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In silico characterization of a novel dehalogenase (DehHX) from the halophile Pseudomonas halophila HX isolated from Tuz Gölü Lake, Turkey: insights into a hypersaline-adapted dehalogenase

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Abstract

Halogenated compounds represent potential long-term threats to human well-being and health and, therefore, the quest for microorganisms capable of degrading these hazardous substances merits urgent consideration. We have isolated a novel dehalogenase-producing bacterium from the hypersaline environment of Tuz Gölü Lake, Turkey and subsequently identified this isolate as Pseudomonas halophila HX. Under optimal culture conditions (pH 8.0, 15% NaCl, 30 °C, 200 rpm, 96 h culture time), the strain almost completely degraded (99.3%) 2,2-dichloropropionic acid (20 mM). The dehalogenase gene (dehHX) of the bacterium was amplified by PCR, and the deduced amino acid sequence of the DehHX was found to belong to a Group I dehalogenase and to share an 82% sequence identity to the dehalogenase DehI of Pseudomonas putida strain PP3. Interestingly, the pI of DehHX was more acidic (pI 3.89) than those of the non-halophilic dehalogenases (average measured pI 5.95). Homology-based structural modeling revealed that the surface of DehHX was unusually negatively charged due to the higher presence of acidic residues, which accounts for the uncommonly low pI seen in DehHX and explains the mechanism of adaptation that contributes to the exceptional halotolerance of the enzyme. The excess surface acidic residues were beneficial in enhancing the water-binding capacity, a crucial feature for preserving the stability and solubility of DehHX in highly saline conditions. In summary, we suggest that bio-prospecting for halogenated compound-degrading microorganisms in highly saline environments is a practical and safe strategy for the bioremediation of contaminated coastal areas.

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Acknowledgments

The Fundamental Research Grant Scheme from the Ministry of Higher Education Malaysia (FRGS R.J130000.7826.4F649) and the Research University Grant Scheme from the Ministry of Education, Malaysia (GUP Q.J130000.2545.09H95) from the Universiti Teknologi, Malaysia supported this work. YK would like to thank Ondokuz Mayiz University for joint financial support of the project (PYO.ZRT.1911.15.001‬‬). MFE thanks the Libyan Government for the scholarship award (Libyan Ministry of Higher Education Scholarship Program No. 700/2007).‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬‬

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  1. Department of Biotechnology and Medical Engineering, Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia (UTM), 81310, Johor Bahru, Malaysia

    Mohamed Faraj Edbeib & Fahrul Huyop

  2. Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia (UTM), 81310, Johor Bahru, Malaysia

    Roswanira Abdul Wahab

  3. Agricultural Biotechnology Department, Faculty of Agriculture, Ondokuz Mayis University, Samsun, Turkey

    Yilmaz Kaya

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  1. Mohamed Faraj Edbeib
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  2. Roswanira Abdul Wahab
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  3. Yilmaz Kaya
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  4. Fahrul Huyop
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Correspondence to Roswanira Abdul Wahab or Fahrul Huyop.

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Edbeib, M.F., Wahab, R.A., Kaya, Y. et al. In silico characterization of a novel dehalogenase (DehHX) from the halophile Pseudomonas halophila HX isolated from Tuz Gölü Lake, Turkey: insights into a hypersaline-adapted dehalogenase. Ann Microbiol 67, 371–382 (2017). https://doi.org/10.1007/s13213-017-1266-2

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