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Peer-reviewedCC BY-NC-NDProceedings of the National Academy of Sciences of the United States of America

Two D-loop resolution systems enable natural genetic transformation in bacteria.

  • Léo Hardy1
  • Violette Morales2,3
  • Clothilde J Rousseau1
  • Mathieu Bergé2,3
  • Fanny Mazzamurro4,5
  • Julie Plantade1
  • Triana N Dalia6
  • Ankur B Dalia6
  • Eduardo P C Rocha4
  • Xavier Charpentier1
  • Patrice Polard2,3
6 affiliations
  1. 1Centre International de Recherche end Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Univ Lyon, Villeurbanne 69100, France.
  2. 2Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative, Centre Nationale de la Recherche Scientifique, Toulouse 31062, France.
  3. 3Université de Toulouse, Toulouse 31062, France.
  4. 4Institut Pasteur, CNRS UMR3525, Microbial Evolutionary Genomics, Université Paris Cité, Paris 75015, France.
  5. 5Collège Doctoral-Sorbonne Université, Paris F-75005, France.
  6. 6Department of Biology, Indiana University, Bloomington, IN 47405.
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Abstract

Natural transformation is a widespread mechanism driving genetic exchanges in bacteria. It proceeds from the capture of extracellular DNA released by other cells. Internalized in linear single strands, this exogenous DNA is ultimately integrated into the genome by homologous recombination. It is unknown how the RecA-directed D-loop intermediate of this dedicated recombination pathway is processed. We report that resolution of the transformation D-loop depends on two endonucleases of opposing phylogenetic distribution in bacteria. One is YraN, which has coevolved and interacts with the ComM helicase, known to extend DNA recombination at the transformation D-loop. The other is CoiA, which is restricted to the Bacillota. CoiA is shown to be a resolvase of the transformation D-loop, extended by the RadA helicase in these species. We demonstrate that both YraN and CoiA act synergistically with their cognate helicases. These findings reveal that bacteria have evolved two helicase/nuclease pairs for the maturation and recombination extension of the transformation D-loop. The wide distribution of this dual system indicates that recombination of exogenous DNA by natural transformation is an ancestral and pervasive feature of bacteria.

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Cite

BibTeXRIS
BibTeX
@article{hardy2026dloop,
  title = {{Two D-loop resolution systems enable natural genetic transformation in bacteria.}},
  author = {Léo Hardy and Violette Morales and Clothilde J Rousseau and Mathieu Bergé and Fanny Mazzamurro and Julie Plantade and Triana N Dalia and Ankur B Dalia and Eduardo P C Rocha and Xavier Charpentier and Patrice Polard},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  year = {2026},
  month = oct,
  doi = {10.1073/pnas.2610795123},
  url = {https://europepmc.org/article/MED/42837456},
  note = {CC BY-NC-ND},
}
RIS
TY  - JOUR
TI  - Two D-loop resolution systems enable natural genetic transformation in bacteria.
AU  - Léo Hardy
AU  - Violette Morales
AU  - Clothilde J Rousseau
AU  - Mathieu Bergé
AU  - Fanny Mazzamurro
AU  - Julie Plantade
AU  - Triana N Dalia
AU  - Ankur B Dalia
AU  - Eduardo P C Rocha
AU  - Xavier Charpentier
AU  - Patrice Polard
PY  - 2026
DA  - 2026/10/06
JO  - Proceedings of the National Academy of Sciences of the United States of America
DO  - 10.1073/pnas.2610795123
UR  - https://europepmc.org/article/MED/42837456
AB  - Natural transformation is a widespread mechanism driving genetic exchanges in bacteria. It proceeds from the capture of extracellular DNA released by other cells. Internalized in linear single strands, this exogenous DNA is ultimately integrated into the genome by homologous recombination. It is unknown how the RecA-directed D-loop intermediate of this dedicated recombination pathway is processed. We report that resolution of the transformation D-loop depends on two endonucleases of opposing phylogenetic distribution in bacteria. One is YraN, which has coevolved and interacts with the ComM helicase, known to extend DNA recombination at the transformation D-loop. The other is CoiA, which is restricted to the Bacillota. CoiA is shown to be a resolvase of the transformation D-loop, extended by the RadA helicase in these species. We demonstrate that both YraN and CoiA act synergistically with their cognate helicases. These findings reveal that bacteria have evolved two helicase/nuclease pairs for the maturation and recombination extension of the transformation D-loop. The wide distribution of this dual system indicates that recombination of exogenous DNA by natural transformation is an ancestral and pervasive feature of bacteria.
SN  - 0027-8424
SN  - 1091-6490
ER  -