An HMM approach expands the landscape of sesquiterpene cyclases across the kingdom Fungi

Abstract

Sesquiterpene cyclases (STC) catalyse the cyclization of the C15 molecule farnesyl diphosphate into a vast variety of mono- or polycyclic hydrocarbons and, for a few enzymes, oxygenated structures, with diverse stereogenic centres. The huge diversity in sesquiterpene skeleton structures in nature is primarily the result of the type of cyclization driven by the STC. Despite the phenomenal impact of fungal sesquiterpenes on the ecology of fungi and their potentials for applications, the fungal sesquiterpenome is largely untapped. The identification of fungal STC is generally based on protein sequence similarity with characterized enzymes. This approach has improved our knowledge on STC in a few fungal species, but it has limited success for the discovery of distant sequences. Besides, the tools based on secondary metabolite biosynthesis gene clusters have shown poor performance for terpene cyclases. Here, we used four sets of sequences of fungal STC that catalyse four types of cyclization, and specific amino acid motives to identify phylogenetically related sequences in the genomes of basidiomycetes fungi from the order Polyporales. We validated that four STC genes newly identified from the genome sequence of Leiotrametes menziesii, each classified in a different phylogenetic clade, catalysed a predicted cyclization of farnesyl diphosphate. We built HMM models and searched STC genes in 656 fungal genomes genomes. We identified 5605 STC genes, which were classified in one of the four clades and had a predicted cyclization mechanism. We noticed that the HMM models were more accurate for the prediction of the type of cyclization catalysed by basidiomycete STC than for ascomycete STC.

Unravelling the Function of the Sesquiterpene Cyclase STC3 in the Life Cycle of <em>Botrytis cinerea</em>

“…The ratio of Bcstc3-homologous proteins per organism was slightly higher in Basidiomycota than in Ascomycota. This difference between phyla has been previously described for terpene synthases and may be related to tandem duplication of the gene clusters in Basidiomycota [46,63,64]. Of the 160 BcStc3 homologous proteins, only one has been previously characterized and crystalized, the terpene cyclase AaTPS of Alternaria alternata [65].…”

Unravelling the Function of the Sesquiterpene Cyclase STC3 in the Lifecycle of Botrytis cinerea

“…Homologous proteins to BcStc3 were identified in 124 fungal species: seven proteins were found in three species of the Agarycomycetes class (Basidiomycota) and the remaining 153 proteins were distributed among 121 Ascomycota species (Table 2). The ratio of BcStc3-homologous proteins per organism was slightly higher in Basidiomycota than in Ascomycota which may be related to the described tandem duplication of the gene clusters in Basidiomycota [39,53,54]. Out of the 160 BcStc3 homologous proteins, only the terpene cyclase AaTPS of Alternaria alternata has been previously characterized [55].…”

“…The three species contain in their genome more than 20 terpene biosynthetic clusters [59,63,64]. This high number of terpene biosynthetic gene clusters, often repeated in tandem, is a characteristic of Basidiomycota and is related to the fact that terpenes and terpenoids are produced more frequently by these fungi than by Ascomycota [53,64,65]. Horizontal gene transfer has been considered one of the primary mechanisms explaining the duplication of these clusters in Basidiomycota and also the transfer of genetic material between phylogenetically unrelated species [53,65,66].…”

“…This high number of terpene biosynthetic gene clusters, often repeated in tandem, is a characteristic of Basidiomycota and is related to the fact that terpenes and terpenoids are produced more frequently by these fungi than by Ascomycota [53,64,65]. Horizontal gene transfer has been considered one of the primary mechanisms explaining the duplication of these clusters in Basidiomycota and also the transfer of genetic material between phylogenetically unrelated species [53,65,66]. For instance, the sesquiterpene cyclase involved in the synthesis of ∆6-protoilludene probably has been horizontally transferred from Basidiomycota to the Ascomycota Diaporthe sp.…”