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Reassembly of shattered chromosomes in Deinococcus radiodurans

Nature volume 443, pages 569–573 (2006)Cite this article

Abstract

Dehydration or desiccation is one of the most frequent and severe challenges to living cells1. The bacterium Deinococcus radiodurans is the best known extremophile among the few organisms that can survive extremely high exposures to desiccation and ionizing radiation, which shatter its genome into hundreds of short DNA fragments2,3,4,5. Remarkably, these fragments are readily reassembled into a functional 3.28-megabase genome. Here we describe the relevant two-stage DNA repair process, which involves a previously unknown molecular mechanism for fragment reassembly called ‘extended synthesis-dependent strand annealing’ (ESDSA), followed and completed by crossovers. At least two genome copies and random DNA breakage are requirements for effective ESDSA. In ESDSA, chromosomal fragments with overlapping homologies are used both as primers and as templates for massive synthesis of complementary single strands, as occurs in a single-round multiplex polymerase chain reaction. This synthesis depends on DNA polymerase I and incorporates more nucleotides than does normal replication in intact cells. Newly synthesized complementary single-stranded extensions become ‘sticky ends’ that anneal with high precision, joining together contiguous DNA fragments into long, linear, double-stranded intermediates. These intermediates require RecA-dependent crossovers to mature into circular chromosomes that comprise double-stranded patchworks of numerous DNA blocks synthesized before radiation, connected by DNA blocks synthesized after radiation.

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Figure 1: DNA repair and synthesis after 7-kGy γ-irradiation of D. radiodurans.
Figure 2: Photolytic fragmentation of shattered D. radiodurans chromosomes reassembled in the presence of BrdU.
Figure 3: Single-cell detection of repair-associated newly synthesized single-stranded DNA by immunofluorescence microscopy.
Figure 4: Two-stage process of reconstitution of shattered chromosomes.

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Acknowledgements

We thank J. Battista for initial help with Deinococcus and for the polA mutant; M. Meselson, B. Wagner, A. Stark, D. Zahradka and members of the M.R. lab for reading this manuscript and/or providing advice; M. Blazevic for technical assistance on γ-irradiation; and Mikula Radman for illustrations. K.Z. held a fellowship from the Necker Institute during work in M.R.'s laboratory. D.S. holds a Boehringer Ingelheim Foundation predoctoral fellowship and A.B.L. is a Marie Curie fellow. The laboratory in the Université de Paris-Descartes was funded by INSERM and the Necker Institute (Mixis/PLIVA contract); that in the Institut de Génétique et Microbiologie by EDF-France and CNRS (GEOMEX); that in the Institut Curie by EDF-France; and that in the Ruder Boskovic Institute by the Croatian Ministry of Science, Education and Sports. Author Contributions Experiments in Figs 1 and 2 and Supplementary Fig. 4 were carried out by K.Z.; those in Fig. 3 by D.S. A.B.L. provided expertise in microscopy; and the global experimental design was by M.R. The results of Fig. 1b, f, were obtained in, and with the scientific and material support of, the Institut de Génétique et Microbiologie; those of Fig. 1a, e, in the Institut Curie; those of refs Figs 1c, d, and Supplementary Fig. 4 in the Ruder Boskovic Institute, and those of Fig. 3 in the Université de Paris-Descartes.

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Authors and Affiliations

  1. Université de Paris-Descartes, Faculté de Médecine, INSERM Site Necker, U571, 156 rue de Vaugirard, 75015, Paris, France

    Ksenija Zahradka, Dea Slade, Ariel B. Lindner & Miroslav Radman

  2. Division of Molecular Biology, Ruder Boskovic Institute, PO Box 180, 10002, Zagreb, Croatia

    Ksenija Zahradka & Mirjana Petranovic

  3. Institut de Génétique et Microbiologie, CNRS UMR8621, CEA LRC42V, Université Paris-Sud, Bâtiment 409, 91405 Cedex, Orsay, France

    Adriana Bailone & Suzanne Sommer

  4. Institut Curie, Section Recherche, UMR 2027 CNRS, Centre Universitaire de Paris-Sud, Bâtiment 110, 91405, Orsay Cedex, France

    Dietrich Averbeck

  5. Mediterranean Institute for Life Sciences, Mestrovicevo setaliste bb, 21000, Split, Croatia

    Miroslav Radman

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  1. Ksenija Zahradka
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Correspondence to Miroslav Radman.

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Supplementary Data

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Supplementary Notes

This file contains Supplementary Methods, Supplementary Results, Supplementary Discussion and additional references. (PDF 93 kb)

Supplementary Figure 1

Analysis of repaired D. radiodurans DNA by 5-BrdU density labelling. (PPT 55 kb)

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Zahradka, K., Slade, D., Bailone, A. et al. Reassembly of shattered chromosomes in Deinococcus radiodurans. Nature 443, 569–573 (2006). https://doi.org/10.1038/nature05160

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