Sökning: onr:"swepub:oai:research.chalmers.se:e627390a-0906-4641-a7ae-d032a5bb60fd" >
An HMM approach exp...
-
Hage, HayatAix-Marseille Université,Aix Marseille University
(författare)
An HMM approach expands the landscape of sesquiterpene cyclases across the kingdom Fungi
- Artikel/kapitelEngelska2023
Förlag, utgivningsår, omfång ...
-
2023
-
electronicrdacarrier
Nummerbeteckningar
-
LIBRIS-ID:oai:research.chalmers.se:e627390a-0906-4641-a7ae-d032a5bb60fd
-
https://research.chalmers.se/publication/535536URI
-
https://doi.org/10.1099/mgen.0.000990DOI
Kompletterande språkuppgifter
-
Språk:engelska
-
Sammanfattning på:engelska
Ingår i deldatabas
Klassifikation
-
Ämneskategori:art swepub-publicationtype
-
Ämneskategori:ref swepub-contenttype
Anmärkningar
-
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 och genrebeteckningar
Biuppslag (personer, institutioner, konferenser, titlar ...)
-
Couillaud, Julie,1992(Swepub:cth)juliec
(författare)
-
Salamov, A.DOE Joint Genome Institute
(författare)
-
Loussouarn-Yvon, MargotAix-Marseille Université,Aix Marseille University
(författare)
-
Durbesson, Fabien
(författare)
-
Ormeño, Elena
(författare)
-
Grisel, SachaAix-Marseille Université,Aix Marseille University
(författare)
-
Duquesne, Katia
(författare)
-
Vincentelli, Renaud
(författare)
-
Grigoriev, IgorLawrence Berkeley National Laboratory,University of California at Berkeley,DOE Joint Genome Institute
(författare)
-
Iacazio, Gilles
(författare)
-
Rosso, Marie NoëlleAix-Marseille Université,Aix Marseille University
(författare)
-
Aix-Marseille UniversitéDOE Joint Genome Institute
(creator_code:org_t)
Sammanhörande titlar
-
Ingår i:Microbial Genomics9:42057-5858
Internetlänk
Hitta via bibliotek
Till lärosätets databas
- Av författaren/redakt...
-
Hage, Hayat
-
Couillaud, Julie ...
-
Salamov, A.
-
Loussouarn-Yvon, ...
-
Durbesson, Fabie ...
-
Ormeño, Elena
-
visa fler...
-
Grisel, Sacha
-
Duquesne, Katia
-
Vincentelli, Ren ...
-
Grigoriev, Igor
-
Iacazio, Gilles
-
Rosso, Marie Noë ...
-
visa färre...
- Om ämnet
-
- NATURVETENSKAP
-
NATURVETENSKAP
-
och Data och informa ...
-
och Bioinformatik
-
- NATURVETENSKAP
-
NATURVETENSKAP
-
och Biologi
-
och Bioinformatik oc ...
-
- NATURVETENSKAP
-
NATURVETENSKAP
-
och Biologi
-
och Genetik
- Artiklar i publikationen
-
Microbial Genomi ...
- Av lärosätet
-
Chalmers tekniska högskola