IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-33503-6.html
   My bibliography  Save this article

Search and processing of Holliday junctions within long DNA by junction-resolving enzymes

Author

Listed:
  • Artur P. Kaczmarczyk

    (Imperial College London
    MRC-London Institute of Medical Sciences)

  • Anne-Cécile Déclais

    (University of Dundee)

  • Matthew D. Newton

    (Imperial College London
    MRC-London Institute of Medical Sciences
    The Francis Crick Institute)

  • Simon J. Boulton

    (The Francis Crick Institute)

  • David M. J. Lilley

    (University of Dundee)

  • David S. Rueda

    (Imperial College London
    MRC-London Institute of Medical Sciences)

Abstract

Resolution of Holliday junctions is a critical intermediate step of homologous recombination in which junctions are processed by junction-resolving endonucleases. Although binding and cleavage are well understood, the question remains how the enzymes locate their substrate within long duplex DNA. Here we track fluorescent dimers of endonuclease I on DNA, presenting the complete single-molecule reaction trajectory for a junction-resolving enzyme finding and cleaving a Holliday junction. We show that the enzyme binds remotely to dsDNA and then undergoes 1D diffusion. Upon encountering a four-way junction, a catalytically-impaired mutant remains bound at that point. An active enzyme, however, cleaves the junction after a few seconds. Quantitative analysis provides a comprehensive description of the facilitated diffusion mechanism. We show that the eukaryotic junction-resolving enzyme GEN1 also undergoes facilitated diffusion on dsDNA until it becomes located at a junction, so that the general resolution trajectory is probably applicable to many junction resolving enzymes.

Suggested Citation

  • Artur P. Kaczmarczyk & Anne-Cécile Déclais & Matthew D. Newton & Simon J. Boulton & David M. J. Lilley & David S. Rueda, 2022. "Search and processing of Holliday junctions within long DNA by junction-resolving enzymes," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-33503-6
    DOI: 10.1038/s41467-022-33503-6
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-33503-6
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-022-33503-6?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Alfredo De Biasio & Alain Ibáñez de Opakua & Gulnahar B. Mortuza & Rafael Molina & Tiago N. Cordeiro & Francisco Castillo & Maider Villate & Nekane Merino & Sandra Delgado & David Gil-Cartón & Irene L, 2015. "Structure of p15PAF–PCNA complex and implications for clamp sliding during DNA replication and repair," Nature Communications, Nature, vol. 6(1), pages 1-12, May.
    2. Leonard Wu & Ian D. Hickson, 2003. "The Bloom's syndrome helicase suppresses crossing over during homologous recombination," Nature, Nature, vol. 426(6968), pages 870-874, December.
    3. Jonathan M. Hadden & Anne-Cécile Déclais & Stephen B. Carr & David M. J. Lilley & Simon E. V. Phillips, 2007. "The structural basis of Holliday junction resolution by T7 endonuclease I," Nature, Nature, vol. 449(7162), pages 621-624, October.
    4. Christian Biertümpfel & Wei Yang & Dietrich Suck, 2007. "Crystal structure of T4 endonuclease VII resolving a Holliday junction," Nature, Nature, vol. 449(7162), pages 616-620, October.
    5. Géraldine Farge & Niels Laurens & Onno D. Broekmans & Siet M.J.L. van den Wildenberg & Linda C.M. Dekker & Martina Gaspari & Claes M. Gustafsson & Erwin J.G. Peterman & Maria Falkenberg & Gijs J.L. Wu, 2012. "Protein sliding and DNA denaturation are essential for DNA organization by human mitochondrial transcription factor A," Nature Communications, Nature, vol. 3(1), pages 1-9, January.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. S. Cohen & A. Guenolé & I. Lazar & A. Marnef & T. Clouaire & D. V. Vernekar & N. Puget & V. Rocher & C. Arnould & M. Aguirrebengoa & M. Genais & N. Firmin & R. A. Shamanna & R. Mourad & V. A. Bohr & V, 2022. "A POLD3/BLM dependent pathway handles DSBs in transcribed chromatin upon excessive RNA:DNA hybrid accumulation," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    2. Anne Margriet Heijink & Colin Stok & David Porubsky & Eleni Maria Manolika & Jurrian K. Kanter & Yannick P. Kok & Marieke Everts & H. Rudolf Boer & Anastasia Audrey & Femke J. Bakker & Elles Wierenga , 2022. "Sister chromatid exchanges induced by perturbed replication can form independently of BRCA1, BRCA2 and RAD51," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    3. Rohit Prakash & Thomas Sandoval & Florian Morati & Jennifer A. Zagelbaum & Pei-Xin Lim & Travis White & Brett Taylor & Raymond Wang & Emilie C. B. Desclos & Meghan R. Sullivan & Hayley L. Rein & Kara , 2021. "Distinct pathways of homologous recombination controlled by the SWS1–SWSAP1–SPIDR complex," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    4. Hyun Huh & Jiayu Shen & Yogeeshwar Ajjugal & Aparna Ramachandran & Smita S. Patel & Sang-Hyuk Lee, 2024. "Sequence-specific dynamic DNA bending explains mitochondrial TFAM’s dual role in DNA packaging and transcription initiation," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    5. Claudia Lancey & Muhammad Tehseen & Souvika Bakshi & Matthew Percival & Masateru Takahashi & Mohamed A. Sobhy & Vlad S. Raducanu & Kerry Blair & Frederick W. Muskett & Timothy J. Ragan & Ramon Crehuet, 2021. "Cryo-EM structure of human Pol κ bound to DNA and mono-ubiquitylated PCNA," Nature Communications, Nature, vol. 12(1), pages 1-14, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-33503-6. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.