Genome-based identification of hydrocarbon-metabolism-associated genes with putative relevance to polyethylene modification in Rhodococcus pyridinivorans AAa3

Polyethylene (PE) is a highly recalcitrant plastic that accumulates extensively in the environment. In this study, Rhodococcus pyridinivorans AAa3 was analysed using hybrid WGS to investigate its genomic features and identify candidate metabolic functions with putative relevance to PE modification. The assembled genome (5,078,411 bp) exhibited high completeness and continuity. Phylogenetic, phylogenomic, and ANI analyses confirmed the strain's classification, with 98.96 % ANI to R. pyridinivorans DSM 44555^T. Genome mining identified diverse oxidative enzymes, including alkane monooxygenases, cytochrome P450s, Baeyer-Villiger monooxygenases, and multicopper oxidases. Analysis of AlkB proteins showed conserved motifs, transmembrane domains, and phylogenetic conservation. Orthology and synteny analyses showed conservation of AlkB proteins and their genomic neighbourhoods, with strain-specific variation. AAa3 contained five MCO genes, placing it toward the upper end of the copy-number distribution across 41 R. pyridinivorans genomes. Molecular docking showed accommodation of n-octane, n-decane, and n-dodecane within the targeted regions of AlkB1 and AlkB2. An AlkX-like TetR-family regulator was identified near alkB2, while targeted motif analysis detected an AlkX-like motif upstream of cytochrome P450 gene ACU6L1_03615. To the best of our knowledge, no previous genome-based study has specifically investigated R. pyridinivorans in the context of PE modification. These findings warrant further experimental investigation.