Comparative analysis of plant lycopene cyclases

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dc.contributor.authorKoç, İbrahim
dc.contributor.authorFiliz, Ertuğrul
dc.contributor.authorTombuloğlu, Hüseyin
dc.date.accessioned2020-04-30T22:41:05Z
dc.date.available2020-04-30T22:41:05Z
dc.date.issued2015
dc.departmentDÜ, Çilimli Meslek Yüksekokulu, Bitkisel ve Hayvansal Üretim Bölümüen_US
dc.descriptionFiliz, Ertugrul/0000-0001-9636-6389; Tombuloglu, Huseyin/0000-0001-8546-2658en_US
dc.descriptionWOS: 000364897700009en_US
dc.descriptionPubMed: 26092704en_US
dc.description.abstractCarotenoids are essential isoprenoid pigments produced by plants, algae, fungi and bacteria. Lycopene cyclase (LYC) commonly cyclize carotenoids, which is an important branching step in the carotenogenesis, at one or both end of the backbone. Plants have two types of LYC (beta-LCY and epsilon-LCY). In this study, plant LYCs were analyzed. Based on domain analysis, all LYCs accommodate lycopene cyclase domain (Pf05834). Furthermore, motif analysis indicated that motifs were conserved among the plants. On the basis of phylogenetic analysis, beta-LCYs and epsilon-LCYs were classified in beta and & groups. Monocot and dicot plants separated from each other in the phylogenetic tree. Subsequently, Oryza sativa Japonica Group and Zea mays of LYCs as monocot plants and Vitis vinifera and Solanum lycopersicum of LYCs as dicot plants were analyzed. According to nucleotide diversity analysis of beta-LCYand epsilon-LCYgenes, nucleotide diversities were found to be pi: 0.30 and pi: 0.25, respectively. The result highlighted beta-LCY genes showed higher nucleotide diversity than a-LCYgenes. LYCs interacting genes and their co-expression partners were also predicted using String server. The obtained data suggested the importance of LYCs in carotenoid metabolism. 3D modeling revealed that depicted structures were similar in O. sativa, Z mays, S. lycopersicum, and V. vinifera beta-LCYs and epsilon-LCYs. Likewise, the predicted binding sites were highly similar between O. sativa, Z mays, S. lycopersicum, and V. vinifera LCYs. Most importantly, analysis elucidated the V/IXGXGXXGXXXA motif for both type of LYC (beta-LCY and epsilon-LCY). This motif related to Rossmann fold domain and probably provides a flat platform for binding of FAD in O. sativa, Z mays, S. lycopersicum, and V vinifera beta-LCYs and epsilon-LCYs with conserved structure. In addition to lycopene cyclase domain, the V/IXGXGXXMOOCA motif can be used for exploring LYCs proteins and to annotate the function of unknown proteins containing lycopene cyclase domain. Overall results indicated that a high degree of conserved signature were observed in plant LYCs. (C) 2015 Elsevier Ltd. All rights reserved.en_US
dc.identifier.doi10.1016/j.compbiolchem.2015.06.001en_US
dc.identifier.endpage92en_US
dc.identifier.issn1476-9271
dc.identifier.issn1476-928X
dc.identifier.scopusqualityQ2en_US
dc.identifier.startpage81en_US
dc.identifier.urihttps://doi.org/10.1016/j.compbiolchem.2015.06.001
dc.identifier.urihttps://hdl.handle.net/20.500.12684/3121
dc.identifier.volume58en_US
dc.identifier.wosWOS:000364897700009en_US
dc.identifier.wosqualityQ3en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakPubMeden_US
dc.indekslendigikaynakScopusen_US
dc.language.isoenen_US
dc.publisherElsevier Sci Ltden_US
dc.relation.ispartofComputational Biology And Chemistryen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/closedAccessen_US
dc.subjectLycopene cyclaseen_US
dc.subjectCarotenoiden_US
dc.subjectRossmann fold domainen_US
dc.subjectBeta caroteneen_US
dc.titleComparative analysis of plant lycopene cyclasesen_US
dc.typeArticleen_US

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