Evidence map›Paper›PMID 33767388›Full record

ArticleNature chemical biology2021

Biomolecular condensates amplify mRNA decapping by biasing enzyme conformation.

Ryan W Tibble, Anaïs Depaix, Joanna Kowalska, Jacek Jemielity, John D Gross

Open access · greenAbstract read
In one paragraph

Article in Nature chemical biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.

0numbers the graph read from it
0cells of the map it votes in
53citing papers in PubMed
5.9field-weighted citation impact, top 3% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

53 citing papers in PubMed, 92 citations in OpenAlex.

  1. Article
  2. Article
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  6. Article
  7. Biomolecular Condensates Dictate the Folding Landscape of Proteins.bioRxiv : the preprint server for biology · 2026
    Article
  8. Review
  9. Sticky interactions govern sequence-dependent dynamics in biomolecular condensates.Proceedings of the National Academy of Sciences of the United States of America · 2026
    Article
  10. Review
  11. Client-scaffold interactions suppress aggregation of a client protein in model condensates.Proceedings of the National Academy of Sciences of the United States of America · 2025
    Article
  12. Article
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  15. COProceedings of the National Academy of Sciences of the United States of America · 2025
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  16. Review
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  20. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors at 2 institutions in 2 countries.

Ryan W TibbleProgram in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0002-4188-3116
Anaïs DepaixDivision of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland.ORCID http://orcid.org/0000-0003-1472-4985
Joanna KowalskaDivision of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland.ORCID http://orcid.org/0000-0002-9174-7999
Jacek JemielityCentre of New Technologies, University of Warsaw, Warsaw, Poland.ORCID http://orcid.org/0000-0001-7633-788X
John D GrossProgram in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, CA, USA. jdgross@cgl.ucsf.edu.ORCID http://orcid.org/0000-0002-1377-4705
University of Warsaw · PLUniversity of California, San Francisco · US

Funding

Structure and Function of the Decapping Enzyme ComplexR01GM078360 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI GROSS, JOHN D · 2009 to 2018
$2.5M
Molecular Mechanisms that Control mRNA Decapping in Biological CondensatesR01GM148881 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI John D Gross · 2023 to 2026
$1.3M
A 600 MHz NMR console and cryoprobe for studies of macromolecules, drug discovery and cancer biomarkersS10OD023455 · OD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI GROSS, JOHN D · 2018 to 2018
$820k
Wide field-of-view Spinning Disk Confocal with Photoactivation and PhotobleachingS10OD017993 · OD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI THORN, KURT · 2015 to 2015
$274k
NIGMS NIH HHS R01 GM078360NIGMS NIH HHS R01 GM148881NIH HHS S10 OD017993NIH HHS S10 OD023455
6 · The paper itself

Abstract

Cells organize biochemical processes into biological condensates. P-bodies are cytoplasmic condensates that are enriched in enzymes important for mRNA degradation and have been identified as sites of both storage and decay. How these opposing outcomes can be achieved in condensates remains unresolved. mRNA decapping immediately precedes degradation, and the Dcp1/Dcp2 decapping complex is enriched in P-bodies. Here, we show that Dcp1/Dcp2 activity is modulated in condensates and depends on the interactions promoting phase separation. We find that Dcp1/Dcp2 phase separation stabilizes an inactive conformation in Dcp2 to inhibit decapping. The activator Edc3 causes a conformational change in Dcp2 and rewires the protein-protein interactions to stimulate decapping in condensates. Disruption of the inactive conformation dysregulates decapping in condensates. Our results indicate that the regulation of enzymatic activity in condensates relies on a coupling across length scales ranging from microns to ångstroms. We propose that this regulatory mechanism may control the functional state of P-bodies and related phase-separated compartments.

Indexed as

Binding SitesCloning, MolecularCytoplasmic GranulesEscherichia coliFluorescent DyesGene ExpressionGenetic VectorsModels, MolecularProtein BindingProtein Conformation, alpha-HelicalProtein Conformation, beta-StrandProtein Interaction Domains and MotifsRecombinant ProteinsRNA CapsRNA StabilitySchizosaccharomycesDcp1 protein, S pombeDcp2 protein, S pombeEdc3 protein, S pombeFluorescent DyesRecombinant ProteinsRNA CapsSchizosaccharomyces pombe Proteins

Identifiers

PMID33767388
PMCPMC8476181
OpenAlexW3139160981

What OpenQuestion holds

Textmetadata
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Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.