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Schüller A, Studt-Reinhold L, Berger H, Silvestrini L, Labuda R, Güldener U, Gorfer M, Bacher M, Doppler M, Gasparotto E, Gattesco A, Sulyok M, Strauss J. Genome analysis of Cephalotrichum gorgonifer and identification of the biosynthetic pathway for rasfonin, an inhibitor of KRAS dependent cancer. Fungal Biol Biotechnol 2023; 10:13. [PMID: 37355668 DOI: 10.1186/s40694-023-00158-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 04/28/2023] [Indexed: 06/26/2023] Open
Abstract
BACKGROUND Fungi are important sources for bioactive compounds that find their applications in many important sectors like in the pharma-, food- or agricultural industries. In an environmental monitoring project for fungi involved in soil nitrogen cycling we also isolated Cephalotrichum gorgonifer (strain NG_p51). In the course of strain characterisation work we found that this strain is able to naturally produce high amounts of rasfonin, a polyketide inducing autophagy, apoptosis, necroptosis in human cell lines and showing anti-tumor activity in KRAS-dependent cancer cells. RESULTS In order to elucidate the biosynthetic pathway of rasfonin, the strain was genome sequenced, annotated, submitted to transcriptome analysis and genetic transformation was established. Biosynthetic gene cluster (BGC) prediction revealed the existence of 22 BGCs of which the majority was not expressed under our experimental conditions. In silico prediction revealed two BGCs with a suite of enzymes possibly involved in rasfonin biosynthesis. Experimental verification by gene-knock out of the key enzyme genes showed that one of the predicted BGCs is indeed responsible for rasfonin biosynthesis. CONCLUSIONS This study identified a biosynthetic gene cluster containing a key-gene responsible for rasfonin production. Additionally, molecular tools were established for the non-model fungus Cephalotrichum gorgonifer which allows strain engineering and heterologous expression of the BGC for high rasfonin producing strains and the biosynthesis of rasfonin derivates for diverse applications.
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Affiliation(s)
- Andreas Schüller
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Campus Tulln, Konrad Lorenz Strasse 24, 3430, Tulln an der Donau, Austria
| | - Lena Studt-Reinhold
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Campus Tulln, Konrad Lorenz Strasse 24, 3430, Tulln an der Donau, Austria
| | - Harald Berger
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Campus Tulln, Konrad Lorenz Strasse 24, 3430, Tulln an der Donau, Austria
| | - Lucia Silvestrini
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Campus Tulln, Konrad Lorenz Strasse 24, 3430, Tulln an der Donau, Austria
- DGforLife, Operations - Research and Development, Via Albert Einstein, Marcallo c.C., 20010, Milan, Italy
| | - Roman Labuda
- Research Platform Bioactive Microbial Metabolites (BiMM), Konrad Lorenz Strasse 24, 3430, Tulln an der Donau, Austria
- Department for Farm Animals and Veterinary Public Health, Institute of Food Safety, Food Technology and Veterinary Public Health, Unit of Food Microbiology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210, Vienna, Austria
| | - Ulrich Güldener
- Department of Bioinformatics, Technical University of Munich, TUM School of Life Sciences Weihenstephan, Freising, Germany
- German Heart Center Munich, Technical University Munich, Lazarettstraße 36, 80636, Munich, Germany
| | - Markus Gorfer
- AIT Austrian Institute of Technology GmbH, Bioresources, 3430, Tulln, Austria
| | - Markus Bacher
- Research Platform Bioactive Microbial Metabolites (BiMM), Konrad Lorenz Strasse 24, 3430, Tulln an der Donau, Austria
- Department of Chemistry, Institute of Chemistry of Renewable Resources, University of Natural Resources and Life Sciences Vienna (BOKU), Konrad-LorenzStraße 24, 3430, Tulln, Austria
| | - Maria Doppler
- Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz Strasse 20, 3430, Tulln an der Donau, Austria
- Core Facility Bioactive Molecules, Screening and Analysis, University of Natural Resources and Life Sciences, Vienna, 3430, Tulln an der Donau, Austria
| | - Erika Gasparotto
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Campus Tulln, Konrad Lorenz Strasse 24, 3430, Tulln an der Donau, Austria
- Research Platform Bioactive Microbial Metabolites (BiMM), Konrad Lorenz Strasse 24, 3430, Tulln an der Donau, Austria
- Department of Biological Chemistry, Faculty of Chemistry, University of Vienna, Josef-Holaubek-Platz 2, 1090, Vienna, Austria
| | - Arianna Gattesco
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Campus Tulln, Konrad Lorenz Strasse 24, 3430, Tulln an der Donau, Austria
- Research Platform Bioactive Microbial Metabolites (BiMM), Konrad Lorenz Strasse 24, 3430, Tulln an der Donau, Austria
| | - Michael Sulyok
- Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz Strasse 20, 3430, Tulln an der Donau, Austria
| | - Joseph Strauss
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Campus Tulln, Konrad Lorenz Strasse 24, 3430, Tulln an der Donau, Austria.
- Research Platform Bioactive Microbial Metabolites (BiMM), Konrad Lorenz Strasse 24, 3430, Tulln an der Donau, Austria.
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Sandoval-Denis M, Guarro J, Cano-Lira JF, Sutton DA, Wiederhold NP, de Hoog GS, Abbott SP, Decock C, Sigler L, Gené J. Phylogeny and taxonomic revision of Microascaceae with emphasis on synnematous fungi. Stud Mycol 2016; 83:193-233. [PMID: 27616803 PMCID: PMC5007882 DOI: 10.1016/j.simyco.2016.07.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
The taxonomy of the synnematous genera Cephalotrichum, Doratomyces and Trichurus, and other related genera Gamsia, Wardomyces and Wardomycopsis, has been controversial and relies mainly on morphological criteria. These are microascaceous saprobic fungi mostly found in air and soil and with a worldwide distribution. In order to clarify their taxonomy and to delineate generic boundaries within the Microascaceae, we studied 57 isolates that include clinical, environmental and all the available ex-type strains of a large set of species by means of morphological, physiological and molecular phylogenetic analyses using DNA sequence data of four loci (the ITS region, and fragments of rDNA LSU, translation elongation factor 1α and β-tubulin). The results demonstrate that Cephalotrichum, Doratomyces and Trichurus are congeneric and the genus Cephalotrichum is accepted here with Echinobotryum as a further synonym. The genera Acaulium and Fairmania, typified by A. albonigrescens and F. singularis, respectively, are distinct from Microascus and Scopulariopsis, Gamsia is distinct from Wardomyces, and Wardomycopsis is confirmed as a separate genus in the Microascaceae. Two new species of Cephalotrichum are described as C. brevistipitatum and C. hinnuleum. Nine new combinations are proposed, i.e. Acaulium acremonium, A. caviariforme, Cephalotrichum asperulum, C. columnare, C. cylindricum, C. dendrocephalum, C. gorgonifer, Gamsia columbina and Wardomyces giganteus. A neotype is designed for C. stemonitis. Lectotypes and epitypes are designated for A. acremonium, A. albonigrescens, C. gorgonifer, C. nanum and W. anomalus. Cephalotrichum cylindricum, C. microsporum, F. singularis and Gamsia columbina are also epitypified with new specimens. Descriptions of the phenotypic features and dichotomous keys for identification are provided for accepted species in the different genera.
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Affiliation(s)
- M Sandoval-Denis
- Unitat de Micologia, Facultat de Medicina, Universitat Rovira i Virgili, Reus, Spain; Faculty of Natural and Agricultural Sciences, Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
| | - J Guarro
- Unitat de Micologia, Facultat de Medicina, Universitat Rovira i Virgili, Reus, Spain
| | - J F Cano-Lira
- Unitat de Micologia, Facultat de Medicina, Universitat Rovira i Virgili, Reus, Spain
| | - D A Sutton
- Fungus Testing Laboratory, Department of Pathology, University of Texas Health Science Center, San Antonio, TX, USA
| | - N P Wiederhold
- Fungus Testing Laboratory, Department of Pathology, University of Texas Health Science Center, San Antonio, TX, USA
| | - G S de Hoog
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - S P Abbott
- Natural Link Mold Lab, Inc., 4900 Mill Street, Suite 3, Reno, NV 89502, USA
| | - C Decock
- Mycothèque de l'Université Catholique de Louvain (MUCL, BCCMTM), Earth and Life Institute - Microbiology (ELIM), Université catholique de Louvain, Croix du Sud 2 bte L7.05.06, B-1348 Louvain-la-Neuve, Belgium
| | - L Sigler
- University of Alberta Microfungus Collection and Herbarium (UAMH), Devonian Botanic Garden, Edmonton, Alberta T6G 2E1, Canada
| | - J Gené
- Unitat de Micologia, Facultat de Medicina, Universitat Rovira i Virgili, Reus, Spain
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