Biological and molecular approaches of the degradation or decolorization potential of the hypersaline Lake Tuz Bacillus megaterium H2 isolate

Abstract

The presence of synthetic dyes in water bodies and soil is one of the major issues affecting the global ecology, possibly impacting societal well-being adversely due to the colorants’ recalcitrance and toxicity. Herein, the study spectrophotometrically monitored the ability of the Bacillus megaterium H2 azoreductase (AzrBmH2) to degrade four synthetic dyes, reactive blue 4, remazol brilliant red, thymol blue, and methyl red, followed by in-silico assessment using GROMACS. We found that the bacterium degraded as much as 60% of all four synthetic dyes at various tested concentrations. The genome analysis revealed five different azoreductase genes, which were then modeled into the AzrBmH21, AzrBmH22/3, and AzrBmH24/5 templates. The AzrBmH2-substrate complexes showed binding energies with all the dyes of between −10.6 to −6.9 kcal/mol and formed 4–6 hydrogen bonds with the predicted catalytic binding residues (His10, Glu 14, Ser 58, Met 99, Val 107, His 183, Asn184 and Gln 191). In contrast, the lowest binding energies were observed for the AzrBmH21-substrates (−10.6 to −7.9). Molecular dynamic simulations revealed that the AzrBmH21-substrate complexes were more stable (RMSD 0.2–0.25 nm, RMSF 0.05 − 0.3 nm) and implied strong bonding with the dyes. The Molecular Mechanics Poisson-Boltzmann Surface Area results also mirrored this outcome, showing the lowest azoreductase-dye binding energy in the order of AzrBmH21-RB4 (−78.18 ± 8.92 kcal/mol), AzrBmH21-RBR (−67.51 ± 7.74 kcal/mol), AzrBmH21-TB (−46.62 ± 5.23 kcal/mol) and AzrBmH21-MR (−40.78 ± 7.87 kcal/mol). In short, the study demonstrated the ability of the B. megaterium H2 to efficiently decolorize the above-said synthetic dyes, conveying the bacterium’s promising use for large-scale dye remediation.

Communicated by Ramaswamy H. Sarma

Keywords:

• Azoreductase
• Bacillus thuringiensis
• molecular docking
• MD simulations
• MM-PBSA
• synthetic dyes

Acknowledgment

The authors express their gratitude to the Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia (UTM), and the Department of Applied Science, , Universitas Negeri Malang, Indonesia, for their support and collaboration in this study. This work was partially funded by the Professional Development Research University through the Research Management Centre of UTM REF No. PY/2022/04640. Habeebat Adekilekun Oyewusi is a researcher of Universiti Teknologi Malaysia under the Post-Doctoral Fellowship Scheme for the project: "Catalytic-Enzyme degradation of toxic environmental pollutants by Bacillus megaterium H2: An in-silico approach.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This work was funded by the Professional Development Research University through the Research Management Centre of UTM for financial support of the project through REF No. PY/2022/04640. Habeebat Adekilekun Oyewusi is a researcher of Universiti Teknologi Malaysia under the Post-Doctoral Fellowship Scheme for the project: ‘Catalytic-Enzyme degradation of toxic environmental pollutants by Bacillus megaterium H2: An in-silico approach’.