Computational Analysis of Some Enzymes Involved in Synthesis of Secondary Metabolites in Camellia Sinensis

Abstract

Tea is one of the most popular beverages worldwide, native to Southeast Asia but currently cultivated in over 35 countries. Studies on its chemical composition reveal that polyphenol metabolites account for 25% to 35% of the total dry weight. Tea has many health benefits owing to secondary metabolites whose level of expression in various tea clones determine tea flavor. The flavor (taste and aroma) and the color of processed tea are used to assess its quality and therefore a detailed analysis of key enzymes involved in the synthesis of secondary metabolites is necessary.  Enzyme PAL (phenylalanine ammonia-lyase) a key enzyme in the phenylpropanoid pathway, playing an important role in the plant development and defense. C4H (cinnamte-4-hydroxylse) an important enzyme in allocating significant amounts of carbon from phenylalanine into the biosynthesis of several metabolites, It maintains activities of the metabolic flux for the operation of the flavanoid pathway. 4CL (4-coumarate: COA ligase) the last enzyme in the general phenylpropanoid pathway that provides precursors for the biosynthesis of a large variety of plant natural products like COA thiol esters of 4-coumarate and other hydroxycinnamate. FLS (flavonol synthase) a key enzyme in flavonol synthesisthat determines the final content of flavonols which play an important role in defense related functions and as potent antioxidants. ANS (anthocyanidin synthase) an enzyme in the biosynthetic pathway to anthocyanin. This study employed a computational approach in the analysis of some of these enzymes to gain insight into the mechanism of synthesis of these bioactive secondary metabolites. Biological databases were used to retrieve amino acid sequences of these key enzymes. Consensus conserved regions in these sequences were identified from highly identical homologs which were useful in modeling the enzymes' three dimensional structures.  A total of 5 key enzymes were analyzed and pockets and cavities in their structures; hence the putative substrate binding sites determined, which gave insight into the enzymes-substrate as well as enzyme cofactor interactions. The preferred orientations of the interactions between substrates and/or co-factors with the enzymes were also simulated through molecular docking.  Analysis of these enzymes revealed unique enzyme structures and very specific substrate and co-factor preference. This analysis offers a platform for optimization of selective expression of these key enzymes through gene expression assays that can potentially alter the quality yield of tea clones.

Keywords: camellia sinensis, Secondary metabolites, Conserved regions, Pockets and cavities, Molecular docking