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An HMM approach exp...
An HMM approach expands the landscape of sesquiterpene cyclases across the kingdom Fungi
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- Hage, Hayat (författare)
- Aix-Marseille Université,Aix Marseille University
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Couillaud, Julie, 1992 (författare)
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- Salamov, A. (författare)
- DOE Joint Genome Institute
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- Loussouarn-Yvon, Margot (författare)
- Aix-Marseille Université,Aix Marseille University
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Durbesson, Fabien (författare)
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Ormeño, Elena (författare)
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- Grisel, Sacha (författare)
- Aix-Marseille Université,Aix Marseille University
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Duquesne, Katia (författare)
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Vincentelli, Renaud (författare)
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- Grigoriev, Igor (författare)
- Lawrence Berkeley National Laboratory,University of California at Berkeley,DOE Joint Genome Institute
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Iacazio, Gilles (författare)
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- Rosso, Marie Noëlle (författare)
- Aix-Marseille Université,Aix Marseille University
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(creator_code:org_t)
- 2023
- 2023
- Engelska.
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Ingår i: Microbial Genomics. - 2057-5858. ; 9:4
- Relaterad länk:
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https://research.cha... (primary) (free)
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https://research.cha...
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- 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.
Ämnesord
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Genetik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Genetics (hsv//eng)
Nyckelord
- terpene synthase
- Polyporales
- genome
- sesquiterpene
- Keywords : fungi
Publikations- och innehållstyp
- art (ämneskategori)
- ref (ämneskategori)
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Hage, Hayat
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Couillaud, Julie ...
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Salamov, A.
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Loussouarn-Yvon, ...
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Durbesson, Fabie ...
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Ormeño, Elena
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visa fler...
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Grisel, Sacha
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Duquesne, Katia
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Vincentelli, Ren ...
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Grigoriev, Igor
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Iacazio, Gilles
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Rosso, Marie Noë ...
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visa färre...
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