Genomic insights on gene clusters and pathways for the biodegradation of plastic compounds: Unravelling the metabolic versatility in a Dietzia kunjamensis IITR165

Abstract

The Dietzia kunjamensis IITR165 bacterium, capable of degrading dibutyl phthalate (DBP), terephthalate (TPA), and polyethylene terephthalate (PET), was studied to uncover its metabolic pathways. Whole-genome analysis revealed a circular chromosome of 3,477,711 bp and a plasmid of 58,850 bp with 70.6 % GC content. Among 3,311 functional genes, phthalate dioxygenase/decarboxylase (padAa1, padAb1, phtB, phtC), alkane monooxygenase (alkB), di-and mono-alkyl phthalate hydrolase, and extra-diol dioxygenase were identified. Gene clusters for terephthalate (tphA1A2A3 and tphB), benzoic acid (benABCD), and catechol (catABCD) were also found. Strain IITR165 metabolized of 1000 mg/L of TPA in 96 h with a half-life of 15.36 h⁻¹, producing phthalic acid (PA), benzoic acid (BA), and catechol as metabolites based on Q-TOF LC/MS-MS analysis. Scanning electron micrograph reveals the extensive biofilm and surface modification of PET sheet after bacterial treatment. A novel PET-hydrolase (PET165) protein, sharing 45.70 % amino acid homology with reported PETases, was discovered, with docking studies showing a conserved catalytic triad (Serine-128, Aspartate-261, and Histidine-287) interacting with the PET ligand. The presence of this novel PET hydrolase and the tpa gene cluster, along with genes involved in nylon, and polystyrene metabolism, indicates versatility of the bacterium useful in treatment of a mixed plastic contaminated ecological niches.