Cited by 116DNA Repair MechanismsUbiquitin and proteasome pathwaysGenomics and Chromatin Dynamics

A conserved mechanism for regulating replisome disassembly in eukaryotes

Open access
Jenkyn-Bedford, Michael, Jones, Morgan L., Baris, Yasemin, Labib, Karim P. M., Cannone, Giuseppe, Yeeles, Joseph T. P., Deegan, Tom D.·2021·Nature

Abstract

Replisome disassembly is the final step of eukaryotic DNA replication and is triggered by ubiquitylation of the CDC45–MCM–GINS (CMG) replicative helicase 1–3 . Despite being driven by evolutionarily diverse E3 ubiquitin ligases in different eukaryotes (SCF Dia2 in budding yeast 1 , CUL2 LRR1 in metazoa 4–7 ), replisome disassembly is governed by a common regulatory principle, in which ubiquitylation of CMG is suppressed before replication termination, to prevent replication fork collapse. Recent evidence suggests that this suppression is mediated by replication fork DNA 8–10 . However, it is unknown how SCF Dia2 and CUL2 LRR1 discriminate terminated from elongating replisomes, to selectively ubiquitylate CMG only after termination. Here we used cryo-electron microscopy to solve high-resolution structures of budding yeast and human replisome–E3 ligase assemblies. Our structures show that the leucine-rich repeat domains of Dia2 and LRR1 are structurally distinct, but bind to a common site on CMG, including the MCM3 and MCM5 zinc-finger domains. The LRR–MCM interaction is essential for replisome disassembly and, crucially, is occluded by the excluded DNA strand at replication forks, establishing the structural basis for the suppression of CMG ubiquitylation before termination. Our results elucidate a conserved mechanism for the regulation of replisome disassembly in eukaryotes, and reveal a previously unanticipated role for DNA in preserving replisome integrity.

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Crossref · 10.1038/s41586-021-04145-3

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  • In budding yeast, previous experiments mapped the POLD3-POLA1 interaction to the location in both proteins predicted by AF-M.

    “in budding yeast, previous experiments mapped this interaction to the location in both proteins predicted by AF-M69,70.”

    From Predictomes, a classifier-curated database of AlphaFold-modeled protein-protein interactions (2025) · cites this paper as [69]

    The Terminated yeast replisome structures section describes Pol-ε and a Dia2–CMG interface, while the Dia2LRR–MCM interface section reports experiments on that interface. Neither addresses a POLD3–POLA1 interaction or compares its experimentally mapped location with an AF-M prediction. Searches for POLD3, POLA1, and the yeast protein names Pol32 and Pol1 found no relevant passage; page numbers were unavailable in our copy. (LLM, conf=0.76)

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Research works printed but not linked: 8

  1. [6]Villa F CUL2LRR1, TRAIP and p97 control CMG helicase disassembly in the mammalian cell cycle EMBO Rep. 2021 22 e52164 10.15252/embr.202052164 33590678 PMC7926238 · DOI
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  4. [36]Martin EC LRRpredictor—a new LRR motif detection method for irregular motifs of plant NLR proteins using an ensemble of classifiers Genes 2020 11 286 10.3390/genes11030286 32182725 PMC7140858 · DOI
  5. [37]Schulman BA Insights into SCF ubiquitin ligases from the structure of the Skp1–Skp2 complex Nature 2000 408 381 386 10.1038/35042620 11099048 · DOI
  6. [38]Xing W SCFFBXL3 ubiquitin ligase targets cryptochromes at their cofactor pocket Nature 2013 496 64 68 10.1038/nature11964 23503662 PMC3618506 · DOI · Paper page
  7. [39]Noguchi Y Cryo-EM structure of Mcm2-7 double hexamer on DNA suggests a lagging-strand DNA extrusion model Proc. Natl Acad. Sci. USA 2017 114 E9529 E9538 10.1073/pnas.1712537114 29078375 PMC5692578 · DOI
  8. [40]Afonine PV Real-space refinement in PHENIX for cryo-EM and crystallography Acta Crystallogr. D 2018 74 531 544 10.1107/S2059798318006551 PMC6096492 29872004 · DOI

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Authors
Jenkyn-Bedford, M., Jones, M. L., Baris, Y., Labib, K. P. M., Cannone, G., Yeeles, J. T. P., & Deegan, T. D.
Affiliations
  • MRC Laboratory of Molecular Biology (GB)
  • University of Dundee (GB)
Corresponding author
  • Yeeles, Joseph T. P.
  • Deegan, Tom D.
Venue
Nature
Published
2021-10-26
Volume
600
Issue
7890
Pages
743-747
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
OpenAlex
W3208795162
Cited by
116
References
33
Citations by year
2026: 17 · 2025: 34 · 2024: 32 · 2023: 26 · 2022: 7
FWCI
5.10
Type
journal article
Language
en
Open access
Locations
  • Nature (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Discovery Research Portal (University of Dundee) (publishedVersion, cc-by)
  • RePEc: Research Papers in Economics (submittedVersion)
  • Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, cc-by)
  • Apollo (University of Cambridge) (submittedVersion, cc-by)
  • Apollo
Funders
  • Wellcome Trust (204678/Z/16/Z)
  • UK Research and Innovation (MC_UP_1201/12)
  • Cancer Research UK (24558)
  • Directorate for Biological Sciences
  • Medical Research Council (MC_UU_12016/13, MC_UP_1201/12, MC_UU_12016, MC_UU_00018/4)
  • Biotechnology and Biological Sciences Research Council
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Keywords
CMG helicase, E3 ubiquitin ligase, ubiquitination, replication termination, leucine-rich repeat domain, replication fork collapse, eukaryotic DNA replication
MeSH terms
DNA, DNA Replication, DNA Helicases, Humans, Cryoelectron Microscopy, Ubiquitin-Protein Ligases, Eukaryota

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