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Volume 9, Issue 4

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

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 , 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.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): genome , Keywords : fungi , Polyporales , sesquiterpene and terpene synthase
Funding
This study was supported by the:
  • Joint Genome Institute (Award DE-SC0019427)
    • Principle Award Recipient: IgorGrigoriev
  • Fondation Aix-Marseille Universite
    • Principle Award Recipient: MargotLoussouarn-Yvon
  • Aix-Marseille Université
    • Principle Award Recipient: JulieCouillaud
  • Groupement de Recherche Génomique Environnementale
    • Principle Award Recipient: HayatHage
  • Conseil Régional Provence-Alpes-Côte d'Azur
    • Principle Award Recipient: HayatHage
  • INRAE
    • Principle Award Recipient: HayatHage
  • Institut Carnot 3BCAR
    • Principle Award Recipient: HayatHage
  • Joint Genome Institute (Award DE-AC02-05CH11231)
    • Principle Award Recipient: IgorGrigoriev
© 2023 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2023-04-19
2024-05-04
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An HMM approach expands the landscape of sesquiterpene cyclases across the kingdom Fungi
M Gen 9, 000990 (2023); https://doi.org/10.1099/mgen.0.000990
/content/journal/mgen/10.1099/mgen.0.000990
/content/journal/mgen/10.1099/mgen.0.000990
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