy by allowing for long gaps","volume":"16","author":"Gotoh","year":"2000","journal-title":"Bioinformatics"},{"key":"2023051309143645400_btu753-B4","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1093\/nar\/gki198","article-title":"MAFFT version 5: improvement in accuracy of multiple sequence alignment","volume":"33","author":"Katoh","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023051309143645400_btu753-B5","doi-asserted-by":"crossref","first-page":"4157","DOI":"10.1016\/S0040-4039(00)74677-6","article-title":"Ustiloxin: a phytotoxin and a mycotoxin from false smut balls on rice panicles","volume":"33","author":"Koiso","year":"1992","journal-title":"Tetrahedron Lett."},{"key":"2023051309143645400_btu753-B6","doi-asserted-by":"crossref","first-page":"765","DOI":"10.7164\/antibiotics.47.765","article-title":"Ustiloxins, antimitotic cyclic peptides from false smut balls on rice panicles caused by Ustilaginoidea virens","volume":"47","author":"Koiso","year":"1994","journal-title":"J. Antibiot. (Tokyo)"},{"key":"2023051309143645400_btu753-B7","doi-asserted-by":"crossref","first-page":"418","DOI":"10.7164\/antibiotics.51.418","article-title":"Isolation and structure of an antimitotic cyclic peptide, ustiloxin F: chemical interrelation with a homologous peptide, ustiloxin B","volume":"51","author":"Koiso","year":"1998","journal-title":"J. Antibiot. (Tokyo)"},{"key":"2023051309143645400_btu753-B8","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"Langmead","year":"2009","journal-title":"Genome Biol."},{"key":"2023051309143645400_btu753-B9","doi-asserted-by":"crossref","first-page":"1157","DOI":"10.1038\/nature04300","article-title":"Genome sequencing and analysis of Aspergillus oryzae","volume":"438","author":"Machida","year":"2005","journal-title":"Nature"},{"key":"2023051309143645400_btu753-B10","doi-asserted-by":"crossref","first-page":"bar009","DOI":"10.1093\/database\/bar009","article-title":"UniProt Knowledgebase: a hub of integrated protein data","volume":"2011","author":"Magrane","year":"2011","journal-title":"Database"},{"key":"2023051309143645400_btu753-B11","doi-asserted-by":"crossref","first-page":"2878","DOI":"10.1093\/bioinformatics\/bth315","article-title":"TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders","volume":"20","author":"Majoros","year":"2004","journal-title":"Bioinformatics"},{"key":"2023051309143645400_btu753-B12","doi-asserted-by":"crossref","first-page":"W339","DOI":"10.1093\/nar\/gkr466","article-title":"antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences","volume":"39","author":"Medema","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023051309143645400_btu753-B13","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/nbt.1754","article-title":"Integrative genomics viewer","volume":"29","author":"Robinson","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"2023051309143645400_btu753-B14","doi-asserted-by":"crossref","first-page":"e00071","DOI":"10.1128\/genomeA.00071-14","article-title":"Genome sequence of the mucoromycotina fungus Umbelopsis isabellina, an effective producer of lipids","volume":"2","author":"Takeda","year":"2014","journal-title":"Genome Announc."},{"key":"2023051309143645400_btu753-B15","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1093\/bioinformatics\/btp120","article-title":"TopHat: discovering splice junctions with RNA-Seq","volume":"25","author":"Trapnell","year":"2009","journal-title":"Bioinformatics"},{"key":"2023051309143645400_btu753-B16","doi-asserted-by":"crossref","first-page":"e84028","DOI":"10.1371\/journal.pone.0084028","article-title":"MIDDAS-M: motif-independent de novo detection of secondary metabolite gene clusters through the integration of genome sequencing and transcriptome data","volume":"8","author":"Umemura","year":"2013","journal-title":"PLoS One"},{"key":"2023051309143645400_btu753-B17","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/j.fgb.2014.04.011","article-title":"Characterization of the biosynthetic gene cluster for the ribosomally synthesized cyclic peptide ustiloxin B in Aspergillus flavus","volume":"68","author":"Umemura","year":"2014","journal-title":"Fungal Genet. Biol."},{"key":"2023051309143645400_btu753-B18","doi-asserted-by":"crossref","first-page":"1287","DOI":"10.1073\/pnas.1115983109","article-title":"Unveiling the biosynthetic puzzle of destruxins in Metarhizium species","volume":"109","author":"Wang","year":"2012","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"2023051309143645400_btu753-B20","doi-asserted-by":"crossref","first-page":"3849","DOI":"10.1038\/ncomms4849","article-title":"Specific adaptation of Ustilaginoidea virens in occupying host florets revealed by comparative and functional genomics","volume":"5","author":"Zhang","year":"2014","journal-title":"Nat. Commun."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/7\/981\/50306033\/bioinformatics_31_7_981.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/7\/981\/50306033\/bioinformatics_31_7_981.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,13]],"date-time":"2023-05-13T09:16:12Z","timestamp":1683969372000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/7\/981\/180410"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,11,19]]},"references-count":19,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2015,4,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu753","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,4,1]]},"published":{"date-parts":[[2014,11,19]]}}}