Genome analysis of Cephalotrichum gorgonifer and identification of the biosynthetic pathway for rasfonin, an inhibitor of KRAS dependent cancer

• Published in: Fungal biology and biotechnology 2023-06, Vol.10 (1), p.13-19, Article 13
• Main Authors: Schüller, Andreas, Studt-Reinhold, Lena, Berger, Harald, Silvestrini, Lucia, Labuda, Roman, Güldener, Ulrich, Gorfer, Markus, Bacher, Markus, Doppler, Maria, Gasparotto, Erika, Gattesco, Arianna, Sulyok, Michael, Strauss, Joseph
• Format: Article
• Language: English
• Subjects: Acids; Analysis; Anticancer properties; Antitumor agents; Apoptosis; Autophagy; Bioactive compounds; Biosynthesis; Cancer; Cells; Cephalotrichum; Doratomyces NG_p51; Environmental monitoring; Food industry; Fungi; Genes; Genetic analysis; Genetic research; Genome analysis; Genomes; Genomics; K-Ras protein; Kinases; Metabolism; Metabolites; Necroptosis; Nitrates; Pharmaceuticals; Phylogenetics; Physiological aspects; Rasfonin; Scientific equipment and supplies industry; Secondary metabolism; Soil microorganisms; Transcriptome analysis; Transcriptomes; Tumor cell lines
• ISSN: 2054-3085; 2054-3085
• DOI: 10.1186/s40694-023-00158-x

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. 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. 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.