title: Comparative analysis of plant lycopene cyclases.
abstract: Carotenoids 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 (β-LCY and ϵ-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, β-LCYs and ϵ-LCYs were classified in β and ϵ 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 β-LCY and ϵ-LCY genes, nucleotide diversities were found to be π: 0.30 and π: 0.25, respectively. The result highlighted β-LCY genes showed higher nucleotide diversity than ϵ-LCY genes. 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 β-LCYs and ϵ-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 (β-LCY and ϵ-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 β-LCYs and ϵ-LCYs with conserved structure. In addition to lycopene cyclase domain, the V/IXGXGXXGXXXA 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.
authors.affiliation: Gebze Technical University, Faculty of Science, Department of Molecular Biology and Genetics, Gebze, Kocaeli, 41400, Turkey; Crop Science, University of Illinois at Urbana-Champaign, United States. Electronic address: koc_ibrahim@yahoo.com.
authors.forename: Ibrahim
authors.initials: I
authors.lastname: Koc
authors.affiliation: Duzce University, Department of Crop and Animal Production, Cilimli Vocational School, 81750, Cilimli, Duzce, Turkey.
authors.forename: Ertugrul
authors.initials: E
authors.lastname: Filiz
authors.affiliation: Department of Biology, Faculty of Science and Arts, Fatih University, Büyükçekmece, İstanbul, Turkey.
authors.forename: Huseyin
authors.initials: H
authors.lastname: Tombuloglu
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D019753:Intramolecular Lyases / Q000235:genetics* / Q000378:metabolism; D019684:Magnoliopsida / Q000201:enzymology / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D060066:Protein Interaction Maps
chemical_list: D010940:Plant Proteins; D019753:Intramolecular Lyases; C070925:lycopene cyclase-isomerase
keywords: Beta carotene; Carotenoid; Lycopene cyclase; Rossmann fold domain