JOURNAL OF TROPICAL LIFE SCIENCE 2021, Vol. 11, No. 1, 67 – 77 http://dx.doi.org/10.11594/jtls.11.01.09 How to cite: Zakary S, Oyewusi HA, Huyop F (2021) Genomic Analysis of Mesorhizobium loti Strain TONO Reveals Dehalogenases for Bioremediation. Journal of Tropical Life Science 11 (1): 67 – 77. doi: 10.11594/jtls.11.01.09. Research Article Genomic Analysis of Mesorhizobium loti Strain TONO Reveals Dehalogenases for Bioremediation Sefatullah Zakary 1, 2 , Habeebat Adekilekun Oyewusi 1, 3 , Fahrul Huyop 1 * 1 Department of Biosciences, Faculty of Sciences, Universiti Teknologi Malaysia, Johor Bahru 81310, Malaysia 2 Department of Botany, Faculty of Biology, Kabul University, Dehburi, Kabul 1006, Afghanistan. 3 Department of Biochemistry, School of Science and Computer Studies, Federal Polytechnic Ado Ekiti, Ado Ekiti PMB 5351, Ekiti State, Nigeria Article history: Submission December 2020 Revised December 2020 Accepted January 2021 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 im- portant 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 an- alyzed. 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 dehalogen- ase is common. Surprisingly, only M. loti strain TONO carries four dehalogenases and therefore it was further characterized. The chromosome of M. loti strain TONO con- tains 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 dehalogen- ase 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 per- mease 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 new type of dehalogenases based on basic molecular structure and functions analysis. Keywords: Genomic analysis, Haloacid dehalogenase, Haloacid permease, Halogen- ated organic compounds, Mesorhizobium loti *Corresponding author: E-mail: fahrul@utm.my Introduction A significant group of halogenated organic compounds such as chlorinated hydrocarbons was produced and extensively utilized in agriculture and various industrial applications. This resulted in severe environmental dilemmas due to their tox- icity and persistence [1]. Fortunately, many bacte- rial species produce dehalogenases that could breakdown these toxic compounds and convert them into harmless products [2]. Most of these bacteria species used organohalides as their sole source of carbon and energy [3]. Dehalogenase catalyzes halogenated organic pollutants' by cleaving of carbon–halogen bonds. Many dehalo- genases were identified, for example haloalkane dehalogenase [4], fluoroacetate dehalogenase [5], haloalkanoic acid dehalogenase [6-8], and 4-chlo- robenzoyl-CoA dehalogenase [9]. Haloalkanoic acid dehalogenase catalyzes haloalkanoic acids