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PreprintCited by 22Bacterial Genetics and BiotechnologyDNA Repair MechanismsEnzyme Structure and Function

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Structural and functional characterization of DdrC, a novel DNA damage-induced nucleoid associated protein involved in DNA compaction

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Banneville, Anne-Sophie, de la Tour, Claire Bouthier, Hognon, Cécilia, Colletier, Jacques-Philippe, Teulon, Jean-Marie, Le Roy, Aline, Pellequer, Jean-Luc, Monari, Antonio, Dehez, François, Confalonieri, Fabrice, Servant, Pascale, Timmins, Joanna·2021·Nucleic Acids Research
DOI 10.1101/2021.10.27.466113PMC PMC9303277

Preprint — published as 10.1093/nar/gkac563

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Abstract

Deinococcus radiodurans is a spherical bacterium well-known for its outstanding resistance to DNA-damaging agents. Exposure to such agents leads to drastic changes in the transcriptome of D. radiodurans . In particular, four Deinococcus -specific genes, known as DNA Damage Response genes, are strongly up-regulated and have been shown to contribute to the resistance phenotype of D. radiodurans . One of these, DdrC, is expressed shortly after exposure to γ-radiation and is rapidly recruited to the nucleoid. In vitro , DdrC has been shown to compact circular DNA, circularize linear DNA, anneal complementary DNA strands and protect DNA from nucleases. To shed light on the possible functions of DdrC in D. radiodurans , we determined the crystal structure of the domain-swapped DdrC dimer at a resolution of 2.2 Å and further characterized its DNA binding and compaction properties. Notably, we show that DdrC bears two asymmetric DNA binding sites located on either side of the dimer and can modulate the topology and level of compaction of circular DNA. These findings suggest that DdrC may be a DNA damage-induced nucleoid-associated protein that enhances nucleoid compaction to limit the dispersion of the fragmented genome and facilitate DNA repair after exposure to severe DNA damaging conditions.

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Metadata

Authors
Banneville, A.-S., de la Tour, C. B., Hognon, C., Colletier, J.-P., Teulon, J.-M., Le Roy, A., Pellequer, J.-L., Monari, A., Dehez, F., Confalonieri, F., Servant, P., & Timmins, J.
Affiliations
Centre National de la Recherche Scientifique (FR)
Corresponding author
Timmins, Joanna
ORCID
Venue
Nucleic Acids Research
Publisher
openRxiv
Published
2021-10-27
Volume
50
Issue
13
Pages
7680-7696
ISSN
0305-1048 (ISSN-L)
DOI
10.1101/2021.10.27.466113
PMC
PMC9303277
OpenAlex
W4284958032
Cited by
22
References
1
Citations by year
2026: 1 · 2025: 2 · 2024: 8 · 2023: 8 · 2022: 3
FWCI
3.17
Type
journal article
Language
en
Open access
Licence
cc-by-nc
Locations
  • Nucleic Acids Research (publishedVersion, cc-by-nc)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • HAL (submittedVersion, cc-by-nc-nd)
Funders
  • Laboratoire d'Excellence SEAM (ANR-11-IDEX-05-02, ANR-11-LABX-086)
  • Agence Nationale de la Recherche (ANR-17-EURE-0003, 11 IDEX 05 02, 11 LABX 086, ANR-17-EURE-, ANR-11-IDEX-0502, ANR 11 LABX 086, ANR 11, ANR-10-LABX-0096, ANR-17, ANR-10, ANR11-LABX, ANR-11-IDEX-0005, ANR-10-INBS-0005, ANR-10-LABX-0049)
  • European Synchrotron Radiation Facility (ID23‐1)
  • Centre National de la Recherche Scientifique (ID23-1, ANR‐17‐EURE‐0003)
  • Commissariat Général à l'Investissement (ANR-11-LABX-086, ANR 11 IDEX 05 02)
  • Commissariat à l'Énergie Atomique et aux Énergies Alternatives
  • French Infrastructure for Integrated Structural Biology (ANR-17-EURE-0003, UMS 3518, ANR-10-INBS-0005, ANR-10-INBS-000502, ANR-10-INBS)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
Keywords
Deinococcus radiodurans, nucleoid-associated proteins, DNA condensation, DNA damage response, radioresistance (biology), crystal structure, DNA binding sites, DNA topology, DNA repair, genome fragmentation
MeSH terms
Bacterial Proteins, DNA Damage, DNA Repair, DNA, Circular, Deinococcus

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