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All Journal Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences
Sefatullah Zakary
Lecturer at Kabul University
Agriculture, Biological Sciences & Forestry Environmental Science

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Genomic Analysis of Mesorhizobium loti Strain TONO Reveals Dehalogenases for Bioremediation Sefatullah Zakary; Habeebat Adekilekun Oyewusi; Fahrul Huyop
Journal of Tropical Life Science Vol. 11 No. 1 (2021)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.11.01.09

Abstract

Halogenated compounds are extensively utilized in different industrial applications such as pesticides and herbicides and cause severe environmental problems because of their toxicity and persistence. Degradation of these compounds by the biological method is a significant method to reduce these recalcitrant. Mesorhizobium loti is important for nitrogen fixation in legume roots. Up to now, there is no report to indicate M. loti can produce dehalogenase enzymes. Thus, a total of twenty-five genomes of M. loti strains from the National Center for Biotechnology Information (NCBI) were analyzed. These strains notably carry dehalogenase genes and were further investigated. The relative ratio of haloalkane and haloacid dehalogenase type II or L-type from all twenty-five genomes was 26% and 74%, respectively, suggesting type II dehalogenase is common. Surprisingly, only M. loti strain TONO carries four dehalogenases and therefore it was further characterized. The chromosome of M. loti strain TONO contains four haloacid dehalogenase type II genes namely, dehLt1 (MLTONO_2099), dehLt2 (MLTONO_3660), dehLt3 (MLTONO_4143), and dehLt4 (MLTONO_6945), and their corresponding enzymes were designated as DehLt1, DehLt2, DehLt3, and DehLt4, respectively. The only haloalkane dehalogenase gene (MLTONO_4828) was located upstream of the dehLt3 gene and its amino acid share 88% identity with DmlA of Mesorhizobium japonicum MAFF 303099. The putative haloacid permease gene designated as dehrPt (MLTONO_0284) was located downstream of the dehLt1 and its amino acids show 69% identity with haloacid permease of Rhizobium sp. RC1. The gene encoding helix-turn-helix (HTH) motif family DNA-binding protein regulator and LysR family transcriptional regulator genes were also identified, possibly for regulatory functions. The genomic studies as such, have good potential to be screened for ne
In Silico Molecular Characterization of a Putative Haloacid Dehalogenase Type II from Genomic of Mesorhizobium loti Strain TONO: In Silico Molecular Characterization of a Putative Haloacid Dehalogenase Type II Sefatullah Zakary; Hamida Mashal; Abdul Rahman Osmani; Habeebat Adekilekun Oyewus; Fahrul Huyop; Muzhgan Mohammad Nasim
Journal of Tropical Life Science Vol. 12 No. 2 (2022)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.12.02.10

Abstract

Halogenated organic compounds are found as waste in the biosphere and can causenumerous dilemmas because of their toxicity and persistence in the environment. Theyplay a major role in the quality of life of both, human beings and other living organisms. Degradation of these compounds by microorganisms is significant to reduce recalcitrant and cost. Thus, in the current study, an in-silico approach was used for homology modelling and docking assessment of a newly identified DehLt4, type IIdehalogenase to predict its ability to degrade selected haloalkanoic acids and haloacetates. The study aimed to establish the catalytic tendencies of the enzyme to optimallydegrade the selected halogenated haloacids. The refined modelled structure of DehLt4using GROMACS 5.1.2 software revealed satisfactory scores of ERRAT (94.73%),Verify3D (90.83%) and PROCHECK (99.05 %) assessments. Active site predictionby blind docking and multiple sequence alignment indicated the catalytic triads forDehLt4 were Asp9-Lys149-Asn175. Both L-2-chloropropionic acid (L-2-CP) and trichloroacetate (TCA) docked with DehLt4 exhibited binding energy of -3.9 kcal/mol.However, the binding energy for D-2-chloropropionic acid (D-2-CP) and monochloroacetate (MCA) was -3.8 kcal/mol and -3.1 kcal/mol, respectively. Thus, the findingsof the study successfully identified the catalytic important residues of DehLt4 for possible pollutant degradation. The in-silico study as such has a good potential for characterization of newly identified dehalogenases based on basic molecular structure andfunctions analysis.Keywords: Dehalogenase, Haloacid dehalogenase, Mesorhizobium loti strain TONO,Protein structure
Co-Authors Abdul Rahman Osmani Fahrul Huyop Fahrul Huyop Habeebat Adekilekun Oyewus Habeebat Adekilekun Oyewusi Hamida Mashal Muzhgan Mohammad Nasim