In Silico Analysis of Polycyclic Aromatic Hydrocarbon (PAH) Degrader from Bordetella petrii Strain P003 Isolated from Contaminated Oil of Kuwait

Bordetella petrii is an environmentally versatile Gram-negative bacterium with hydrocarbon-degrading capabilities, yet its genetic and metabolic characteristics remain poorly characterized. This study investigated the genomic features of a PAH-degrading Bordetella petrii strain P003 isolated from contaminated oil in Kuwait using bioinformatic approaches. The genome of B. petrii P003 was sequenced and analyzed for genomic islands, comparative genomics, and PAH degradation pathways. The draft genome assembly of B. petrii P003 was 5,011,660 bp with 49 contigs and 68.67% GC content. It contained 4687 coding sequences, 5 rRNAs, and 56 tRNAs. Prediction of genomic islands (GIs) revealed that strain P003 possessed 99 GIs, whereas the reference B. pertii DSM 12,804 had 58 unique GIs. Comparative genomics showed 279 locally collinear blocks with the reference strain. The P003 genome encoded multiple genes involved in PAH, naphthalene, and benzoate degradation pathways, including an 8-gene PAH operon (pht4, ph2, pht5, pht3, pcaG, pcaH, nahAb/nagAb/ndoA/nbzA). We found that pcaG and pcaH encode the enzymes responsible for the breakdown of PAH, protocatechuate 3,4-dioxygenase, alpha and beta subunits (EC: 1.13.11.3). The genomic analysis of B. petrii P003 provides insights into its PAH degradation capabilities and potential for bioremediation applications. The strain possesses an expanded repertoire of aromatic compound degradation genes compared to reference strains, suggesting enhanced metabolic versatility for degrading environmental pollutants.