Cited by 112DNA Repair MechanismsGenomics and Chromatin DynamicsMicrotubule and mitosis dynamics

In silico protein interaction screening uncovers DONSON’s role in replication initiation

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Lim, Yang, Tamayo-Orrego, Lukas, Schmid, Ernst, Tarnauskaite, Zygimante, Kochenova, Olga V., Gruar, Rhian, Muramatsu, Sachiko, Lynch, Luke +7 more·2023·Science

Abstract

CDC45-MCM2-7-GINS (CMG) helicase assembly is the central event in eukaryotic replication initiation. In yeast, a multi-subunit “pre-loading complex” (pre-LC) accompanies GINS to chromatin-bound MCM2-7, leading to CMG formation. Here, we report that DONSON, a metazoan protein mutated in microcephalic primordial dwarfism, is required for CMG assembly in vertebrates. Using AlphaFold to screen for protein-protein interactions followed by experimental validation, we show that DONSON scaffolds a vertebrate pre-LC containing GINS, TOPBP1, and DNA pol ε. Our evidence suggests that DONSON docks the pre-LC onto MCM2-7, delivering GINS to its binding site in CMG. A patient-derived DONSON mutation compromises CMG assembly and recapitulates microcephalic dwarfism in mice. These results unify our understanding of eukaryotic replication initiation, implicate defective CMG assembly in microcephalic dwarfism, and illustrate how in silico protein-protein interaction screening accelerates mechanistic discovery.

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Crossref · 10.1126/science.adi3448

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  • In proteome wide screens, SPOC readily identified STK19, USP37, and DONSON partners whose function we validated.

    “The power of SPOC is illustrated by the fact that in proteome wide screens, it readily identified STK19, USP37, and DONSON partners whose function we validated23,54,56.”

    From Predictomes, a classifier-curated database of AlphaFold-modeled protein-protein interactions (2025) · cites this paper as [23]

    The Results section (“Ab initio prediction of protein function using AlphaFold-Multimer”; page unavailable) reports a proteome-wide DONSON interactor screen, and the Discussion says its predicted functional partners were experimentally validated. But the paper describes the method as AF-M, not SPOC, and says identifying CMG assembly as DONSON’s function from the proteome-wide screen was clearest after a second, structure-guided round of predictions. This source supports the DONSON example, not the STK19 or USP37 examples attributed to the other citations. (LLM, conf=0.84)

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Research works printed but not linked: 1

  1. [36]Day M TopBP1 utilises a bipartite GINS binding mode to activate the replicative helicase. bioRxiv, (2023).

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Authors
Lim, Y., Tamayo-Orrego, L., Schmid, E., Tarnauskaite, Z., Kochenova, O. V., Gruar, R., Muramatsu, S., Lynch, L., Schlie, A. V., Carroll, P. L., Chistol, G., Reijns, M. A. M., Kanemaki, M. T., Jackson, A. P., & Walter, J. C.
Affiliations
  • Harvard University (US)
  • Institute of Genetics and Cancer (GB)
  • MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK.
  • Howard Hughes Medical Institute (US)
  • National Institute of Genetics (JP)
  • Stanford Medicine (US)
Corresponding author
  • Lim, Yang
  • Tamayo-Orrego, Lukas
  • Jackson, Andrew P.
  • Walter, Johannes C.
Venue
Science
Published
2023-09-22
Volume
381
Issue
6664
Pages
eadi3448-eadi3448
ISSN
  • 0036-8075 (ISSN-L)
  • 1095-9203
OpenAlex
W4385925982
Cited by
112
References
82
Citations by year
2026: 29 · 2025: 37 · 2024: 39 · 2023: 7
FWCI
9.98
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Science (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion, cc-by)
  • Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, cc-by)
Funders
  • National Science Foundation (2144481, CREST, 2140743, CAREER)
  • Howard Hughes Medical Institute
  • European Commission (HORIZON2020)
  • National Institutes of Health
  • Medical Research Council (MC_UU_00035/10)
  • Japan Society for the Promotion of Science (21H04719, JP23H04925, CREST, JP21H0419)
  • National Heart, Lung, and Blood Institute (R01HL098316)
  • National Institute of General Medical Sciences (GM147060, T32GM007276, R35GM147060)
  • Core Research for Evolutional Science and Technology (JPMJCR21E6)
  • H2020 European Research Council (788093)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Microtubule and mitosis dynamics
Keywords
DNA replication initiation, MCM2-7 complex, GINS, TopBP1, DNA polymerase epsilon, protein-protein interaction screening, AlphaFold
MeSH terms
Animals, Computer Simulation, DNA Replication, DNA-Binding Proteins, Dwarfism, Humans, Microcephaly, Nuclear Proteins, Saccharomyces cerevisiae, Xenopus laevis, Cell Cycle Proteins, Protein Interaction Mapping, Saccharomyces cerevisiae Proteins, Mice, Minichromosome Maintenance Proteins

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