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Novel approach in whole genome mining and transcriptome analysis reveal conserved RiPPs in Trichoderma spp

BACKGROUND: Ribosomally 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 RiPP...

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Autores principales: Vignolle, Gabriel A., Mach, Robert L., Mach-Aigner, Astrid R., Derntl, Christian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7099791/
https://www.ncbi.nlm.nih.gov/pubmed/32216757
http://dx.doi.org/10.1186/s12864-020-6653-6
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author Vignolle, Gabriel A.
Mach, Robert L.
Mach-Aigner, Astrid R.
Derntl, Christian
author_facet Vignolle, Gabriel A.
Mach, Robert L.
Mach-Aigner, Astrid R.
Derntl, Christian
author_sort Vignolle, Gabriel A.
collection PubMed
description BACKGROUND: Ribosomally 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. RESULTS: Here 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. CONCLUSION: We 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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spelling pubmed-70997912020-03-30 Novel approach in whole genome mining and transcriptome analysis reveal conserved RiPPs in Trichoderma spp Vignolle, Gabriel A. Mach, Robert L. Mach-Aigner, Astrid R. Derntl, Christian BMC Genomics Methodology Article BACKGROUND: Ribosomally 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. RESULTS: Here 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. CONCLUSION: We 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. BioMed Central 2020-03-27 /pmc/articles/PMC7099791/ /pubmed/32216757 http://dx.doi.org/10.1186/s12864-020-6653-6 Text en © The Author(s). 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Methodology Article
Vignolle, Gabriel A.
Mach, Robert L.
Mach-Aigner, Astrid R.
Derntl, Christian
Novel approach in whole genome mining and transcriptome analysis reveal conserved RiPPs in Trichoderma spp
title Novel approach in whole genome mining and transcriptome analysis reveal conserved RiPPs in Trichoderma spp
title_full Novel approach in whole genome mining and transcriptome analysis reveal conserved RiPPs in Trichoderma spp
title_fullStr Novel approach in whole genome mining and transcriptome analysis reveal conserved RiPPs in Trichoderma spp
title_full_unstemmed Novel approach in whole genome mining and transcriptome analysis reveal conserved RiPPs in Trichoderma spp
title_short Novel approach in whole genome mining and transcriptome analysis reveal conserved RiPPs in Trichoderma spp
title_sort novel approach in whole genome mining and transcriptome analysis reveal conserved ripps in trichoderma spp
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7099791/
https://www.ncbi.nlm.nih.gov/pubmed/32216757
http://dx.doi.org/10.1186/s12864-020-6653-6
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