Discovery of Highly Conserved Evolutionary Regions in Polyhydroxyalkanoate Synthase (PhaC) From Pseudomonas sp. Using Bioinformatics and In-silico Approaches

Abstract

- Microbial polyesters such as polyhydroxyalkanoates (PHAs) are biopolymers with unique physicochemical and thermal properties that can replace synthetic polymers from the environment. The ability of these polymers to aid multiple processes in pharmaceuticals, drug delivery systems, and bioplastic materials has increased their worth in the polymer industry. Polyhydroxyalkanoate synthase (PhaC) has a crucial role in the biosynthesis of PHA and is produced by various microbes. Pseudomonas strains have a high potential to produce PhaC. Due to limited structural, functional, and phylogenetic studies of the PhaC, its important evolutionary and underlying molecular functional characteristics remain unknown. This study envisaged finding out the phylogenetic relation, conserved motifs, and 3D structural coherence in PhaC for various species of the Pseudomonas . Three highly regions conserved evolutionary regions named R1, R2, and R3 were identified in forty strains of Pseudomonas including five conserved regions in each phylogenetic group formed. R1 with amino acid sequence of (Arg-263)-(Glu-264)-(Trp-265)-(Gly-266)-(Leu-267), R2 with (Phe-367)-(Ala-368)-(Trp-369)-(Met-370)-(Arg-371)-(Pro-372)-(Asn-373)-(Asp-374)-(Leu-375)-(Ile-376) and R3 having (Asp-452)-(His-453)-(Ile-454)-(Thr-455)-(Pro-456)-(Trp-457) amino acid sequence were determined. Ramachandran plot analysis for the PhaC of P. fluorescens, P. stutzeri, P. putida, P. aeruginosa , and P. syringae suggested that nearly 87% of the residues of PhaC are in favored regions with 11-12% in additionally allowed and 1-2% in allowed regions. This study has confirmed for the first time the presence of three highly conserved in the PhaC protein of the Pseudomonas genus additionally with conserved sites in each phylogenetic group that can help in understanding and improving the function of this protein in the future. Comparative analysis of PhaC 3-D structures for Chromobacterium sp. USM2 and Ralstonia eutropha with the predicted structures of PhaC of Pseudomonas strains was performed. It showed that the binding ability of the catalytic site of Pseudomonas strains is different as compared to that already predicted in Chromobacterium sp. USM2 (PDB ID 6K3C), Ralstonia