Sequence analysis, structure prediction, and functional validation of phaC1/phaC2 genes of Pseudomonas sp. LDC-25 and its importance in polyhydroxyalkanoate accumulation

Abstract

Polyhydroxyalkanoates (PHAs) are attractive biomaterials in both conventional medical devices and tissue engineering. PHA synthase is responsible for catalyzing the formation of Polyhydroxyalkanoates (PHA), but its structural information is limited. Hence, this study focuses to predict 3D model for phaC1 and phaC2 genes of field-soil strain Pseudomonas sp. LDC-25 and to validate the functional properties through in vitro studies. The phaC1/phaC2 genes were amplified, cloned, and sequenced. The sequence analysis showed > 90% homology to phaC loci and presence of alpha/beta hydrolase fold, but phaC2 loci of LDC-25 exhibits variation in the conserved residue (Ser is replaced by Ala). Threading approach demonstrated that Carboxylesterase (d1tqha) can be used as the modeling template. The predicted models showed the presence of conserved residues at 122 (G), 205 (S), and 236 (S). In vitro studies also supported that PHA accumulation ability was less in Pseudomonas sp. LDC-25 compared to other field isolate, Pseudomonas sp. LDC-5. FT-IR spectrum showed PHA specific peaks at 1735.62 cm(-1). Results of this study would help to detect the functional domains of the protein in order to elucidate their structure/function characteristics with special emphasis on invariant conserved residues.