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      Organohalide Respiring Bacteria and Reductive Dehalogenases: Key Tools in Organohalide Bioremediation

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          Abstract

          Organohalides are recalcitrant pollutants that have been responsible for substantial contamination of soils and groundwater. Organohalide-respiring bacteria (ORB) provide a potential solution to remediate contaminated sites, through their ability to use organohalides as terminal electron acceptors to yield energy for growth (i.e., organohalide respiration). Ideally, this process results in non- or lesser-halogenated compounds that are mostly less toxic to the environment or more easily degraded. At the heart of these processes are reductive dehalogenases (RDases), which are membrane bound enzymes coupled with other components that facilitate dehalogenation of organohalides to generate cellular energy. This review focuses on RDases, concentrating on those which have been purified (partially or wholly) and functionally characterized. Further, the paper reviews the major bacteria involved in organohalide breakdown and the evidence for microbial evolution of RDases. Finally, the capacity for using ORB in a bioremediation and bioaugmentation capacity are discussed.

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          The many faces of vitamin B12: catalysis by cobalamin-dependent enzymes.

          Vitamin B12 is a complex organometallic cofactor associated with three subfamilies of enzymes: the adenosylcobalamin-dependent isomerases, the methylcobalamin-dependent methyltransferases, and the dehalogenases. Different chemical aspects of the cofactor are exploited during catalysis by the isomerases and the methyltransferases. Thus, the cobalt-carbon bond ruptures homolytically in the isomerases, whereas it is cleaved heterolytically in the methyltransferases. The reaction mechanism of the dehalogenases, the most recently discovered class of B12 enzymes, is poorly understood. Over the past decade our understanding of the reaction mechanisms of B12 enzymes has been greatly enhanced by the availability of large amounts of enzyme that have afforded detailed structure-function studies, and these recent advances are the subject of this review.
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            The diversity of naturally produced organohalogens.

            More than 3800 organohalogen compounds, mainly containing chlorine or bromine but a few with iodine and fluorine, are produced by living organisms or are formed during natural abiogenic processes, such as volcanoes, forest fires, and other geothermal processes. The oceans are the single largest source of biogenic organohalogens, which are biosynthesized by myriad seaweeds, sponges, corals, tunicates, bacteria, and other marine life. Terrestrial plants, fungi, lichen, bacteria, insects, some higher animals, and even humans also account for a diverse collection of organohalogens.
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              Overview of organohalide-respiring bacteria and a proposal for a classification system for reductive dehalogenases.

              Organohalide respiration is an anaerobic bacterial respiratory process that uses halogenated hydrocarbons as terminal electron acceptors during electron transport-based energy conservation. This dechlorination process has triggered considerable interest for detoxification of anthropogenic groundwater contaminants. Organohalide-respiring bacteria have been identified from multiple bacterial phyla, and can be categorized as obligate and non-obligate organohalide respirers. The majority of the currently known organohalide-respiring bacteria carry multiple reductive dehalogenase genes. Analysis of a curated set of reductive dehalogenases reveals that sequence similarity and substrate specificity are generally not correlated, making functional prediction from sequence information difficult. In this article, an orthologue-based classification system for the reductive dehalogenases is proposed to aid integration of new sequencing data and to unify terminology.
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                Author and article information

                Contributors
                Journal
                Front Microbiol
                Front Microbiol
                Front. Microbiol.
                Frontiers in Microbiology
                Frontiers Media S.A.
                1664-302X
                01 March 2016
                2016
                : 7
                : 249
                Affiliations
                [1] 1School of Biotechnology and Biomolecular Sciences, University of New South Wales Sydney, NSW, Australia
                [2] 2Department of Molecular Biology and Genetics, Istanbul University Istanbul, Turkey
                [3] 3Department of Biotechnology, Mannheim University of Applied Sciences Mannheim, Germany
                Author notes

                Edited by: Gavin Collins, National University of Ireland, Ireland

                Reviewed by: Jun-Jie Zhang, Wuhan Institute of Virology, China; Christopher L. Hemme, University of Rhode Island, USA

                *Correspondence: Christopher P. Marquis c.marquis@ 123456unsw.edu.au

                This article was submitted to Microbiotechnology, Ecotoxicology and Bioremediation, a section of the journal Frontiers in Microbiology

                Article
                10.3389/fmicb.2016.00249
                4771760
                26973626
                dbbaefef-c7b2-4270-89cf-45a2da77fa51
                Copyright © 2016 Jugder, Ertan, Bohl, Lee, Marquis and Manefield.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 09 December 2015
                : 15 February 2016
                Page count
                Figures: 3, Tables: 2, Equations: 0, References: 96, Pages: 12, Words: 8716
                Funding
                Funded by: Australian Research Council 10.13039/501100000923
                Award ID: LP130100454
                Funded by: University of New South Wales 10.13039/501100001773
                Categories
                Microbiology
                Review

                Microbiology & Virology
                reductive dehalogenase,organohalide respiration,bioremediation,dehalobacter,dehalococcoides

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