Mining of ring-hydroxylating dioxygenase genes from PAH contaminated soil metagenome

Bacteria tend to initiate PAH degradation by the action of multi-component aromatic ring dioxygenases which comprising a reductase, a ferredoxin and terminal ring-hydroxylating dioxygenase. The potential for PAH degradation by the ring-hydroxylating dioxygenases in a PAH contaminated soil was assess...

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Main Authors:	Mohd Ashaari, Mardiana, Storey, Sean, Doyle, Evelyn
Format:	Conference or Workshop Item
Language:	English English
Published:	2015
Subjects:	QR Microbiology
Online Access:	http://irep.iium.edu.my/48215/ http://irep.iium.edu.my/48215/2/Mardiana%27s_poster_ACB2015.pdf http://irep.iium.edu.my/48215/19/48215%20abstract.pdf

id	iium-48215
recordtype	eprints
spelling	iium-482152019-04-03T04:15:42Z http://irep.iium.edu.my/48215/ Mining of ring-hydroxylating dioxygenase genes from PAH contaminated soil metagenome Mohd Ashaari, Mardiana Storey, Sean Doyle, Evelyn QR Microbiology Bacteria tend to initiate PAH degradation by the action of multi-component aromatic ring dioxygenases which comprising a reductase, a ferredoxin and terminal ring-hydroxylating dioxygenase. The potential for PAH degradation by the ring-hydroxylating dioxygenases in a PAH contaminated soil was assessed using metagenomic approaches. A metagenomic library was constructed from PAH contaminated soil and dioxygenase gene activity was examined by function-based screening of the library. An agar plate assay resulted in 3 positive fosmid clones out of 18,048 clones screened. Sequence-based screening of the metagenomic library was conducted by amplifying a ring hydoxylating gene (RHD) for both Gram positive and Gram negative bacteria. The RHD gene specific for Gram negative bacteria was amplified in 14 fosmid clones but none of the clones tested positive for the gene associated with Gram positive bacteria. Although not detected in the metagenomic library, high levels (≈300,000 copies per ng DNA extracted) and expression (82,704 copies per ng cDNA) of the RHD gene from Gram positive bacteria were detected in the contaminated soil using quantitative PCR. In addition, metatranscriptomic analysis confirmed the expression of RHD gene for Gram positive bacteria which could be mapped to a phenanthrene degradation pathway. This study provides deeper understanding on the ring-hydroxylating dioxygenases involved in PAH biodegradation. This information may be useful in the development of bioremediation strategies through bioengineering of these enzymes. 2015 Conference or Workshop Item NonPeerReviewed application/pdf en http://irep.iium.edu.my/48215/2/Mardiana%27s_poster_ACB2015.pdf application/pdf en http://irep.iium.edu.my/48215/19/48215%20abstract.pdf Mohd Ashaari, Mardiana and Storey, Sean and Doyle, Evelyn (2015) Mining of ring-hydroxylating dioxygenase genes from PAH contaminated soil metagenome. In: ASIAN Congress on Biotechnology 2015, 15th-19th Nov. 2015, Kuala Lumpur. (Unpublished)
repository_type	Digital Repository
institution_category	Local University
institution	International Islamic University Malaysia
building	IIUM Repository
collection	Online Access
language	English English
topic	QR Microbiology
spellingShingle	QR Microbiology Mohd Ashaari, Mardiana Storey, Sean Doyle, Evelyn Mining of ring-hydroxylating dioxygenase genes from PAH contaminated soil metagenome
description	Bacteria tend to initiate PAH degradation by the action of multi-component aromatic ring dioxygenases which comprising a reductase, a ferredoxin and terminal ring-hydroxylating dioxygenase. The potential for PAH degradation by the ring-hydroxylating dioxygenases in a PAH contaminated soil was assessed using metagenomic approaches. A metagenomic library was constructed from PAH contaminated soil and dioxygenase gene activity was examined by function-based screening of the library. An agar plate assay resulted in 3 positive fosmid clones out of 18,048 clones screened. Sequence-based screening of the metagenomic library was conducted by amplifying a ring hydoxylating gene (RHD) for both Gram positive and Gram negative bacteria. The RHD gene specific for Gram negative bacteria was amplified in 14 fosmid clones but none of the clones tested positive for the gene associated with Gram positive bacteria. Although not detected in the metagenomic library, high levels (≈300,000 copies per ng DNA extracted) and expression (82,704 copies per ng cDNA) of the RHD gene from Gram positive bacteria were detected in the contaminated soil using quantitative PCR. In addition, metatranscriptomic analysis confirmed the expression of RHD gene for Gram positive bacteria which could be mapped to a phenanthrene degradation pathway. This study provides deeper understanding on the ring-hydroxylating dioxygenases involved in PAH biodegradation. This information may be useful in the development of bioremediation strategies through bioengineering of these enzymes.
format	Conference or Workshop Item
author	Mohd Ashaari, Mardiana Storey, Sean Doyle, Evelyn
author_facet	Mohd Ashaari, Mardiana Storey, Sean Doyle, Evelyn
author_sort	Mohd Ashaari, Mardiana
title	Mining of ring-hydroxylating dioxygenase genes from PAH contaminated soil metagenome
title_short	Mining of ring-hydroxylating dioxygenase genes from PAH contaminated soil metagenome
title_full	Mining of ring-hydroxylating dioxygenase genes from PAH contaminated soil metagenome
title_fullStr	Mining of ring-hydroxylating dioxygenase genes from PAH contaminated soil metagenome
title_full_unstemmed	Mining of ring-hydroxylating dioxygenase genes from PAH contaminated soil metagenome
title_sort	mining of ring-hydroxylating dioxygenase genes from pah contaminated soil metagenome
publishDate	2015
url	http://irep.iium.edu.my/48215/ http://irep.iium.edu.my/48215/2/Mardiana%27s_poster_ACB2015.pdf http://irep.iium.edu.my/48215/19/48215%20abstract.pdf
first_indexed	2023-09-18T21:08:26Z
last_indexed	2023-09-18T21:08:26Z
_version_	1777411090537250816

Mining of ring-hydroxylating dioxygenase genes from PAH contaminated soil metagenome

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