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<p>A halotolerant, Gram-negative bacterial isolate, designated PNPBRP5(2), was obtained from pond water and identified as a <i>Pseudomonas</i> species via 16S rRNA gene sequencing. The optimum p-nitrophenol (PNP) concentration for degradation was determined to be 0.5&#xa0;mM, with 98% of the compound degraded within 60&#xa0;h by this strain. PNP degradation occurred through <i>p</i>-benzoquinone (PBQ) as a hydrolytic intermediate accompanied by the release of nitrite. Chemotaxis assays revealed positive responses toward PNP, PBQ, and 4-aminophenol (4AP), with the strongest response observed for 4AP (Chemotactic Index (CI): 6.67 at 200&#xa0;µM), followed by PNP (CI: 4.64 at 250 µM) and PBQ (CI: 3.2 at 150 µM). Growth-based studies under catabolic conditions revealed the utilization of all assessed compounds as the sole carbon (C) source, indicating that the strain possesses genetic information for the mineralization of all three examined xenobiotic compounds. To investigate the molecular basis of PNP biodegradation, homology models of p-nitrophenol-4-monooxygenase (<i>pnpA</i>) were generated, retrieved from the Protein Data Bank (PDB), validated, and subjected to docking studies to elucidate enzyme–substrate interactions at the atomic level. This integrative approach advances beyond prior studies by providing a more comprehensive understanding of the molecular basis of PNP degradation. Overall, the strain PNPBRP5(2) demonstrated strong chemotactic behavior and efficient degradation of PNP and related compounds, highlighting its biotechnological potential for bioremediation of PNP-contaminated aquatic environments.</p>

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Integrative bioinformatics and chemotactic insights into p-nitrophenol bioremediation by halotolerant aquatic Pseudomonas sp. strain PNPBRP5(2)

  • 期刊论文

  • 发表日期：

    2025年10月18日

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  • Sk Aftabul Alam,
  • Biswajit Khan,
  • Debabrata Karmakar,
  • Rajkumar Mandal,
  • Pradipta Saha

摘要

A halotolerant, Gram-negative bacterial isolate, designated PNPBRP5(2), was obtained from pond water and identified as a Pseudomonas species via 16S rRNA gene sequencing. The optimum p-nitrophenol (PNP) concentration for degradation was determined to be 0.5 mM, with 98% of the compound degraded within 60 h by this strain. PNP degradation occurred through p-benzoquinone (PBQ) as a hydrolytic intermediate accompanied by the release of nitrite. Chemotaxis assays revealed positive responses toward PNP, PBQ, and 4-aminophenol (4AP), with the strongest response observed for 4AP (Chemotactic Index (CI): 6.67 at 200 µM), followed by PNP (CI: 4.64 at 250 µM) and PBQ (CI: 3.2 at 150 µM). Growth-based studies under catabolic conditions revealed the utilization of all assessed compounds as the sole carbon (C) source, indicating that the strain possesses genetic information for the mineralization of all three examined xenobiotic compounds. To investigate the molecular basis of PNP biodegradation, homology models of p-nitrophenol-4-monooxygenase (pnpA) were generated, retrieved from the Protein Data Bank (PDB), validated, and subjected to docking studies to elucidate enzyme–substrate interactions at the atomic level. This integrative approach advances beyond prior studies by providing a more comprehensive understanding of the molecular basis of PNP degradation. Overall, the strain PNPBRP5(2) demonstrated strong chemotactic behavior and efficient degradation of PNP and related compounds, highlighting its biotechnological potential for bioremediation of PNP-contaminated aquatic environments.