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Watanabe N, Mitsukuni K, Sato T, Zhang J, Ono A, Suzuki T. RNA-Seq analysis of the fruiting bodies and mycelia of angel-wing mushroom Pleurocybella porrigens that cause acute encephalopathy. BMC Res Notes 2024; 17:204. [PMID: 39049055 PMCID: PMC11270884 DOI: 10.1186/s13104-024-06860-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Accepted: 07/10/2024] [Indexed: 07/27/2024] Open
Abstract
OBJECTIVE In 2004, after consuming angel-wing mushrooms, Pleurocybella porrigens, 59 incidents of food poisoning were reported in Japan. Consequently, 17 individuals died of acute encephalopathy. In 2023, we proved that a lectin, pleurocybelline, and pleurocybellaziridine from this mushroom caused damage to the brains of mice. Although we reported genomic and transcriptomic data of P. porrigens in 2013, the assembly quality of the transcriptomic data was inadequate for accurate functional annotation. Thus, we obtained detailed transcriptomic data on the fruiting bodies and mycelia of this mushroom using Illumina NovaSeq 6000. RESULTS De novo assembly data indicated that the N50 lengths for the fruiting bodies and mycelia were improved compared with those previously reported. The differential expression analysis between the fruiting bodies and the mycelia revealed that 1,937 and 1,555 genes were significantly up-regulated in the fruiting bodies and the mycelia, respectively. The biological functions of P. porrigens transcripts, including PA biosynthetic pathways, were investigated using BLAST search, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes pathway analysis. The obtained results revealed L-valine, a predicted precursor of PA, is biosynthesized in the fruiting bodies and mycelia. Furthermore, real-time RT-PCR was performed to evaluate the accuracy of the results of differential expression analysis.
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Affiliation(s)
- Nozomu Watanabe
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, 321-8505, Japan
| | - Keisuke Mitsukuni
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, 321-8505, Japan
| | - Takumi Sato
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, 321-8505, Japan
| | - Jili Zhang
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, 321-8505, Japan
| | - Akiko Ono
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, 321-8505, Japan
- Faculty of Global Interdisciplinary Science and Innovation, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Tomohiro Suzuki
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, 321-8505, Japan.
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Possible molecular mechanism for acute encephalopathy by angel-wing mushroom ingestion – Involvement of three constituents in onset –. Toxicon 2023; 221:106958. [DOI: 10.1016/j.toxicon.2022.106958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/05/2022] [Accepted: 10/24/2022] [Indexed: 11/12/2022]
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Kawagishi H. Chemical elucidation of acute encephalopathy by ingestion of angel-wing mushroom (Pleurocybella porrigens) - involvement of three constituents in onset. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2023; 99:191-197. [PMID: 37518008 DOI: 10.2183/pjab.99.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/01/2023]
Abstract
The mushroom, Pleurocybella porrigens, is widely consumed in Japan; however, in autumn 2004, acute encephalopathy due to ingestion of the mushroom in a large group of patients was reported in Japan. We have continued working on the mushroom to clarify the mechanisms underlying the acute encephalopathy that occurred due to its consumption. The data collected to date have shown that three compounds, pleurocybelline (PC), a Pleurocybella porrigens lectin (PPL), and pleurocybellaziridine (PA), in the mushroom are potentially responsible for the onset of the disease; PC that exhibit lethal activity in mice and PPL formed a complex, and the complex of the two components exhibited proteolytic activity and disrupted the blood-brain barrier. Although PA was not isolated directly from the mushroom, the existence of this compound in the mushroom was predicted. The compound was chemically synthesized and its endogeneity in the mushroom was demonstrated. Furthermore, PA exhibited toxicity to oligodendrocytes.
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Affiliation(s)
- Hirokazu Kawagishi
- Faculty of Agriculture, Shizuoka University
- Research Institute for Mushroom Science, Shizuoka University
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Suzuki T. Genetic sequence analysis and characterization of bioactive compounds in mushroom-forming fungi. Biosci Biotechnol Biochem 2021; 85:8-12. [PMID: 33577662 DOI: 10.1093/bbb/zbaa067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 10/26/2020] [Indexed: 11/12/2022]
Abstract
Mushroom-forming fungi produce unique bioactive compounds that have potential applications as medicines, supplements, and agrochemicals. Thus, it is necessary to clarify the biosynthetic pathways of these compounds using genome and transcriptome analyses. This review introduces some of our research on bioactive compounds isolated from mushrooms, as well as genetic analysis with next-generation sequencing.
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Affiliation(s)
- Tomohiro Suzuki
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Japan
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He MQ, Zhao RL, Hyde KD, Begerow D, Kemler M, Yurkov A, McKenzie EHC, Raspé O, Kakishima M, Sánchez-Ramírez S, Vellinga EC, Halling R, Papp V, Zmitrovich IV, Buyck B, Ertz D, Wijayawardene NN, Cui BK, Schoutteten N, Liu XZ, Li TH, Yao YJ, Zhu XY, Liu AQ, Li GJ, Zhang MZ, Ling ZL, Cao B, Antonín V, Boekhout T, da Silva BDB, De Crop E, Decock C, Dima B, Dutta AK, Fell JW, Geml J, Ghobad-Nejhad M, Giachini AJ, Gibertoni TB, Gorjón SP, Haelewaters D, He SH, Hodkinson BP, Horak E, Hoshino T, Justo A, Lim YW, Menolli N, Mešić A, Moncalvo JM, Mueller GM, Nagy LG, Nilsson RH, Noordeloos M, Nuytinck J, Orihara T, Ratchadawan C, Rajchenberg M, Silva-Filho AGS, Sulzbacher MA, Tkalčec Z, Valenzuela R, Verbeken A, Vizzini A, Wartchow F, Wei TZ, Weiß M, Zhao CL, Kirk PM. Notes, outline and divergence times of Basidiomycota. FUNGAL DIVERS 2019. [DOI: 10.1007/s13225-019-00435-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
AbstractThe Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.
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Wakimoto T. Toward the Dark Matter of Natural Products. CHEM REC 2017; 17:1124-1134. [DOI: 10.1002/tcr.201700009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences; Hokkaido University; Kita 12, Nishi 6, Kita-ku Sapporo 060-0812 Japan
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Brereton NJB, Gonzalez E, Marleau J, Nissim WG, Labrecque M, Joly S, Pitre FE. Comparative Transcriptomic Approaches Exploring Contamination Stress Tolerance in Salix sp. Reveal the Importance for a Metaorganismal de Novo Assembly Approach for Nonmodel Plants. PLANT PHYSIOLOGY 2016; 171:3-24. [PMID: 27002060 PMCID: PMC4854704 DOI: 10.1104/pp.16.00090] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 03/20/2016] [Indexed: 05/09/2023]
Abstract
Metatranscriptomic study of nonmodel organisms requires strategies that retain the highly resolved genetic information generated from model organisms while allowing for identification of the unexpected. A real-world biological application of phytoremediation, the field growth of 10 Salix cultivars on polluted soils, was used as an exemplar nonmodel and multifaceted crop response well-disposed to the study of gene expression. Sequence reads were assembled de novo to create 10 independent transcriptomes, a global transcriptome, and were mapped against the Salix purpurea 94006 reference genome. Annotation of assembled contigs was performed without a priori assumption of the originating organism. Global transcriptome construction from 3.03 billion paired-end reads revealed 606,880 unique contigs annotated from 1588 species, often common in all 10 cultivars. Comparisons between transcriptomic and metatranscriptomic methodologies provide clear evidence that nonnative RNA can mistakenly map to reference genomes, especially to conserved regions of common housekeeping genes, such as actin, α/β-tubulin, and elongation factor 1-α. In Salix, Rubisco activase transcripts were down-regulated in contaminated trees across all 10 cultivars, whereas thiamine thizole synthase and CP12, a Calvin Cycle master regulator, were uniformly up-regulated. De novo assembly approaches, with unconstrained annotation, can improve data quality; care should be taken when exploring such plant genetics to reduce de facto data exclusion by mapping to a single reference genome alone. Salix gene expression patterns strongly suggest cultivar-wide alteration of specific photosynthetic apparatus and protection of the antenna complexes from oxidation damage in contaminated trees, providing an insight into common stress tolerance strategies in a real-world phytoremediation system.
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Affiliation(s)
- Nicholas J B Brereton
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
| | - Emmanuel Gonzalez
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
| | - Julie Marleau
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
| | - Werther Guidi Nissim
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
| | - Michel Labrecque
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
| | - Simon Joly
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
| | - Frederic E Pitre
- Institut de recherche en biologie végétale, University of Montreal, Montreal QC H1X 2B2, Canada (N.J.B.B., E.G., J.M., M.L., S.J., F.E.P.); andMontreal Botanical Garden, Montreal, QC H1X 2B2, Canada (W.G.N., M.L., S.J., F.E.P.)
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The Acute Encephalopathy Induced by Intake of Sugihiratake Mushroom in the Patients with Renal Damage Might Be Associated with the Intoxication of Cyanide and Thiocyanate. Food Saf (Tokyo) 2015. [DOI: 10.14252/foodsafetyfscj.2014036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Yamamoto N, Suzuki T, Kobayashi M, Dohra H, Sasaki Y, Hirai H, Yokoyama K, Kawagishi H, Yano K. A-WINGS: an integrated genome database for Pleurocybella porrigens (Angel's wing oyster mushroom, Sugihiratake). BMC Res Notes 2014; 7:866. [PMID: 25465051 PMCID: PMC4289373 DOI: 10.1186/1756-0500-7-866] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Accepted: 11/21/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The angel's wing oyster mushroom (Pleurocybella porrigens, Sugihiratake) is a well-known delicacy. However, its potential risk in acute encephalopathy was recently revealed by a food poisoning incident. To disclose the genes underlying the accident and provide mechanistic insight, we seek to develop an information infrastructure containing omics data. In our previous work, we sequenced the genome and transcriptome using next-generation sequencing techniques. The next step in achieving our goal is to develop a web database to facilitate the efficient mining of large-scale omics data and identification of genes specifically expressed in the mushroom. FINDINGS This paper introduces a web database A-WINGS (http://bioinf.mind.meiji.ac.jp/a-wings/) that provides integrated genomic and transcriptomic information for the angel's wing oyster mushroom. The database contains structure and functional annotations of transcripts and gene expressions. Functional annotations contain information on homologous sequences from NCBI nr and UniProt, Gene Ontology, and KEGG Orthology. Digital gene expression profiles were derived from RNA sequencing (RNA-seq) analysis in the fruiting bodies and mycelia. The omics information stored in the database is freely accessible through interactive and graphical interfaces by search functions that include 'GO TREE VIEW' browsing, keyword searches, and BLAST searches. CONCLUSIONS The A-WINGS database will accelerate omics studies on specific aspects of the angel's wing oyster mushroom and the family Tricholomataceae.
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Affiliation(s)
| | | | | | | | | | | | | | - Hirokazu Kawagishi
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Kawasaki 214-8571, Japan.
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