1
|
Steinert K, Atanasoff-Kardjalieff AK, Messner E, Gorfer M, Niehaus EM, Humpf HU, Studt-Reinhold L, Kalinina SA. Tools to make Stachybotrys chartarum genetically amendable: Key to unlocking cryptic biosynthetic gene clusters. Fungal Genet Biol 2024; 172:103892. [PMID: 38636782 DOI: 10.1016/j.fgb.2024.103892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 04/12/2024] [Accepted: 04/13/2024] [Indexed: 04/20/2024]
Abstract
The soil and indoor fungus Stachybotrys chartarum can induce respiratory disorders, collectively referred to as stachybotryotoxicosis, owing to its prolific production of diverse bioactive secondary metabolites (SMs) or mycotoxins. Although many of these toxins responsible for the harmful effects on animals and humans have been identified in the genus Stachybotrys, however a number of SMs remain elusive. Through in silico analyses, we have identified 37 polyketide synthase (PKS) genes, highlighting that the chemical profile potential of Stachybotrys is far from being fully explored. Additionally, by leveraging phylogenetic analysis of known SMs produced by non-reducing polyketide synthases (NR-PKS) in other filamentous fungi, we showed that Stachybotrys possesses a rich reservoir of untapped SMs. To unravel natural product biosynthesis in S. chartarum, genetic engineering methods are crucial. For this purpose, we have developed a reliable protocol for the genetic transformation of S. chartarum and applied it to the ScPKS14 biosynthetic gene cluster. This cluster is homologous to the already known Claviceps purpurea CpPKS8 BGC, responsible for the production of ergochromes. While no novel SMs were detected, we successfully applied genetic tools, such as the generation of deletionand overexpression strains of single cluster genes. This toolbox can now be readily employed to unravel not only this particular BGC but also other candidate BGCs present in S. chartarum, making this fungus accessible for genetic engineering.
Collapse
Affiliation(s)
| | - Anna K Atanasoff-Kardjalieff
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln an der Donau, Austria
| | - Elias Messner
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln an der Donau, Austria
| | - Markus Gorfer
- Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Eva-Maria Niehaus
- Institute of Food Chemistry, University of Münster, Münster, Germany
| | - Hans-Ulrich Humpf
- Institute of Food Chemistry, University of Münster, Münster, Germany
| | - Lena Studt-Reinhold
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln an der Donau, Austria.
| | | |
Collapse
|
2
|
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] [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.
Collapse
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.
| |
Collapse
|
3
|
Huth L, Ash GJ, Idnurm A, Kiss L, Vaghefi N. The "Bipartite" Structure of the First Genome of Ampelomyces quisqualis, a Common Hyperparasite and Biocontrol Agent of Powdery Mildews, May Point to Its Evolutionary Origin from Plant Pathogenic Fungi. Genome Biol Evol 2021; 13:evab182. [PMID: 34363471 PMCID: PMC8382677 DOI: 10.1093/gbe/evab182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2021] [Indexed: 12/27/2022] Open
Abstract
Powdery mildews are among the most important plant pathogens worldwide, which are often attacked in the field by mycoparasitic fungi belonging to the genus Ampelomyces. The taxonomy of the genus Ampelomyces is unresolved, but well-supported molecular operational taxonomic units were repeatedly defined suggesting that the genus may include at least four to seven species. Some Ampelomyces strains were commercialized as biocontrol agents of crop pathogenic powdery mildews. However, the genomic mechanisms underlying their mycoparasitism are still poorly understood. To date, the draft genome of a single Ampelomyces strain, designated as HMLAC 05119, has been released. We report a high-quality, annotated hybrid draft genome assembly of A. quisqualis strain BRIP 72107, which, based on phylogenetic analyses, is not conspecific with HMLAC 05119. The constructed genome is 40.38 Mb in size, consisting of 24 scaffolds with an N50 of 2.99 Mb and 96.2% completeness. Our analyses revealed "bipartite" structure of Ampelomyces genomes, where GC-balanced genomic regions are interspersed by longer or shorter stretches of AT-rich regions. This is also a hallmark of many plant pathogenic fungi and provides further evidence for evolutionary affinity of Ampelomyces species to plant pathogenic fungi. The high-quality genome and annotation produced here provide an important resource for future genomic studies of mycoparasitisim to decipher molecular mechanisms underlying biocontrol processes and natural tritrophic interactions.
Collapse
Affiliation(s)
- Lauren Huth
- Centre for Crop Health, University of Southern Queensland, Darling Heights, Queensland, Australia
| | - Gavin J Ash
- Centre for Crop Health, University of Southern Queensland, Darling Heights, Queensland, Australia
| | - Alexander Idnurm
- School of BioSciences, University of Melbourne, Parkville, Victoria, Australia
| | - Levente Kiss
- Centre for Crop Health, University of Southern Queensland, Darling Heights, Queensland, Australia
| | - Niloofar Vaghefi
- Centre for Crop Health, University of Southern Queensland, Darling Heights, Queensland, Australia
| |
Collapse
|