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Advances in molecular interactions on the Rhizoctonia solani-sugar beet pathosystem. FUNGAL BIOL REV 2023. [DOI: 10.1016/j.fbr.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Schafhauser T, Wibberg D, Binder A, Rückert C, Busche T, Wohlleben W, Kalinowski J. Genome Assembly and Genetic Traits of the Pleuromutilin-Producer Clitopilus passeckerianus DSM1602. J Fungi (Basel) 2022; 8:jof8080862. [PMID: 36012850 PMCID: PMC9410065 DOI: 10.3390/jof8080862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 11/16/2022] Open
Abstract
The gilled mushroom Clitopilus passeckerianus (Entolomataceae, Agaricales, Basidiomycota) is well known to produce the terpenoid pleuromutilin, which is the biotechnological basis for medically important antibiotics such as lefamulin and retapamulin. Their unique mode of action and good tolerance entails an increasing demand of pleuromutilin-derived antibiotics in veterinary and human health care. Surprisingly, despite their pharmaceutical importance, no genome sequence is available of any pleuromutilin-producing fungus. Here, we present the high-quality draft genome sequence of the pleuromutilin-producer C. passeckerianus DSM1602 including functional genome annotation. More precisely, we employed a hybrid assembly strategy combining Illumina sequencing and Nanopore sequencing to assemble the mitochondrial genome as well as the nuclear genome. In accordance with the dikaryotic state of the fungus, the nuclear genome has a diploid character. Interestingly, the mitochondrial genome appears duplicated. Bioinformatic analysis revealed a versatile secondary metabolism with an emphasis on terpenoid biosynthetic enzymes in C. passeckerianus and also in related strains. Two alleles of biosynthetic gene clusters for pleuromutilin were found in the genome of C. passeckerianus. The pleuromutilin genes were reassembled with yeast-specific elements for heterologous expression in Saccharomyces cerevisiae. Our work lays the foundation for metabolic strain engineering towards higher yields of the valuable compound pleuromutilin.
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Affiliation(s)
- Thomas Schafhauser
- Mikrobiologie und Biotechnologie, Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tuebingen, Germany
- Correspondence: (T.S.); (J.K.)
| | - Daniel Wibberg
- Centrum für Biotechnologie, CeBiTec, Universität Bielefeld, Universitätsstr. 27, 33615 Bielefeld, Germany
- Institute of Bio- and Geosciences IBG-5, Computational Metagenomics, Forschungszentrum Jülich GmbH, 52425 Juelich, Germany
| | - Antonia Binder
- Mikrobiologie und Biotechnologie, Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tuebingen, Germany
- Institut für Mikrobiologie, Technische Universität Dresden, Zellescher Weg 20b, 01062 Dresden, Germany
| | - Christian Rückert
- Centrum für Biotechnologie, CeBiTec, Universität Bielefeld, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Tobias Busche
- Centrum für Biotechnologie, CeBiTec, Universität Bielefeld, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Wolfgang Wohlleben
- Mikrobiologie und Biotechnologie, Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tuebingen, Germany
- Cluster of Excellence EXC 2124—Controlling Microbes to Fight Infections, 72076 Tuebingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, 72076 Tuebingen, Germany
| | - Jörn Kalinowski
- Centrum für Biotechnologie, CeBiTec, Universität Bielefeld, Universitätsstr. 27, 33615 Bielefeld, Germany
- Correspondence: (T.S.); (J.K.)
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Seventeen Ustilaginaceae High-Quality Genome Sequences Allow Phylogenomic Analysis and Provide Insights into Secondary Metabolite Synthesis. J Fungi (Basel) 2022; 8:jof8030269. [PMID: 35330271 PMCID: PMC8951962 DOI: 10.3390/jof8030269] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 02/04/2023] Open
Abstract
The family of Ustilaginaceae belongs to the order of Basidiomycetes. Despite their plant pathogenicity causing, e.g., corn smut disease, they are also known as natural producers of value-added chemicals such as extracellular glycolipids, organic acids, and polyols. Here, we present 17 high-quality draft genome sequences (N50 > 1 Mb) combining third-generation nanopore and second-generation Illumina sequencing. The data were analyzed with taxonomical genome-based bioinformatics methods such as Percentage of Conserved Proteins (POCP), Average Nucleotide Identity (ANI), and Average Amino Acid Identity (AAI) analyses indicating that a reclassification of the Ustilaginaceae family might be required. Further, conserved core genes were determined to calculate a phylogenomic core genome tree of the Ustilaginaceae that also supported the results of the other phylogenomic analysis. In addition, to genomic comparisons, secondary metabolite clusters (e.g., itaconic acid, mannosylerythritol lipids, and ustilagic acid) of biotechnological interest were analyzed, whereas the sheer number of clusters did not differ much between species.
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Genomic and Experimental Analysis of the Insecticidal Factors Secreted by the Entomopathogenic Fungus Beauveria pseudobassiana RGM 2184. J Fungi (Basel) 2022; 8:jof8030253. [PMID: 35330256 PMCID: PMC8952764 DOI: 10.3390/jof8030253] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 02/22/2022] [Accepted: 02/26/2022] [Indexed: 02/04/2023] Open
Abstract
The entomopathogenic fungus Beauveria pseudobassiana strain RGM 2184 can reach a maximum efficacy of 80% against the quarantine pest Lobesia botrana in field assays. In this study, the RGM 2184 genome was sequenced, and genome mining analyses were performed to predict the factors involved in its insecticidal activity. Additionally, the metabolic profiling of the RMG 2184 culture’s supernatants was analyzed by mass spectrometry, and the insecticidal activity from one of these extracts was evaluated in Galleria mellonella larvae. The genome analysis resulted in 114 genes encoding for extracellular enzymes, four biosynthetic gene clusters reported as producers of insecticidal and bactericidal factors (oosporein, beauvericin, desmethylbassianin, and beauveriolide), 20 toxins, and at least 40 undescribed potential biocontrol factors (polyketides and nonribosomal peptides). Comparative genomic analysis revealed that 65–95% of these genes are Beauveria genus-specific. Metabolic profiling of supernatant extracts from RGM 2184 cultures exhibited secondary metabolites such as beauveriolide, oosporein, inflatin C, and bassiatin. However, a number of detected metabolites still remain undescribed. The metabolite extract caused 79% mortality of Galleria mellonella larvae at 28 days. The results of this research lay the groundwork for the study of new insecticidal molecules.
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