ArticleBMC genomics2020
Novel approach in whole genome mining and transcriptome analysis reveal conserved RiPPs in Trichoderma spp.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 25 citations in OpenAlex.
- EngineeringAIMS microbiology · 2026Review
- A class of benzofuranoindoline-bearing heptacyclic fungal RiPPs with anticancer activities.Nature chemical biology · 2025Article
- Biocontrol Potential of NativeJournal of fungi (Basel, Switzerland) · 2025Article
- Fungal Metabolomics: A Comprehensive Approach to Understanding Pathogenesis in Humans and Identifying Potential Therapeutics.Journal of fungi (Basel, Switzerland) · 2025Review
- Review
- Comparative Genomics of Fungi in Nectriaceae Reveals Their Environmental Adaptation and Conservation Strategies.Journal of fungi (Basel, Switzerland) · 2024Article
- Characterization of the Biosynthetic Gene Cluster for the Ribosomally Synthesized Cyclic Peptide Epichloëcyclins inJournal of agricultural and food chemistry · 2023Article
- Characterization of Peptaibols Produced by a Marine Strain of the FungusMetabolites · 2023Article
- Application of Gene Knockout and Heterologous Expression Strategy in Fungal Secondary Metabolites Biosynthesis.Marine drugs · 2022Review
- Exploring fungal RiPPs from the perspective of chemical ecology.Fungal biology and biotechnology · 2022Review
- Biosynthetic Potential of the Endophytic Fungus Helotiales sp. BL73 Revealed via Compound Identification and Genome Mining.Applied and environmental microbiology · 2022Article
- Review
- Molecular methods unravel the biosynthetic potential ofRSC advances · 2021Review
- New developments in RiPP discovery, enzymology and engineering.Natural product reports · 2021Review
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
backgroundRibosomally synthesized and post-translationally modified peptides (RiPPs) are a highly diverse group of secondary metabolites (SM) of bacterial and fungal origin. While RiPPs have been intensively studied in bacteria, little is known about fungal RiPPs. In Fungi only six classes of RiPPs are described. Current strategies for genome mining are based on these six known classes. However, the genes involved in the biosynthesis of theses RiPPs are normally organized in biosynthetic gene clusters (BGC) in fungi.
resultsHere we describe a comprehensive strategy to mine fungal genomes for RiPPs by combining and adapting existing tools (e.g. antiSMASH and RiPPMiner) followed by extensive manual curation based on conserved domain identification, (comparative) phylogenetic analysis, and RNASeq data. Deploying this strategy, we could successfully rediscover already known fungal RiPPs. Further, we analysed four fungal genomes from the Trichoderma genus. We were able to find novel potential RiPP BGCs in Trichoderma using our unconventional mining approach.
conclusionWe demonstrate that the unusual mining approach using tools developed for bacteria can be used in fungi, when carefully curated. Our study is the first report of the potential of Trichoderma to produce RiPPs, the detected clusters encode novel uncharacterized RiPPs. The method described in our study will lead to further mining efforts in all subdivisions of the fungal kingdom.
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