Preserving Genome Integrity: The DdrA Protein of Deinococcus radiodurans R1

Harris, Dennis; Tanaka, Masashi; Saveliev, S. V.; Jolivet, Edmond; Earl, Ashlee M.; Cox, Michael M.; Battista, John R.

doi:10.1371/journal.pbio.0020304

Cited by 109 publications

(136 citation statements)

References 36 publications

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“…Protein samples were concentrated by ammonium sulfate precipitation, resuspended, and dialyzed into elution buffer (25 mM Tris-acetate, 80% cation-10% glycerol-500 mM NaCl-1 mM dithiothreitol [DTT]). The characterization of purified DdrA protein has been described previously (13). The identity of DdrA157 protein was verified by accurate mass determination (calculated mass, 17,428.7 Da; determined mass, 17,430.0 Da) and trypsin digest fingerprinting of a protein sample (42% coverage).…”

Section: Methodsmentioning

confidence: 99%

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The Stable, Functional Core of DdrA from Deinococcus radiodurans R1 Does Not Restore Radioresistance In Vivo

2008

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DdrA protein binds to and protects 3 DNA ends and is essential for preserving the genome integrity of Deinococcus radiodurans following treatment by gamma radiation in an environment lacking nutrients. Limited proteolysis was used to identify a stable and functional protein core, designated DdrA157, consisting of the first 157 residues of the protein. In vitro, the biochemical differences between wild-type and mutant proteins were modest. DdrA exhibits a strong bias in binding DNA with 3 extensions but not with 5 extensions. The mutant DdrA157 exhibited a greater affinity for 5 DNA ends but still bound to 3 ends more readily. However, when we replaced the wild-type ddrA gene with the mutant gene for ddrA157, the resulting D. radiodurans strain became almost as sensitive to gamma radiation as the ddrA knockout strain. These results suggest that while the stable protein core DdrA157 is functional for DNA binding and protection assays in vitro, the carboxyl terminus is required for important functions in vivo. The C terminus may therefore be required for protein or DNA interactions or possibly as a regulatory region for DNA binding or activities not yet identified.

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Section: Methodsmentioning

confidence: 99%

“…The DdrA protein of D. radiodurans is among a group of the most highly upregulated gene products, following IR treatment (13). Previously, we had characterized DdrA as a component of a DNA end protection system in D. radiodurans that would prevent nucleolytic degradation of DNA in the absence of nutrients.…”

mentioning

confidence: 99%

The Stable, Functional Core of DdrA from Deinococcus radiodurans R1 Does Not Restore Radioresistance In Vivo

2008

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“…DdrA protects 3Ј ssDNA overhangs from degradation by E. coli exonuclease I (239), presumably ensuring long-lived recombination substrates and the recycling of RecA (277). Its absence results in excessive DNA degradation following radiation exposure (239). Hence, DdrA is proposed to preserve genome integrity by protecting DNA fragments generated by ionizing radiation from nuclease degradation, particularly when nutrients are scarce and when DNA repair processes are hindered as a result (239).…”

Section: Recombinational Processes In D Radiodurans Dna Repairmentioning

confidence: 99%

“…Hence, DdrA is proposed to preserve genome integrity by protecting DNA fragments generated by ionizing radiation from nuclease degradation, particularly when nutrients are scarce and when DNA repair processes are hindered as a result (239). The disruption of this gene results in only modest sensitivity to ionizing radiation and to MMC but causes a substantial increase in DNA degradation (239) (Fig. 8).…”

Section: Recombinational Processes In D Radiodurans Dna Repairmentioning

confidence: 99%

Oxidative Stress Resistance inDeinococcus radiodurans

Slade

Radman

2011

Microbiol Mol Biol Rev

659

639

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SUMMARY Deinococcus radiodurans is a robust bacterium best known for its capacity to repair massive DNA damage efficiently and accurately. It is extremely resistant to many DNA-damaging agents, including ionizing radiation and UV radiation (100 to 295 nm), desiccation, and mitomycin C, which induce oxidative damage not only to DNA but also to all cellular macromolecules via the production of reactive oxygen species. The extreme resilience of D. radiodurans to oxidative stress is imparted synergistically by an efficient protection of proteins against oxidative stress and an efficient DNA repair mechanism, enhanced by functional redundancies in both systems. D. radiodurans assets for the prevention of and recovery from oxidative stress are extensively reviewed here. Radiation- and desiccation-resistant bacteria such as D. radiodurans have substantially lower protein oxidation levels than do sensitive bacteria but have similar yields of DNA double-strand breaks. These findings challenge the concept of DNA as the primary target of radiation toxicity while advancing protein damage, and the protection of proteins against oxidative damage, as a new paradigm of radiation toxicity and survival. The protection of DNA repair and other proteins against oxidative damage is imparted by enzymatic and nonenzymatic antioxidant defense systems dominated by divalent manganese complexes. Given that oxidative stress caused by the accumulation of reactive oxygen species is associated with aging and cancer, a comprehensive outlook on D. radiodurans strategies of combating oxidative stress may open new avenues for antiaging and anticancer treatments. The study of the antioxidation protection in D. radiodurans is therefore of considerable potential interest for medicine and public health.

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“…The products of additional genes specifically conserved in Deinococcus are also involved in DNA repair and radiation tolerance. These include PprA (reported to stimulate ligase activity) (Narumi et al, 2004), DdrA (an oligomeric ring-forming protein involved in DNA extremity protection) (Harris et al, 2004;Gutsche et al, 2008), DdrB, DdrC and DdrD (functions unknown) de Groot et al, 2009) and IrrE (regulator of recA and pprA expression) (Earl et al, 2002a;Hua et al, 2003;Lu et al, 2009;Vujicic-Zagar et al, 2009). Homologues of DNA repair photolyases and specialized translesion synthesis (TLS) DNA polymerases have not been identified in D. radiodurans and D. geothermalis.…”

Section: Introductionmentioning

confidence: 99%

Mutagenic lesion bypass and two functionally different RecA proteins in Deinococcus deserti

Dulermo

Fochesato

Blanchard

et al. 2009

Molecular Microbiology

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SummaryRecA is essential for extreme radiation tolerance in Deinococcus radiodurans. Interestingly, Sahara bacterium Deinococcus deserti has three recA genes (recAC, recAP1, recAP3) that code for two different RecA proteins (RecAC, RecAP). Moreover, and in contrast to other sequenced Deinococcus species, D. deserti possesses homologues of translesion synthesis (TLS) DNA polymerases, including ImuY and DnaE2. Together with a lexA homologue, imuY and dnaE2 form a gene cluster similar to a widespread RecA/LexA-controlled mutagenesis cassette. After having developed genetic tools, we have constructed mutant strains to characterize these recA and TLS polymerase genes in D. deserti. Both RecAC and RecAP are functional and allow D. deserti to survive, and thus repair massive DNA damage, after exposure to high doses of radiation. D. deserti is mutable by UV, which requires ImuY, DnaE2 and RecAC, but not RecAP. RecAC, but not RecAP, facilitates induced expression of imuY and dnaE2 following UV exposure. We propose that the extra recAP1 and recAP3 genes may provide higher levels of RecA protein for efficient error-free repair of DNA damage, without further increasing error-prone lesion bypass by ImuY and DnaE2, whereas limited TLS may contribute to adaptation to harsh conditions by generating genetic variability.

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Preserving Genome Integrity: The DdrA Protein of Deinococcus radiodurans R1

Cited by 109 publications

References 36 publications

The Stable, Functional Core of DdrA from Deinococcus radiodurans R1 Does Not Restore Radioresistance In Vivo

The Stable, Functional Core of DdrA from Deinococcus radiodurans R1 Does Not Restore Radioresistance In Vivo

Oxidative Stress Resistance inDeinococcus radiodurans

Mutagenic lesion bypass and two functionally different RecA proteins in Deinococcus deserti

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