Evidence map›Paper›PMID 41335470›Full record

ArticleNucleic acids research2025

eIF2D promotes 40S ribosomal subunit recycling during intrinsic ribosome destabilization.

Kazuya Ichihara, Taichi Shiraishi, Yuhei Chadani, Yuki Kito, Chisa Shiraishi, Mina Hirata, Yuta Takahashi, Akinao Kobo, Atsushi Hatano, Masaki Matsumoto and 9 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nucleic acids research, 2025. 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. Article
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

19 authors.

Kazuya IchiharaDivision of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan.ORCID 0000-0002-9354-452X
Taichi ShiraishiDivision of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan.
Yuhei ChadaniFaculty of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 700-8530, Japan.
Yuki KitoDivision of Cell Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan.
Chisa ShiraishiDivision of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan.
Mina HirataDivision of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan.
Yuta TakahashiDivision of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan.
Akinao KoboSchool of Life Science and Technology, Institute of Science Tokyo, Yokohama 226-8501, Japan.
Atsushi HatanoDepartment of Omics and Systems Biology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan.
Masaki MatsumotoDepartment of Omics and Systems Biology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan.
Kodai MachidaGraduate School of Engineering, University of Hyogo, Himeji 671-2280, Japan.
Hiroaki ImatakaGraduate School of Engineering, University of Hyogo, Himeji 671-2280, Japan.
Atsushi ToyodaAdvanced Genomics Center, National Institute of Genetics, Shizuoka 411-8540, Japan.ORCID 0000-0002-0728-7548
Emi Mishiro-SatoInstitute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya 464-8601, Japan.
Takayuki NojimaMedical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan.
Takuhiro ItoLaboratory for Translation Structural Biology, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.ORCID 0000-0003-3704-5205
Hideki TaguchiSchool of Life Science and Technology, Institute of Science Tokyo, Yokohama 226-8501, Japan.ORCID 0000-0002-6612-9339
Keiichi I NakayamaDivision of Cell Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan.
Akinobu MatsumotoDivision of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan.ORCID 0000-0002-4077-3935

Funding

Fusion Oriented Research for disruptive Science and Technology JPMJFR2312Japan Science and Technology AgencyJapan Society for the Promotion of ScienceMinistry of Education 20H05928Ministry of Education 23H00378Ministry of Education 24K18054
6 · The paper itself

Abstract

Although eukaryotic initiation factor 2D (eIF2D) is implicated in translation initiation, reinitiation, and ribosome recycling, its precise role remains unclear. Here, we show that eIF2D promotes 40S ribosome recycling during intrinsic ribosome destabilization (IRD), a process in which ribosomes stochastically destabilize while translating proteins with consecutive acidic amino acids at their NH2-terminus. Unrecycled 40S ribosomes accumulate in eIF2D-deficient cells, leading to 80S ribosome stalling. Selective translation complex profiling (TCP-seq) reveals that eIF2D preferentially associates with IRD-prone regions. The winged helix domain, unique to eIF2D but absent in MCTS1-DENR, enhances its binding to 40S subunits, but likely clashes with ABCE1 during stop-codon-associated recycling. Loss of eIF2D reduces the expression of IRD-inducing proteins, including splicing factors. Together, these findings define a previously unappreciated role for eIF2D in 40S recycling and clarify its mechanistic divergence from the MCTS1-DENR complex.

Indexed as

Eukaryotic Initiation Factor-2RibosomesRibosome Subunits, Small, EukaryoticSaccharomyces cerevisiae ProteinsHumansPeptide Chain Initiation, TranslationalProtein BindingProtein BiosynthesisSaccharomyces cerevisiaeEukaryotic Initiation Factor-2Saccharomyces cerevisiae Proteins

Identifiers

PMID41335470
PMCPMC12673854

What OpenQuestion holds

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Registered trials

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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.