Functional genomic analysis and molecular modeling of a novel alkalotolerant dehalogenase enzyme from Bacillus megaterium DehLBHSl

Abstract

Extreme environments, such as alkaline lakes, are at risk of contamination by halogenated compounds. These halogenated products are recalcitrant toxicants posing hazards to human health and the environment, thus urgently need to be studied. In this research, an alkalotolerant bacterium was successfully isolated from the Turkish Blue Lake. The Biolog GEN III system and 16S rRNA analysis identified the bacterium as Bacillus megaterium strain BHS1. The BHS1 was able to use 2,2-dichloropropionic acid (2,2-DCP) as its sole carbon source and was found to grow well in alkaline conditions (pH 7.0-14.0) when supplemented with 2,2-DCP from 20 to 60 mM. This bacterium was also characterized at the genomic level using the HiSeq platform by de novo assembly. Genomic data were analyzed to demarcate DNA regions containing protein-coding genes and their functions. The present study showed the de novo assembly of the BHS1 genomic sequence unveiled a genome size of ~ 5.37 Mb with the average G + C content of 38% successfully. The predicted nuclear genome harbors 5,509 protein-coding genes, 1,353 tRNA genes, 67 rRNA genes and 6 non-coding (mRNA) genes. Genomic analysis suggested that BHS1 encodes a DehLBHS1 dehalogenase enzyme. Deduced amino acid sequence showed that it belongs to Group II dehalogenase with sequence identity (38.4%) to the previously described DehL-DEX YL. Homology modeling using I-TASSER was used to recreate the structure of the enzyme. Compared to other non-alkalophilic dehalogenases with a pI of 6.0, DehLBHS1, which had a theoretical pI of 6.66 in this study, showed a greater tendency to originate from a natural ecosystem rather than from a polluted environment. Homology-based structural modeling revealed that the surface charge of DehLBHS1 was negative, signifying that Bacillus megaterium has evolutionarily adapted to an alkaline environment. Findings from this study construed that bioprospecting for an effective halogen-degrading alkalotolerant bacteria in highly alkaline environments could be a safer and more stable means of bioremediation of polluted areas.