Genomic and structural elucidation of multi-heavy metal tolerance in the p-nitrophenol-degrading bacterium Pseudomonas asiatica strain PNPG3

Pseudomonas asiatica strain PNPG3 demonstrated broad-spectrum heavy-metal tolerance, with minimum inhibitory concentrations (MICs) of 800, 400, 4, and 6 µg/mL (ppm) for arsenite, cadmium (Cd), cobalt (Co), and nickel (Ni), respectively. When exposed to 1 mM arsenite, strain PNPG3 retained approximately 89% of its p-nitrophenol (PNP) degradation efficiency relative to the PNP-only baseline, mineralizing 86% of 0.5 mM PNP within 66 h and releasing 0.41 mM nitrite, indicating strong catabolic resilience under combined PNP–arsenite stress. Genome analysis identified a distinct arsenic (As) tolerance and biotransformation gene cluster on contig 1, comprising coordinated transport, regulatory, and metabolic components, including an ArsR/SmtB family transcriptional regulator and an ArsJ-associated glyceraldehyde-3-phosphate dehydrogenase, suggesting the presence of a specialized and potentially novel As detoxification mechanism. Comparative genomics further revealed conservation of key abiotic and biotic stress response genes, along with metabolic pathways supporting degradation of styrene, dioxins, polycyclic aromatic hydrocarbons, cyanate, and diverse aromatic xenobiotics. Chromate reductase (ChrR) and arsenate reductase (ArsC), key enzymes involved in the biotransformation of Cr (VI) to Cr (III) and arsenate [As(V)] to arsenite [As(III)], respectively, were modeled, characterized, and validated, followed by docking analyses to elucidate heavy-metal interactions at their active sites. Molecular dynamics simulation (MDS) indicated that the ArsC–arsenate complex exhibited higher structural stability and compactness, with limited conformational fluctuations, implied greater robustness of arsenate reduction compared to Cr(VI) reduction under in situ metal stress conditions. Overall, the phenotypic robustness and genomic potential of strain PNPG3 underscore its strong capacity for heavy-metal tolerance, PNP biodegradation, and arsenate biotransformation, highlighting its promise for scalable bioremediation applications.