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Lutfia A, Munir E, Yurnaliza Y, Basyuni M. Chemical analysis and anticancer activity of sesterterpenoid from an endophytic fungus Hypomontagnella monticulosa Zg15SU and its host Zingiber griffithii Baker. Heliyon 2021; 7:e06292. [PMID: 33665446 PMCID: PMC7900702 DOI: 10.1016/j.heliyon.2021.e06292] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/22/2020] [Accepted: 02/11/2021] [Indexed: 11/26/2022] Open
Abstract
Zingiber griffithii Baker is one of the native Zingiberaceous species in a tropical forest of North Sumatra, Indonesia. Zingiberaceous species have been intensively studied and reported as herbal ingredients in ethnomedicine and currently their endophytic fungal associates were studied for pharmacological importance. Fifteen endophytic fungi were isolated from Zingiber griffithii following morphological and molecular characterization. All isolates exhibited antibacterial properties to at least one of the tested pathogenic bacteria Staphylococcus aureus, Escherichia coli, Methicilin-resistant S. aureus (MRSA), and Enteropathogenic E. coli (EPEC). The isolate, identified as Hypomontagnella monticulosa strain Zg15SU (syn. Hypoxylon monticulosum Mont.) based on its rDNA/ITS sequence, displayed antibacterial activities to all tested pathogens. The EtOAc extract of the H. monticulosum Zg15SU showed the highest activity for gram-negative bacteria, the E. coli and EPEC, while the extract of Z. griffithii rhizome displayed activity only for E. coli. The gas chromatography-mass spectrometry analysis (GC-MS) indicated a major portion of similar compounds found in both the endophytic fungus and plant extract, revealing the compounds of oleic acid, cyclononasiloxane, octadecamethyl, and eicosanoic acid Furthermore, purification and structural elucidation on the EtOAc extract of both Z. griffithii rhizome and H. monticulosa Zg15SU yielded two bioactive compounds: a novel compound, griffithiiene, a terpenoid-alkaloid bearing the skeleton of a scalarane (1) and scalaradial (2) which were confirmed by 1H- (500 MHz) and 13C-NMR (125 MHz) spectroscopy. Importantly, the elucidated compounds showed a cytotoxicity activity against cancer cell lines, the Panc-1, NBT-T2, and HCT116 based on in vitro MTT proliferation assay. This is the first report of Z. griffithii harboring an endophytic fungus, H. monticulosa, which produced potential antibacterial and anticancer metabolites along with its host to be utilized for future prospects.
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Affiliation(s)
- Anisa Lutfia
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Sumatera Utara, Medan, 20155, Indonesia
| | - Erman Munir
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Sumatera Utara, Medan, 20155, Indonesia
| | - Yurnaliza Yurnaliza
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Sumatera Utara, Medan, 20155, Indonesia
| | - Mohammad Basyuni
- Department of Forestry, Faculty of Forestry, Universitas Sumatera Utara, Medan, 20155, Indonesia
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Collado J, Platas G, Peláez F. Identification of an endophytic Nodulisporium sp. from Quercus ilex in central Spain as the anamorph of Biscogniauxia mediterranea by rDNA sequence analysis and effect of different ecological factors on distribution of the fungus. Mycologia 2019. [DOI: 10.1080/00275514.2001.12063222] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Javier Collado
- Centro de Investigación Básica. NPDD-Merck Research Laboratories, Merck, Sharp & Dohme de España S. A. Josefa Valcárcel 38, E-28027 Madrid, Spain
| | - Gonzalo Platas
- Centro de Investigación Básica. NPDD-Merck Research Laboratories, Merck, Sharp & Dohme de España S. A. Josefa Valcárcel 38, E-28027 Madrid, Spain
| | - Fernando Peláez
- Centro de Investigación Básica. NPDD-Merck Research Laboratories, Merck, Sharp & Dohme de España S. A. Josefa Valcárcel 38, E-28027 Madrid, Spain
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3
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Exploration of Macrofungi in Sub-Tropical Semi-Evergreen Indian Forest Ecosystems. Fungal Biol 2018. [DOI: 10.1007/978-3-030-02622-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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4
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Leman-Loubière C, Le Goff G, Retailleau P, Debitus C, Ouazzani J. Sporothriolide-Related Compounds from the Fungus Hypoxylon monticulosum CLL-205 Isolated from a Sphaerocladina Sponge from the Tahiti Coast. JOURNAL OF NATURAL PRODUCTS 2017; 80:2850-2854. [PMID: 29043802 DOI: 10.1021/acs.jnatprod.7b00714] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Two sporothriolide-related compounds were obtained from an extract of the fungus Hypoxylon monticulosum CLL-205, isolated from a Sphaerocladina sponge collected from the Tahiti coast. Compound 2 is a deoxy analogue of sporothric acid (4). Compound 3 is a newly reported unusual scaffold combining sporothriolide (1) and trienylfuranol A (5) moieties, through a Diels-Alderase-type reaction. Various experimental and analytical arguments supported the biocatalytic origin of compound 3. The structures of the isolated compounds were elucidated using 1D and 2D NMR, HRMS, and IR data. The structure and the absolute configuration of 3 were unambiguously confirmed by a single-crystal X-ray diffraction analysis.
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Affiliation(s)
- Charlotte Leman-Loubière
- Centre National de la Recherche Scientifique, Institut de Chimie des Substances Naturelles ICSN , Avenue de la Terrasse, 91198 Gif-sur-Yvette, Cedex, France
| | - Géraldine Le Goff
- Centre National de la Recherche Scientifique, Institut de Chimie des Substances Naturelles ICSN , Avenue de la Terrasse, 91198 Gif-sur-Yvette, Cedex, France
| | - Pascal Retailleau
- Centre National de la Recherche Scientifique, Institut de Chimie des Substances Naturelles ICSN , Avenue de la Terrasse, 91198 Gif-sur-Yvette, Cedex, France
| | - Cécile Debitus
- LEMAR, IRD, CNRS, IFREMER, Université de Bretagne Occidentale, IUEM, Technopole Brest-Iroise , Rue Dumont d'Urville, 29280 Plouzané, France
| | - Jamal Ouazzani
- Centre National de la Recherche Scientifique, Institut de Chimie des Substances Naturelles ICSN , Avenue de la Terrasse, 91198 Gif-sur-Yvette, Cedex, France
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5
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Towards a natural classification and backbone tree for Graphostromataceae, Hypoxylaceae, Lopadostomataceae and Xylariaceae. FUNGAL DIVERS 2017. [DOI: 10.1007/s13225-017-0388-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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6
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Wendt L, Sir EB, Kuhnert E, Heitkämper S, Lambert C, Hladki AI, Romero AI, Luangsa-ard JJ, Srikitikulchai P, Peršoh D, Stadler M. Resurrection and emendation of the Hypoxylaceae, recognised from a multigene phylogeny of the Xylariales. Mycol Prog 2017. [DOI: 10.1007/s11557-017-1311-3] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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7
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Acero FJ, González V, Sánchez-Ballesteros J, Rubio V, Checa J, Bills GF, Salazar O, Platas G, Peláez F. Molecular phylogenetic studies on the Diatrypaceae based on rDNA-ITS sequences. Mycologia 2017. [DOI: 10.1080/15572536.2005.11832975] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | | | | | - Víctor Rubio
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB-CSIC), Campus Cantoblanco, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Julia Checa
- Departamento de Biología Vegetal, Universidad de Alcalá de Henares, Madrid 28871, Spain
| | | | | | | | - Fernando Peláez
- Centro de Investigación Básica, Merck Sharp and Dohme de España S. A., Josefa Valcárcel 38, Madrid 28027, Spain
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Affiliation(s)
| | - Yu-Ming Ju
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Jack D. Rogers
- Department of Plant Pathology, Washington State University, Pullman, Washington 99164-6430
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Ju YM, Hsieh HM, Ho MC, Szu DH, Fang MJ. Theissenia rogersii sp. nov. and phylogenetic position of Theissenia. Mycologia 2017. [DOI: 10.1080/15572536.2007.11832555] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | | | | | | | - Mei-Jane Fang
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 115, Taiwan
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Zhang N, Castlebury LA, Miller AN, Huhndorf SM, Schoch CL, Seifert KA, Rossman AY, Rogers JD, Kohlmeyer J, Volkmann-Kohlmeyer B, Sung GH. An overview of the systematics of the Sordariomycetes based on a four-gene phylogeny. Mycologia 2017. [DOI: 10.1080/15572536.2006.11832635] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Ning Zhang
- Department of Plant Pathology, NYSAES, Cornell University, Geneva, New York 14456
| | - Lisa A. Castlebury
- Systematic Botany & Mycology Laboratory, USDA-ARS, Beltsville, Maryland 20705
| | - Andrew N. Miller
- Center for Biodiversity, Illinois Natural History Survey, Champaign, Illinois 61820
| | - Sabine M. Huhndorf
- Department of Botany, The Field Museum of Natural History, Chicago, Illinois 60605
| | - Conrad L. Schoch
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
| | - Keith A. Seifert
- Biodiversity (Mycology and Botany), Agriculture and Agri-Food Canada, Ottawa, Ontario, K1A 0C6 Canada
| | - Amy Y. Rossman
- Systematic Botany & Mycology Laboratory, USDA-ARS, Beltsville, Maryland 20705
| | - Jack D. Rogers
- Department of Plant Pathology, Washington State University, Pullman, Washington 99164
| | | | - Brigitte Volkmann-Kohlmeyer
- Institute of Marine Sciences, University of North Carolina at Chapel Hill, Morehead City, North Carolina 28557
| | - Gi-Ho Sung
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
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11
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Detection of Edible Mushroom Species by Using Molecular Markers. Fungal Biol 2017. [DOI: 10.1007/978-3-319-34106-4_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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12
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Shamim M, Kumar P, Kumar RR, Kumar M, Kumar RR, Singh KN. Assessing Fungal Biodiversity Using Molecular Markers. Fungal Biol 2017. [DOI: 10.1007/978-3-319-34106-4_15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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13
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Phylogenetic and chemotaxonomic resolution of the genus Annulohypoxylon (Xylariaceae) including four new species. FUNGAL DIVERS 2016. [DOI: 10.1007/s13225-016-0377-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Daranagama DA, Camporesi E, Jeewon R, Liu X, Stadler M, Lumyong S, Hyde KD. Taxonomic Rearrangement ofAnthostomella(Xylariaceae) Based on a Multigene Phylogeny and Morphology. CRYPTOGAMIE MYCOL 2016. [DOI: 10.7872/crym/v37.iss4.2016.509] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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15
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Raimondo ML, Lops F, Carlucci A. Charcoal Canker of Pear, Plum, and Quince Trees Caused by Biscogniauxia rosacearum sp. nov. in Southern Italy. PLANT DISEASE 2016; 100:1813-1822. [PMID: 30682981 DOI: 10.1094/pdis-09-15-1037-re] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The genus Biscogniauxia is paraphyletic to members of the family Xylariaceae and includes at least 52 species to date that are mainly pathogens of dicotyledonous angiosperm trees. Most of these are forest trees, such as those in the genera Acacia, Acer, Alnus, Eucalyptus, Fraxinus, Populus, and Quercus, and other species of minor importance. Biscogniauxia spp. have been reported as endophytes or secondary invaders that attack only stressed plants. During a survey in rosaceous orchards in southern Italy, several charcoal cankers were observed and stroma samples were collected. A collection of 31 Biscogniauxia isolates was analyzed. Their phylogenetic relationships were determined through study of the internal transcribed spacer, β-tubulin, and actin gene sequences. Combining morphological, cultural, and molecular data, a new species of Biscogniauxia is described here as Biscogniauxia rosacearum. This new species was isolated for the first time from rosaceous hosts in Apulia. Pathogenicity tests showed that it causes symptoms on stems when artificially inoculated and produces stromata on the bark surface.
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Affiliation(s)
- Maria Luisa Raimondo
- Department of Sciences, Agriculture, Food and the Environment, University of Foggia, 71121 Foggia, Italy
| | - Francesco Lops
- Department of Sciences, Agriculture, Food and the Environment, University of Foggia, 71121 Foggia, Italy
| | - Antonia Carlucci
- Department of Sciences, Agriculture, Food and the Environment, University of Foggia, 71121 Foggia, Italy
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16
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de Almeida DAC, Gusmão LFP, Miller AN. Taxonomy and molecular phylogeny of Diatrypaceae (Ascomycota, Xylariales) species from the Brazilian semi-arid region, including four new species. Mycol Prog 2016. [DOI: 10.1007/s11557-016-1194-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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17
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Paradigm Shift in Plant Disease Diagnostics: A Journey from Conventional Diagnostics to Nano-diagnostics. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27312-9_11] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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18
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Daranagama DA, Camporesi E, Tian Q, Liu X, Chamyuang S, Stadler M, Hyde KD. Anthostomella is polyphyletic comprising several genera in Xylariaceae. FUNGAL DIVERS 2015. [DOI: 10.1007/s13225-015-0329-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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19
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Cheng X, Li W, Cai L. Molecular phylogeny of Ascotricha, including two new marine algae-associated species. Mycologia 2015; 107:490-504. [PMID: 25724998 DOI: 10.3852/14-210] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 02/11/2015] [Indexed: 11/10/2022]
Abstract
Phylogenetic analyses based on a broad taxonomic sampling of Ascotricha were conducted using the sequences of nuc rDNA region encompassing the internal transcribed spacers 1 and 2, along with the 5.8S rDNA (ITS), partial nuc 18S rDNA (18S) and partial β-tubulin gene (TUB2). Hypoxyloid Xylariaceae and xylarioid Xylariaceae were inferred as two distinct lineages in the Xylariaceae in the combined ITS-TUB2 phylogeny. Within xylarioid Xylariaceae species of Ascotricha form a monophyletic group. Two new marine algae-associated fungi, Ascotricha longipila and A. parvispora, are described on the basis of morphological and molecular characters and the combination, A. sinuosa, is proposed. A synopsis of the morphological characters and a dichotomous key to Ascotricha species are provided.
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Affiliation(s)
- Xiaoli Cheng
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Wei Li
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, University of Chinese Academy of Sciences, Beijing 100101, China
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Kuhnert E, Surup F, Sir EB, Lambert C, Hyde KD, Hladki AI, Romero AI, Stadler M. Lenormandins A—G, new azaphilones from Hypoxylon lenormandii and Hypoxylon jaklitschii sp. nov., recognised by chemotaxonomic data. FUNGAL DIVERS 2015. [DOI: 10.1007/s13225-014-0318-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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21
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Raja HA, Kaur A, El-Elimat T, Figueroa M, Kumar R, Deep G, Agarwal R, Faeth SH, Cech NB, Oberlies NH. Phylogenetic and chemical diversity of fungal endophytes isolated from Silybum marianum (L) Gaertn. (milk thistle). Mycology 2015; 6:8-27. [PMID: 26000195 PMCID: PMC4409047 DOI: 10.1080/21501203.2015.1009186] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 01/13/2015] [Indexed: 01/30/2023] Open
Abstract
Use of the herb milk thistle (Silybum marianum) is widespread, and its chemistry has been studied for over 50 years. However, milk thistle endophytes have not been studied previously for their fungal and chemical diversity. We examined the fungal endophytes inhabiting this medicinal herb to determine: (1) species composition and phylogenetic diversity of fungal endophytes; (2) chemical diversity of secondary metabolites produced by these organisms; and (3) cytotoxicity of the pure compounds against the human prostate carcinoma (PC-3) cell line. Forty-one fungal isolates were identified from milk thistle comprising 25 operational taxonomic units based on BLAST search via GenBank using published authentic sequences from nuclear ribosomal internal transcribed spacer sequence data. Maximum likelihood analyses of partial 28S rRNA gene showed that these endophytes had phylogenetic affinities to four major classes of Ascomycota, the Dothideomycetes, Sordariomycetes, Eurotiomycetes, and Leotiomycetes. Chemical studies of solid-substrate fermentation cultures led to the isolation of four new natural products. In addition, 58 known secondary metabolites, representing diverse biosynthetic classes, were isolated and characterized using a suite of nuclear magnetic resonance and mass spectrometry techniques. Selected pure compounds were tested against the PC-3 cell line, where six compounds displayed cytotoxicity.
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Affiliation(s)
- Huzefa A. Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC27402, USA
| | - Amninder Kaur
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC27402, USA
| | - Tamam El-Elimat
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC27402, USA
| | - Mario Figueroa
- Facultad de Química, Universidad Nacional Autónoma de México, Mexico, DF04510, Mexico
| | - Rahul Kumar
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Denver, Aurora, CO80045, USA
| | - Gagan Deep
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Denver, Aurora, CO80045, USA
| | - Rajesh Agarwal
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Denver, Aurora, CO80045, USA
| | - Stanley H. Faeth
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC27402, USA
| | - Nadja B. Cech
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC27402, USA
| | - Nicholas H. Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC27402, USA
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The capability of endophytic fungi for production of hemicellulases and related enzymes. BMC Biotechnol 2013; 13:94. [PMID: 24175970 PMCID: PMC3840621 DOI: 10.1186/1472-6750-13-94] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 09/12/2013] [Indexed: 11/22/2022] Open
Abstract
Background There is an imperative necessity for alternative sources of energy able to reduce the world dependence of fossil oil. One of the most successful options is ethanol obtained mainly from sugarcane and corn fermentation. The foremost residue from sugarcane industry is the bagasse, a rich lignocellulosic raw material uses for the production of ethanol second generation (2G). New cellulolytic and hemicellulytic enzymes are needed, in order to optimize the degradation of bagasse and production of ethanol 2G. Results The ability to produce hemicellulases and related enzymes, suitable for lignocellulosic biomass deconstruction, was explored using 110 endophytic fungi and 9 fungi isolated from spoiled books in Brazil. Two initial selections were performed, one employing the esculin gel diffusion assay, and the other by culturing on agar plate media with beechwood xylan and liquor from the hydrothermal pretreatment of sugar cane bagasse. A total of 56 isolates were then grown at 29°C on steam-exploded delignified sugar cane bagasse (DEB) plus soybean bran (SB) (3:1), with measurement of the xylanase, pectinase, β-glucosidase, CMCase, and FPase activities. Twelve strains were selected, and their enzyme extracts were assessed using different substrates. Finally, the best six strains were grown under xylan and pectin, and several glycohydrolases activities were also assessed. These strains were identified morphologically and by sequencing the internal transcribed spacer (ITS) regions and the partial β-tubulin gene (BT2). The best six strains were identified as Aspergillus niger DR02, Trichoderma atroviride DR17 and DR19, Alternaria sp. DR45, Annulohypoxylon stigyum DR47 and Talaromyces wortmannii DR49. These strains produced glycohydrolases with different profiles, and production was highly influenced by the carbon sources in the media. Conclusions The selected endophytic fungi Aspergillus niger DR02, Trichoderma atroviride DR17 and DR19, Alternaria sp. DR45, Annulohypoxylon stigyum DR47 and Talaromyces wortmannii DR49 are excellent producers of hydrolytic enzymes to be used as part of blends to decompose sugarcane biomass at industrial level.
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New Hypoxylon species from Martinique and new evidence on the molecular phylogeny of Hypoxylon based on ITS rDNA and β-tubulin data. FUNGAL DIVERS 2013. [DOI: 10.1007/s13225-013-0264-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Suwannasai N, Martín MP, Phosri C, Sihanonth P, Whalley AJS, Spouge JL. Fungi in Thailand: a case study of the efficacy of an ITS barcode for automatically identifying species within the Annulohypoxylon and Hypoxylon genera. PLoS One 2013; 8:e54529. [PMID: 23390499 PMCID: PMC3563529 DOI: 10.1371/journal.pone.0054529] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 12/13/2012] [Indexed: 11/20/2022] Open
Abstract
Thailand, a part of the Indo-Burma biodiversity hotspot, has many endemic animals and plants. Some of its fungal species are difficult to recognize and separate, complicating assessments of biodiversity. We assessed species diversity within the fungal genera Annulohypoxylon and Hypoxylon, which produce biologically active and potentially therapeutic compounds, by applying classical taxonomic methods to 552 teleomorphs collected from across Thailand. Using probability of correct identification (PCI), we also assessed the efficacy of automated species identification with a fungal barcode marker, ITS, in the model system of Annulohypoxylon and Hypoxylon. The 552 teleomorphs yielded 137 ITS sequences; in addition, we examined 128 GenBank ITS sequences, to assess biases in evaluating a DNA barcode with GenBank data. The use of multiple sequence alignment in a barcode database like BOLD raises some concerns about non-protein barcode markers like ITS, so we also compared species identification using different alignment methods. Our results suggest the following. (1) Multiple sequence alignment of ITS sequences is competitive with pairwise alignment when identifying species, so BOLD should be able to preserve its present bioinformatics workflow for species identification for ITS, and possibly therefore with at least some other non-protein barcode markers. (2) Automated species identification is insensitive to a specific choice of evolutionary distance, contributing to resolution of a current debate in DNA barcoding. (3) Statistical methods are available to address, at least partially, the possibility of expert misidentification of species. Phylogenetic trees discovered a cryptic species and strongly supported monophyletic clades for many Annulohypoxylon and Hypoxylon species, suggesting that ITS can contribute usefully to a barcode for these fungi. The PCIs here, derived solely from ITS, suggest that a fungal barcode will require secondary markers in Annulohypoxylon and Hypoxylon, however. The URL http://tinyurl.com/spouge-barcode contains computer programs and other supplementary material relevant to this article.
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Affiliation(s)
- Nuttika Suwannasai
- Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, Thailand
| | - María P. Martín
- Department of Mycology, Real Jardín Botánico-CSIC, Plaza de Murillo 2, Madrid, Spain
| | - Cherdchai Phosri
- Microbiology Programme, Faculty of Science and Technology, Pibulsongkram Rajabhat University, Phitsanulok, Thailand
| | - Prakitsin Sihanonth
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Anthony J. S. Whalley
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - John L. Spouge
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, United States of America
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Wurzburger N, Higgins BP, Hendrick RL. Ericoid mycorrhizal root fungi and their multicopper oxidases from a temperate forest shrub. Ecol Evol 2012; 2:65-79. [PMID: 22408727 PMCID: PMC3297179 DOI: 10.1002/ece3.67] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Revised: 10/13/2011] [Accepted: 10/14/2011] [Indexed: 12/03/2022] Open
Abstract
Ericoid mycorrhizal fungi (ERM) may specialize in capturing nutrients from their host's litter as a strategy for regulating nutrient cycles in terrestrial ecosystems. In spite of their potential significance, we know little about the structure of ERM fungal communities and the genetic basis of their saprotrophic traits (e.g., genes encoding extracellular enzymes). Rhododendron maximum is a model ERM understory shrub that influences the nutrient cycles of montane hardwood forests in the southern Appalachians (North Carolina, USA). We sampled ERM roots of R. maximum from organic and mineral soil horizons and identified root fungi by amplifying and sequencing internal transcribed spacer (ITS) ribosomal DNA (rDNA) collected from cultures and clones. We observed 71 fungal taxa on ERM roots, including known symbionts Rhizoscyphus ericae and Oidiodendron maius, putative symbionts from the Helotiales, Chaetothyriales, and Sebacinales, ectomycorrhizal symbionts, and saprotrophs. Supporting the idea that ERM fungi are adept saprotrophs, richness of root-fungi was greater in organic than in mineral soil horizons. To study the genetic diversity of oxidative enzymes that contribute to decomposition, we amplified and sequenced a portion of genes encoding multicopper oxidases (MCOs) from ERM ascomycetes. Most fungi possessed multiple copies of MCO sequences with strong similarities to known ferroxidases and laccases. Our findings indicate that R. maximum associates with a taxonomically and ecologically diverse fungal community. The study of MCO gene diversity and expression may be useful for understanding how ERM root fungi regulate the cycling of nutrients between the host plant and the soil environment.
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Affiliation(s)
- Nina Wurzburger
- Odum School of Ecology, University of GeorgiaAthens, Georgia
| | - Brian P Higgins
- Department of Microbiology, University of GeorgiaAthens, Georgia
- Georgia Health Sciences University - University of Georgia Medical PartnershipAthens, Georgia
| | - Ronald L Hendrick
- School of Environment and Natural Resources, The Ohio State UniversityColumbus, Ohio
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Alam N, Kim JH, Shim MJ, Lee UY, Lee TS. Mycelial Propagation and Molecular Phylogenetic Relationships of Commercially Cultivated Agrocybe cylindracea based on ITS Sequences and RAPD. MYCOBIOLOGY 2010; 38:89-96. [PMID: 23956633 PMCID: PMC3741571 DOI: 10.4489/myco.2010.38.2.089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Accepted: 04/16/2010] [Indexed: 06/02/2023]
Abstract
This study evaluated the optimal vegetative growth conditions and molecular phylogenetic relationships of eleven strains of Agrocybe cylindracea collected from different ecological regions of Korea, China and Taiwan. The optimal temperature and pH for mycelial growth were observed at 25℃ and 6. Potato dextrose agar and Hennerberg were the favorable media for vegetative growth, whereas glucose tryptone was unfavorable. Dextrin, maltose, and fructose were the most effective carbon sources. The most suitable nitrogen sources were arginine and glycine, whereas methionine, alanine, histidine, and urea were least effective for the mycelial propagation of A. cylindracea. The internal transcribed spacer (ITS) regions of rDNA were amplified using PCR. The sequence of ITS2 was more variable than that of ITS1, while the 5.8S sequences were identical. The reciprocal homologies of the ITS sequences ranged from 98 to 100%. The strains were also analyzed by random amplification of polymorphic DNA (RAPD) using 20 arbitrary primers. Fifteen primers efficiently amplified the genomic DNA. The average number of polymorphic bands observed per primer was 3.8. The numbers of amplified bands varied based on the primers and strains, with polymorphic fragments ranging from 0.1 to 2.9 kb. The results of RAPD analysis were similar to the ITS region sequences. The results revealed that RAPD and ITS techniques were well suited for detecting the genetic diversity of all A. cylindracea strains tested.
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Affiliation(s)
- Nuhu Alam
- Department of Biology, University of Incheon, Incheon 406-840, Korea
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Hastrup ACS, Læssøe T. Camillea (Xylariaceae, Ascomycota), including two new species, along a trans-Andean altitude gradient in Ecuador. Mycol Prog 2009. [DOI: 10.1007/s11557-009-0601-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Persoh D, Melcher M, Graf K, Fournier J, Stadler M, Rambold G. Molecular and morphological evidence for the delimitation of Xylaria hypoxylon. Mycologia 2009; 101:256-68. [PMID: 19397200 DOI: 10.3852/08-108] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Xylaria hypoxylon, the type species of Xylaria (Xylariaceae, Sordariomycetes), was first described by Linnaeus as Clavaria hypoxylon from Sweden. Saccardo and other mycologists assumed a cosmopolitan distribution for this species. However, contradictory reports in the literature on its morphoanatomical characters and strongly inconsistent rDNA sequence data attributed to this species in GenBank suggested the existence of an unresolved species complex. To address this lack of clarity, molecular and morphological characters of numerous specimens and corresponding cultures of X. hypoxylon and related taxa from Europe were studied. Newly obtained 5.8S/ITS nrDNA sequence data were compared with published data and sequences of reference strains. European populations of X. hypoxylon from various hosts exhibited consistent rDNA sequence data and a relatively uniform holomorphic morphology, except for one specimen from Sweden that deviated in its ascospore morphology. Some samples from western United States showed DNA sequence data being identical to those of specimens from Europe, confirming a North American occurrence of X. hypoxylon. DNA sequences and morphology of other extra-European material however showed substantial deviations. Definitely not conspecific with the European material examined in this study is a strain, assigned to X. hypoxylon, the DNA sequence data of which have been used in various phylogenetic studies as a representative of Xylariaceae and Xylariales respectively. This material probably represents X longiana.
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Affiliation(s)
- Derek Persoh
- University of Bayreuth, Department of Mycology, Universitätsstrasse 30, D-95447 Bayreuth, Germany.
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Recognition of hypoxyloid and xylarioid Entonaema species and allied Xylaria species from a comparison of holomorphic morphology, HPLC profiles, and ribosomal DNA sequences. Mycol Prog 2008. [DOI: 10.1007/s11557-008-0553-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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32
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Bitzer J, Læssøe T, Fournier J, Kummer V, Decock C, Tichy HV, Piepenbring M, Peršoh D, Stadler M. Affinities of Phylacia and the daldinoid Xylariaceae, inferred from chemotypes of cultures and ribosomal DNA sequences. ACTA ACUST UNITED AC 2008; 112:251-70. [DOI: 10.1016/j.mycres.2007.07.004] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2007] [Revised: 06/15/2007] [Accepted: 07/11/2007] [Indexed: 11/25/2022]
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Okane I, Nakagiri A. Taxonomy of an anamorphic xylariaceous fungus from a termite nest found together with Xylaria angulosa. MYCOSCIENCE 2007. [DOI: 10.1007/s10267-007-0361-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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34
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Tang AMC, Jeewon R, Hyde KD. Phylogenetic relationships of Nemania plumbea sp. nov. and related taxa based on ribosomal ITS and RPB2 sequences. ACTA ACUST UNITED AC 2007; 111:392-402. [PMID: 17512179 DOI: 10.1016/j.mycres.2007.01.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2006] [Revised: 12/02/2006] [Accepted: 01/10/2007] [Indexed: 11/29/2022]
Abstract
During a survey fungal diversity of xylariaceous fungi in Thailand, a new Nemania species, N. plumbea, was identified. Nemania plumbea is characterized by soft-textured grey stromata on a persistent mat of white hyphae, pale brown ascospores with a short germ-slit on the more convex side. It also produces a Geniculosporium-like anamorph in culture. In order to evaluate its phylogenetic relationships among related species and genera, ITS-5.8S rDNA and RPB2 were analysed separately and simultaneously. Results from the phylogenetic analyses indicate that there is close phylogenetic association between N. plumbea and N. aenea. A preliminary account into the natural grouping of Xylariaceae based on ITS-5.8S rDNA and RPB2 sequences is also discussed.
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Affiliation(s)
- Alvin M C Tang
- Centre for Research in Fungal Diversity, Department of Ecology & Biodiversity, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
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Stadler M, Fournier J. Pigment chemistry, taxonomy and phylogeny of the Hypoxyloideae (Xylariaceae). Rev Iberoam Micol 2007; 23:160-70. [PMID: 17196023 DOI: 10.1016/s1130-1406(06)70037-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The Hypoxyloideae (Xylariaceae with Nodulisporium-like anamorphs) were evaluated by a morphological and HPLC-based chemotaxonomic survey of more than 2000 specimens and cultures. Conspecificity of recent records with ancient type specimens were established in many cases by HPLC, since their characteristic metabolites may remain stable for over 200 years. Most constitute novel natural products that were identified in the course of concurrent "mycochemical" studies. A comparison of HPLC profiles considering relationships within the Hypoxyloideae as inferred from the biogenesis of these pigments agreed fairly with concurrent molecular phylogenetic studies, based on sequences of actin, beta-tubulin, and 5.8S/ITS nrDNA genes. Anamorphic morphology and secondary metabolism of cultures agreed well at generic level and above. A combination of chemical and morphological traits is favored over PCR-based approaches for species discrimination, if only relatively few taxa of these diverse genera have been sequenced. An overview on the chemical structures and biological activities of the characteristic metabolites is provided, their ecological importance is discussed, and the utility of chemotaxonomy to support and predict phylogenetic relationships in the Hypoxyloidae is demonstrated. A polythetic approach is most useful to elucidate the phylogeny of the Xylariaceae. Chemotaxonomy to assess fungal biodiversity has considerable utility.
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Affiliation(s)
- Marc Stadler
- InterMed Discovery GMBH, BioMedizinZentrum, 44227 Dortmund, Germany.
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García D, Stchigel AM, Cano J, Calduch M, Hawksworth DL, Guarro J. Molecular phylogeny of Coniochaetales. ACTA ACUST UNITED AC 2006; 110:1271-89. [PMID: 17081739 DOI: 10.1016/j.mycres.2006.07.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2005] [Revised: 06/01/2006] [Accepted: 07/07/2006] [Indexed: 11/26/2022]
Abstract
Although the taxonomy of ascomycetes has changed dramatically, generic delimitation within the recently proposed order Coniochaetales has not been resolved. In order to clarify the phylogenetic relationships of genera in the Coniochaetaceae, we performed a molecular study based on the analyses of the sequences of the partial SSU and of the variable domains of the LSU rDNA genes. The phylogenetic trees obtained do not support the monophyly of the genera Coniochaeta, Coniochaetidium, Ephemeroascus, and Poroconiochaeta. A morphological study confirmed that there were not enough differences to distinguish these genera, and the latter three are treated as synonyms of Coniochaeta. The phialidic anamorph proved to be an informative phylogenetic character in Coniochaetales, while that the type of ascomata (cleistothecial or perithecial) and the ornamentation of the ascospore walls were of little taxonomic value at the generic level. The circumscription of the genus Coniochaeta is revised. The genera Coniocessia and Coniolariella are proposed as new within the order Xylariales to accommodate Coniochaeta nodulisporioides, and C. gamsii, respectively. The taxonomic position of Synaptospora and Wallrothiella subiculosa are also discussed.
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MESH Headings
- Ascomycota/classification
- Ascomycota/genetics
- Ascomycota/ultrastructure
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Microscopy, Electron, Scanning
- Molecular Sequence Data
- Phylogeny
- RNA, Ribosomal, 28S/genetics
- Sequence Analysis, DNA
- Spores, Fungal/cytology
- Spores, Fungal/genetics
- Spores, Fungal/ultrastructure
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Affiliation(s)
- Dania García
- Instituto de Investigaciones Fundamentales en Agricultura Tropical Alejandro de Humboldt, calle 1 esq.2, Santiago de las Vegas, Boyeros, C. de La Habana, Cuba
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Luchi N, Capretti P, Pinzani P, Orlando C, Pazzagli M. Real-time PCR detection of Biscogniauxia mediterranea in symptomless oak tissue. Lett Appl Microbiol 2006; 41:61-8. [PMID: 15960754 DOI: 10.1111/j.1472-765x.2005.01701.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS Real-time PCR, based on TaqMan chemistry, was used to detect Biscogniauxia mediterranea, a fungal pathogen that after a long endophytic phase may cause charcoal disease in oak trees. METHODS AND RESULTS Specific primers and probe were designed and tested on axenic cultures of B. mediterranea and other fungi commonly colonizing oaks. Twig samples were collected in Tuscany from apparently healthy oaks (Quercus cerris, Quercus ilex and Quercus pubescens) growing near trees infected with the fungus. Twigs were divided into two groups: one for isolation in agar plates, and one for real-time PCR after DNA extraction. The detection limit of the assay was 0.01 pg/DNA, whereas the amounts of fungal DNA detected in asymptomatic tissue were >0.5 pg microg(-1) total DNA extracted. In the apparently healthy twigs the frequency of isolation found on agar was 25.0%, much lower than that with real-time PCR (96.4%). CONCLUSIONS Real-time PCR is a sensitive and fast technique able to specifically detect and quantify the DNA of B. mediterranea in oak tissue. SIGNIFICANCE AND IMPACT OF THE STUDY This diagnostic method is a precise tool to localize fungi in symptomless plant tissues and promises to advance our understanding of fungal infection during their latent phase.
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Affiliation(s)
- N Luchi
- Dipartimento di Biotecnologie Agrarie, Sezione di Patologia vegetale, Università degli Studi di Firenze, Piazzale delle Cascine, Florence, Italy
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Quang DN, Hashimoto T, Asakawa Y. Inedible mushrooms: a good source of biologically active substances. CHEM REC 2006; 6:79-99. [PMID: 16565983 DOI: 10.1002/tcr.20074] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the course of our investigation on biologically active substances from inedible mushrooms in Japan, Germany, and Vietnam, we studied the chemical constituents of 22 species belonging to five families: Scutigeraceae, Polyporaceae, Xylariaceae, Thelephoraceae, and Paxillaceae. Various types of chemical substances were purified and characterized based on the modern spectroscopic methods and also on chemical reactions. These metabolites have shown a broad activity in many biological systems, such as antimicrobial, nematicidal, inhibition of NO production, anti-human immunodeficiency virus, tumor necrosis factor-alpha, and antioxidant activities. These isolated metabolites did not only show interesting activities, but also are employed as chemical markers supported for chemosystematics of these families. This review paper deals with the chemical constituents of 22 species, their biological activities, and also a discussion on chemosystematics.
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Affiliation(s)
- Dang Ngoc Quang
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima 770-8514, Japan
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39
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Hypomiltin, a novel azaphilone from Hypoxylon hypomiltum, and chemotypes in Hypoxylon sect. Hypoxylon as inferred from analytical HPLC profiling. Mycol Prog 2005. [DOI: 10.1007/s11557-006-0108-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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40
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Quang DN, Hashimoto T, Fournier J, Stadler M, Radulović N, Asakawa Y. Sassafrins A–D, new antimicrobial azaphilones from the fungus Creosphaeria sassafras. Tetrahedron 2005. [DOI: 10.1016/j.tet.2004.12.031] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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41
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Shimono Y, Kato M, Takamatsu S. Molecular phylogeny of Russulaceae (Basidiomycetes; Russulales) inferred from the nucleotide sequences of nuclear large subunit rDNA. MYCOSCIENCE 2004. [DOI: 10.1007/s10267-004-0189-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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42
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Platas G, Ruibal C, Collado J. Size and sequence heterogeneity in the ITS1 of Xylaria hypoxylon isolates. ACTA ACUST UNITED AC 2004; 108:71-5. [PMID: 15035507 DOI: 10.1017/s0953756203008815] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
During a survey of 375 strains of the Xylariales, one isolate (F127076) was observed to have an ITS1 size of 833 bp. This size exceeds the average ITS1 size in the Xylariales (mean = 209 +/- 57 bp). Comparison of the DNA sequence with GenBank and with a proprietary DNA database revealed low homology with Xylaria hypoxylon ATCC 42768, and with one undescribed Xylaria species. When the ITS2 sequence was compared, these isolates were 96-98% homologous. Sequences of other variable genes confirmed the relatedness among these strains. A closer observation of the ITS sequence of this isolate revealed the presence of three repeated domains of 250 bp plus one truncated domain, showing 52-75% homology. Sequence similarity suggests that the repeated domain is derived from the fusion of the ITS1 with a DNA fragment derived from the gamma-glutamyltranspeptidase gene. This example suggests that the rate of evolution of ITS1 can be independent of the rate of evolution of other genes, even when this variability is not a result of slipped strand misspairing events like in other Xylariales. This observation also indicates that recombination with other nuclear genes could participate in the evolution of the internal transcribed spacer.
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Affiliation(s)
- Gonzalo Platas
- Centro de Investigacíon Básica, Merck Sharp & Dohme de España, S.A. Josefa Valcarcel 38, E-28027, Madrid, Spain.
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43
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Bridge PD, Roberts PJ, Spooner BM, Panchal G. On the unreliability of published DNA sequences. THE NEW PHYTOLOGIST 2003; 160:43-48. [PMID: 33873520 DOI: 10.1046/j.1469-8137.2003.00861.x] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
• Here, the reliability of published fungal nucleic acid sequences is tested by the critical re-evaluation of 206 named sequences obtained from public-access databases. • Sequences from the ribosomal RNA (rRNA) gene cluster were examined as these are commonly used to establish fungal phylogeny and evolution, and are also increasingly employed in the identification of fungi from nonculture based studies. • Fifty-one rRNA internal transcribed spacer (ITS) sequences were obtained for species of Amanita, 55 ITS sequences were obtained for species of Phoma and 100 rRNA small subunit sequences were obtained from representative genera of the order Helotiales. In each case, the fungal group was selected partly on the basis of sequences deposited by three or more laboratories in order to avoid sample bias. The results suggest that up to 20% of the sequences available for each group may be unreliable, and this proportion is supported by additional informal observations.
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Affiliation(s)
- Paul D Bridge
- School of Biological and Chemical Sciences, Birkbeck College, Malet Street, London WC1E 7HX, UK
- Mycology Section, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
- Present address, British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Rd, Cambridge CB3 0ET, UK
| | - Peter J Roberts
- Mycology Section, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Brian M Spooner
- Mycology Section, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Gita Panchal
- School of Biological and Chemical Sciences, Birkbeck College, Malet Street, London WC1E 7HX, UK
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Macrocarpones, novel metabolites from stromata of Hypoxylon macrocarpum, and new evidence on the chemotaxonomy of Hypoxylon species. Mycol Prog 2002. [DOI: 10.1007/s11557-006-0021-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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45
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Lu L, Li J, Cang Y. PCR-based sensitive detection of medicinal fungi Hericium species from ribosomal internal transcribed spacer (ITS) sequences. Biol Pharm Bull 2002; 25:975-80. [PMID: 12186429 DOI: 10.1248/bpb.25.975] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Based on phylogenetic analysis of rDNA internal transcribed spacer (ITS) sequences, a pair of specific primers were designed for differentiating the Chinese traditional medicine Hericium species from other mushrooms by PCR. PCR was performed, with total DNAs as a template at an annealing temperature of 52-57 degrees C. Positive amplification was obtained from H. erinaceus with all DNA templates from different resources, but not from other related species. The result indicated that H. erinaceus could be clearly distinguished from other fungi by detection PCR, and no incorrect discrimination was found under the same reaction conditions. The primers were also successfully employed to identify H. erinaceus with different tissue types.
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Affiliation(s)
- Ling Lu
- College of Life Science, Nanjing Normal University, PR China.
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