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      A Decade of Biochemical and Structural Studies of the DNA Repair Machinery of Deinococcus radiodurans: Major Findings, Functional and Mechanistic Insight and Challenges

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          Translated abstract

          The Deinococcus radiodurans bacterium is extremely resistant to ionising radiation and desiccation and can withstand a 200-fold higher radiation dose than most other bacteria with no loss of viability. The mechanisms behind this extreme resistance are not fully understood, but it is clear that several factors contribute to this phenotype. Efficient scavenging of reactive oxygen species and repair of damaged DNA are two of these. In this review, we summarise the results from a decade of structural and functional studies of the DNA repair machinery of Deinococcus radiodurans and discuss how these studies have contributed to an improved understanding of the molecular mechanisms underlying DNA repair and to the outstanding resistance of Deinococcus radiodurans to DNA damaging agents.

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          Repair of oxidative damage to DNA: enzymology and biology.

          B Demple, L. Harrison (1994)
          Article 0 comments Cited 182 times – based on 0 reviews     Review now
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            Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics.

            K Minton, Roger Daly, Roman Tatusov … (2001)
            The bacterium Deinococcus radiodurans shows remarkable resistance to a range of damage caused by ionizing radiation, desiccation, UV radiation, oxidizing agents, and electrophilic mutagens. D. radiodurans is best known for its extreme resistance to ionizing radiation; not only can it grow continuously in the presence of chronic radiation (6 kilorads/h), but also it can survive acute exposures to gamma radiation exceeding 1,500 kilorads without dying or undergoing induced mutation. These characteristics were the impetus for sequencing the genome of D. radiodurans and the ongoing development of its use for bioremediation of radioactive wastes. Although it is known that these multiple resistance phenotypes stem from efficient DNA repair processes, the mechanisms underlying these extraordinary repair capabilities remain poorly understood. In this work we present an extensive comparative sequence analysis of the Deinococcus genome. Deinococcus is the first representative with a completely sequenced genome from a distinct bacterial lineage of extremophiles, the Thermus-Deinococcus group. Phylogenetic tree analysis, combined with the identification of several synapomorphies between Thermus and Deinococcus, supports the hypothesis that it is an ancient group with no clear affinities to any of the other known bacterial lineages. Distinctive features of the Deinococcus genome as well as features shared with other free-living bacteria were revealed by comparison of its proteome to the collection of clusters of orthologous groups of proteins. Analysis of paralogs in Deinococcus has revealed several unique protein families. In addition, specific expansions of several other families including phosphatases, proteases, acyltransferases, and Nudix family pyrophosphohydrolases were detected. Genes that potentially affect DNA repair and recombination and stress responses were investigated in detail. Some proteins appear to have been horizontally transferred from eukaryotes and are not present in other bacteria. For example, three proteins homologous to plant desiccation resistance proteins were identified, and these are particularly interesting because of the correlation between desiccation and radiation resistance. Compared to other bacteria, the D. radiodurans genome is enriched in repetitive sequences, namely, IS-like transposons and small intergenic repeats. In combination, these observations suggest that several different biological mechanisms contribute to the multiple DNA repair-dependent phenotypes of this organism.
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              At the heart of the chromosome: SMC proteins in action.

              Tatsuya Hirano (2006)
              Structural maintenance of chromosomes (SMC) proteins are ubiquitous in organisms from bacteria to humans, and function as core components of the condensin and cohesin complexes in eukaryotes. SMC proteins adopt a V-shaped structure with two long arms, each of which has an ATP-binding head domain at the distal end. It is important to understand how these uniquely designed protein machines interact with DNA strands and how such interactions are modulated by the ATP-binding and -hydrolysis cycle. An emerging idea is that SMC proteins use a diverse array of intramolecular and intermolecular protein-protein interactions to actively fold, tether and manipulate DNA strands.
              Article 0 comments Cited 154 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Joanna Timmins
                Journal
                Journal ID (nlm-ta): Comput Struct Biotechnol J
                Journal ID (iso-abbrev): Comput Struct Biotechnol J
                Title: Computational and Structural Biotechnology Journal
                Publisher: Research Network of Computational and Structural Biotechnology
                ISSN (Electronic): 2001-0370
                Publication date PMC-release: 07 April 2016
                Publication date Collection: 2016
                Publication date (Electronic): 07 April 2016
                Volume: 14
                Pages: 168-176
                Affiliations
                [a ]Université Grenoble Alpes, Institut de Biologie Structurale, F-38044 Grenoble, France
                [b ]CNRS, IBS, F-38044 Grenoble, France
                [c ]CEA, IBS, F-38044 Grenoble, France
                [d ]The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT the Arctic University of Norway, N-9037 Tromsø, Norway
                [e ]Instituto de Tecnologia Quimica e Biologica (ITQB), Universidade Nova de Lisboa, Av da Republica (EAN), 2780-157 Oeiras, Portugal
                Author notes
                [* ]Corresponding author at: Institut de Biologie Structurale, 71 avenue des Martyrs, CS10090, 38044 Grenoble Cedex 9. Tel.: + 33 457 428 678.Institut de Biologie Structurale71 avenue des MartyrsCS10090Grenoble Cedex 938044France joanna.timmins@ 123456ibs.fr
                Article
                Publisher ID: S2001-0370(16)30012-5
                DOI: 10.1016/j.csbj.2016.04.001
                PMC ID: 5128194
                PubMed ID: 27924191
                SO-VID: 0577c715-eaf6-4e89-8b81-ee743d3dbfc6
                Copyright © © 2016 The Authors
                License:

                This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

                History
                Date received : 29 February 2016
                Date revision received : 2 April 2016
                Date accepted : 7 April 2016
                Categories
                Subject: Short Survey

                Data availability:

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