Evidence map›Paper›PMID 39675003›Full record

ArticleCell reports2024

Analyses of translation factors Dbp1 and Ded1 reveal the cellular response to heat stress to be separable from stress granule formation.

Naohiro Kuwayama, Emily Nicole Powers, Matej Siketanc, Camila Ines Sousa, Kendra Reynaud, Marko Jovanovic, Maria Hondele, Nicholas Thomas Ingolia, Gloria Ann Brar

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell reports, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
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

1 citing paper in PubMed.

  1. Regulation of RNA-binding proteins by small biomolecules.Nature reviews. Molecular cell biology · 2026
    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

9 authors.

Naohiro KuwayamaDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
Emily Nicole PowersDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
Matej SiketancBiozentrum, Center for Molecular Life Sciences, University of Basel, 4056 Basel, Switzerland.
Camila Ines SousaDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
Kendra ReynaudDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
Marko JovanovicDepartment of Biological Sciences, Columbia University, New York, NY 10027, USA.
Maria HondeleBiozentrum, Center for Molecular Life Sciences, University of Basel, 4056 Basel, Switzerland.
Nicholas Thomas IngoliaDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA; Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
Gloria Ann BrarDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA; Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA. Electronic address: gabrar@berkeley.edu.

Funding

MOLECULAR BIOPHYSICS TRAINING GRANTT32GM008295 · NIGMS · UNIVERSITY OF CALIFORNIA BERKELEY · PI HURLEY, JAMES H, WEMMER, DAVID E · 1989 to 2022
$8.1M
Molecular Biology Across Scales Training ProgramT32GM148378 · NIGMS · UNIVERSITY OF CALIFORNIA BERKELEY · PI David Bilder, Elcin Unal · 2023 to 2026
$7.3M
Illuminating the gene regulatory strategies underlying yeast meiosis and beyondR35GM134886 · NIGMS · UNIVERSITY OF CALIFORNIA BERKELEY · PI Gloria Ann Brar · 2020 to 2026
$3.1M
Regulation of Protein Production Dynamics:RNA Binding Proteins and the Ribosome CodeR35GM128802 · NIGMS · COLUMBIA UNIV NEW YORK MORNINGSIDE · PI JOVANOVIC, MARKO · 2018 to 2022
$2.3M
Functional genomics of the dynamic molecular network controlling mRNA translation and decayR01GM130996 · NIGMS · UNIVERSITY OF CALIFORNIA BERKELEY · PI INGOLIA, NICHOLAS T · 2019 to 2022
$1.2M
NIGMS NIH HHS R01 GM130996NIGMS NIH HHS R35 GM128802NIGMS NIH HHS R35 GM134886NIGMS NIH HHS T32 GM008295NIGMS NIH HHS T32 GM148378
6 · The paper itself

Abstract

Ded1 and Dbp1 are paralogous conserved DEAD-box ATPases involved in translation initiation in yeast. In long-term starvation states, Dbp1 expression increases and Ded1 decreases, whereas in cycling mitotic cells, Dbp1 is absent. Inserting DBP1 in place of DED1 cannot replace Ded1 function in supporting mitotic translation, partly due to inefficient translation of the DBP1 coding region. Global translation measurements, activity of mRNA-tethered proteins, and growth assays show that-even at matched protein levels-Ded1 is better than Dbp1 at activating translation, especially for mRNAs with structured 5' leaders. Heat-stressed cells normally downregulate translation of structured housekeeping transcripts and halt growth, but neither occurs in Dbp1-expressing cells. This failure to halt growth in response to heat is not based on deficient stress granule formation or failure to reduce bulk translation. Rather, it depends on heat-triggered loss of Ded1 function mediated by an 11-amino-acid interval within its intrinsically disordered C terminus.

Indexed as

DEAD-box RNA HelicasesHeat-Shock ResponseProtein BiosynthesisSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsCytoplasmic GranulesRNA, MessengerStress GranulesDEAD-box RNA HelicasesDED1 protein, S cerevisiaeRNA, MessengerSaccharomyces cerevisiae ProteinsCP: Molecular biologyDbp1DDX3DEAD-box helicaseDed1heat stressribosome profilingstress granulesTranslationtranslation initiation

Identifiers

PMID39675003
PMCPMC11759133

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.