Comparative analyses of squalene synthase (SQS) proteins in poplar and pine by using bioinformatics tools

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dc.contributor.authorFiliz, Ertuğrul
dc.contributor.authorÖzyiğit, İbrahim İlker
dc.contributor.authorVatansever, Recep
dc.date.accessioned2020-04-30T22:41:04Z
dc.date.available2020-04-30T22:41:04Z
dc.date.issued2016
dc.departmentDÜ, Çilimli Meslek Yüksekokulu, Bitkisel ve Hayvansal Üretim Bölümüen_US
dc.descriptionFiliz, Ertugrul/0000-0001-9636-6389; Ozyigit, Ibrahim Ilker/0000-0002-0825-5951en_US
dc.descriptionWOS: 000388376600007en_US
dc.description.abstractSqualene synthase (SQS, EC 2.5.1.21) is a major enzyme in biosynthesis of isoprenoid (farnesyl pyrophosphate (FPP) squalene). In the present study, we have analyzed SQS enzymes of black cottonwood (Populus trichocarpa, hereafter Pt) and Masson's pine (Pinus massoniana, hereafter Pm) using bioinformatics tools. PtSQS and PmSQS sequences were found to have very similar physicochemical properties with "squalene/phytoene synthase" domain structure (PF00494). PtSQS sequence was 47.3 kDa weight and 413 amino acids long with a pI value of 6.86, while PmSQS was 46.6 kDa weight and 409 amino acids long with a pI of 7.92. Alignment of SQS protein sequences in 15 plant species showed a highly similar conserved pattern and included (DTVED81)-D-77 and (DYLED217)-D-213 motifs, which are rich in aspartic acids, for FPP binding sites. In phylogenetic tree, monocots and polycot were clearly separated from dicots with high bootstrap value (99 %). A total of 10 interaction partners were predicted for PtSQS and PmSQS proteins. Nine of them were hypothetical proteins (related with phytosterol biosynthesis), while one was putative uncharacterized protein. Similar 3D structures and identical binding sites were predicted for pine and poplar. In docking, FPP-PtSQS was found to make 8 H bonds with Asp81, Asp217, Glu80, and Gln206 residues in poplar with highest affinity while FPP-PmSQS made 7 H bonds with Arg49, Arg74, Ser48, and Val47 residues in pine with highest affinity. The results of this study will provide valuable theoretical knowledge for future studies of identification and characterization of SQS genes and proteins in various tree species and will provide an insight for studies of biotechnological manipulation of sterol biosynthesis pathway to enhance the plant stress tolerance and productivity.en_US
dc.identifier.doi10.1007/s11295-016-0992-0en_US
dc.identifier.issn1614-2942
dc.identifier.issn1614-2950
dc.identifier.issue2en_US
dc.identifier.scopusqualityQ1en_US
dc.identifier.urihttps://doi.org/10.1007/s11295-016-0992-0
dc.identifier.urihttps://hdl.handle.net/20.500.12684/3117
dc.identifier.volume12en_US
dc.identifier.wosWOS:000388376600007en_US
dc.identifier.wosqualityQ1en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakScopusen_US
dc.language.isoenen_US
dc.publisherSpringer Heidelbergen_US
dc.relation.ispartofTree Genetics & Genomesen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/closedAccessen_US
dc.subjectPhytosterolen_US
dc.subjectMolecular dockingen_US
dc.subject3D structureen_US
dc.subjectProtein-protein interactionen_US
dc.titleComparative analyses of squalene synthase (SQS) proteins in poplar and pine by using bioinformatics toolsen_US
dc.typeArticleen_US

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