Cloning and Bioinformatics Investigation on CCD4a and CCD4b Genes from Iranian Saffron (Crocus sativus L.)

Saffron is one of the most expensive spices and natural colors used in various food, pharmaceutical and cosmetic industries. In recent years, a family of enzymes that digest carotenoid substrates into double bonds are identified and introduced in plants. This family is of enzymes Carotenoid Cleavage Dioxygenase (CCD) enzymes. In this study, two isoforms of this gene were cloned and sequenced due to the importance of CCD genes in biosynthesis of apocarotenoids. Bioinformatics analyses including phylogenetic relationships and protein structures were evaluated. 3D modeling of these proteins was done by homologous modeling and using the Swiss Model database after selecting the appropriate pattern. The Ramachandran plot was drawn in order to validate the structure of the 3D model. The results show that the two CCD4a and CCD4b isoforms have both exons and one intron. In silico analysis, the physicochemical properties of CsCCD4a and CsCCD4b proteins also show that the proteins derived from these two isoforms are similar in terms of molecular weight, amino acids, isoelectric points, aliphatic index, instability index and solubility. The results of study of 3D structures resulted in proposal of similar structures for two isoforms. The results of this study can provide valuable information on the behavior and response of CCD4 enzyme in the pathway for synthesis of apricotines in saffron, and these results can be useful in future protein engineering programs.