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

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 successfu...

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Main Author:	Abdul Wahhab, Batool Hazim
Format:	Thesis
Language:	English
Published:	2021
Subjects:	Q Science (General)
Online Access:	http://eprints.utm.my/id/eprint/101801/1/BatoolHazimAbdulPFS2021.pdf.pdf
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spelling	my-utm-ep.1018012023-07-10T09:30:39Z Functional genomic analysis and molecular modeling of a novel alkalotolerant dehalogenase enzyme from Bacillus megaterium DehLBHSl 2021 Abdul Wahhab, Batool Hazim Q Science (General) 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. 2021 Thesis http://eprints.utm.my/id/eprint/101801/ http://eprints.utm.my/id/eprint/101801/1/BatoolHazimAbdulPFS2021.pdf.pdf application/pdf en public http://dms.library.utm.my:8080/vital/access/manager/Repository/vital:146277 phd doctoral Universiti Teknologi Malaysia Faculty of Science
institution	Universiti Teknologi Malaysia
collection	UTM Institutional Repository
language	English
topic	Q Science (General)
spellingShingle	Q Science (General) Abdul Wahhab, Batool Hazim Functional genomic analysis and molecular modeling of a novel alkalotolerant dehalogenase enzyme from Bacillus megaterium DehLBHSl
description	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.
format	Thesis
qualification_name	Doctor of Philosophy (PhD.)
qualification_level	Doctorate
author	Abdul Wahhab, Batool Hazim
author_facet	Abdul Wahhab, Batool Hazim
author_sort	Abdul Wahhab, Batool Hazim
title	Functional genomic analysis and molecular modeling of a novel alkalotolerant dehalogenase enzyme from Bacillus megaterium DehLBHSl
title_short	Functional genomic analysis and molecular modeling of a novel alkalotolerant dehalogenase enzyme from Bacillus megaterium DehLBHSl
title_full	Functional genomic analysis and molecular modeling of a novel alkalotolerant dehalogenase enzyme from Bacillus megaterium DehLBHSl
title_fullStr	Functional genomic analysis and molecular modeling of a novel alkalotolerant dehalogenase enzyme from Bacillus megaterium DehLBHSl
title_full_unstemmed	Functional genomic analysis and molecular modeling of a novel alkalotolerant dehalogenase enzyme from Bacillus megaterium DehLBHSl
title_sort	functional genomic analysis and molecular modeling of a novel alkalotolerant dehalogenase enzyme from bacillus megaterium dehlbhsl
granting_institution	Universiti Teknologi Malaysia
granting_department	Faculty of Science
publishDate	2021
url	http://eprints.utm.my/id/eprint/101801/1/BatoolHazimAbdulPFS2021.pdf.pdf
_version_	1776100774838796288

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

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