Comparative analysis of plant lycopene cyclases

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 (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.