In silico identification and characterisation of putative biphenyl degradation mechanism in gut-derived Pediococcus...

Polychlorinated biphenyls (PCBs) persist in the environment and bioaccumulate through the food chain. Probiotic microorganisms offer a potential strategy to reduce PCB uptake in livestock guts. This study aimed to identify and characterise potential biphenyl degradation capabilities in Pediococcus pentosaceus QS-GN03_1, isolated from the gut of the cockroach, Periplaneta americana for application as a PCB-detoxifying probiotic feed additive. Whole-genome sequencing yielded an approximately 1.86 Mbp assembly with 98.3 % BUSCO completeness. Genomic annotation revealed the presence of a putative biphenyl-2,3-diol 1,2-dioxygenase (BphC; PPBPHCIII) homologue. Compositional analysis surrounding this gene identified atypical genomic singatures and nearby IS481/ISNCY insertion sequence which suggests this gene locus was acquired through horizontal gene transfer independent of other bph genes. Promoter analysis affirmed PPBPHCIII possesses promoter elements and adopts a structure highly similar to functional BphC enzymes from the Protein Data Bank (RMSD 1.357 Å against Pseudomonas BphC PDB ID: 1EIR benchmark). Molecular docking and 100 ns averaged molecular dynamics (MD) simulations indicated stable binding of 2,3-dichlorobiphenyl ligand within a conserved active site coordinated by Fe (II), primarily via electrostatic and hydrophobic interactions. However, the free ligand binding energy calculations predicted a weaker binding affinity for PPBPHCIII compared to the functionally verified 1EIR complex which the difference was primarily due to fewer hydrogen bonds formations. While QS-GN03_1 lacks independent PCB mineralisation capabilities, the isolated presence of a highly ameliorated bphC gene suggests and ancient horizontal acquisition of a larger Bph operon, followed by reductive evolution due to lack of selective pressure. The discovery of native IS30-family insertion sequences within its genome offers synthetic biology opportunity for chromosomal integration of a complete Bph operon, allowing the generation of QS-GN03_1 with complete PCB degradation capability.