Genome-wide characterization of PAL, C4H, and 4CL genes regulating the phenylpropanoid pathway in Vanilla planifolia

Phenylalanine ammonia lyase (PAL), cinnamate 4-hydroxylase (C4H) and 4-coumarate: CoA ligase (4CL) genes encodes the enzymes catalyzing the steps of the phenylpropanoid pathway which is responsible for the biosynthesis of a diverse range of therapeutically important phenylpropanoids. In the present study, identification and characterization of the PAL, C4H and 4CL gene family in an economically and medicinally important orchid species, Vanilla planifolia was done. Six PAL, two C4H and five 4CL proteins have been identified in Vanilla planifolia. All the amino acid residues related to the enzymatic activity were found to be conserved in all the identified proteins. Subcellular localization of VplPAL, VplC4H and Vpl4CL proteins predicted their location in the cytoplasm, endoplasmic reticulum and peroxisome, respectively. Alpha helices and random coils predominated the secondary structure of these proteins. Gene structure analysis showed the presence of two introns in C4H genes while PAL and 4CL genes had one and four introns present, respectively in the majority of members. The analysis of promoter sequences predicted cis-regulatory elements regulated by light, plant growth and development, phytohormones and abiotic and biotic stress conditions. Expression profiling of genes revealed variable relative expression for all the identified genes in various vegetative and reproductive tissues, suggesting their overall role in growth and development.