Bioinformatical Analyses of cinnamyl alcohol dehydrogenase (CAD) proteins from higher plant species

Abstract

Cinnamyl alcohol dehydrogenase (CAD) (EC 1.1.1.195) is an enzyme functioning in the reduction of various phenylpropenyl aldehyde derivatives which are precursors in lignin and lignan production. Species-specific CAD genes have been extensively identified in recent years. In this study, we used bioinformatics tools to characterize and classify plant CADs. The amino acid and nucleotide sequences of 16 CADs from different plant species were used to compare their physiological properties, phylogeny, and conserved motifs. For this purpose, sequence, phylogenetical, structural analyses of proteins were conducted using various servers. All plant CADs had the characteristic alcohol dehydrogenase (PF08240) and zinc-binding dehydrogenase domains (PF00107). According to the physicochemical analysis, it was revealed that the most of plant CADs (81.25%) were in acidic character. Sequence length (aa) and molecular weight (kDa) of CAD proteins were found in range of 356 -367 and 38.6-40.5 respectively. The highest sequence similarities were found between Sorghum bicolor and Zea mays (95.3%), Panicum virgatum and Sorghum bicolor (90.9%), and Oryza sativa and Zea mays (87.1%) respectively. Plant CADs showed divergent exon-intron structures in which exon numbers were ranged from two to six. Four monocot species (S. bicolor, P. virgatum, Z. mays, and O. sativa) have four exons, whereas Brachypodium distachyon contains only two exons. Phylogenetic analysis revealed that the CAD proteins mainly divided into two groups. The highest bootstrap values were found as follows: Fragaria vesca-Prunus persica clade (100%), Glycine maxMedicago truncatula (81%), and S. bicolor-Z. mays (72%). The 3D structures of plant CADs showed that Oryza and Vitis had the most divergent structures when compared to the other plant species. Eventually, the data represented here contribute to studies aiming at evaluating the plant CADs extensively and at identifying new CAD genes in other plants.