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

Abstract

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.

New developments in RiPP discovery, enzymology and engineering

“…227 The bioinformatic analysis of fungal genomes also resulted in the discovery of new or proposed compounds. 17,228 Precursor peptides containing a signal peptide and repeated core peptides were observed frequently in the neighborhood of homologs of the UstYa and UstYb proteins and as many as 96 ustiloxin precursor peptide/UstY pairs were identied. 17 At least 38 different types of repeat sequences were reported that may produce a wide variety of post-translationally modied products.…”

Molecular methods unravel the biosynthetic potential of Trichoderma species

“…is surely expected to grow rapidly. And while the biosynthetic gene clusters of Trichoderma have been shown to be highly programmed and quite challenging to manipulate, recent advances in metabolic engineering strategies, genome mining and comparative analysis tools 27,44,71,81,[123][124][125][126][127][128] can help resolve this and help explore and exploit the full potential of this genus.…”

“…also produce ribosomally synthesized and post translationally modified peptides (RiPP). 44 Fungal polyketide synthases are classified based on their catalytic domain structure into three different types; highly reducing polyketide synthases (hr-PKS), partially reducing polyketide synthases (pr-PKS) and non-reducing polyketide synthases (nr-PKS). Highly reducing polyketide synthases usually synthesize highly reduced, often linear, products and the others synthetize aromatic compounds with phenol groups.…”

The evolutionary history of the lethal amanitin biosynthesis genes in Amanita rubescens complex edible mushrooms and its potential health risk

“…Most of the secondary metabolite pathways of fungal organisms are encoded by biosynthetic or metabolic gene clusters (BGC or MGC) (Rokas et al, 2020;Vignolle et al, 2020). We showed that in the POPD genes neighborhood three different superfamilies related to secondary metabolite transport were found: MATE (multidrug and toxic compound extrusion), MFS (major facilitator superfamily) and ATP-binding cassette proteins transporter (ABC).…”