Evidence map›Paper›PMID 36543799›Full record

ArticleNature communications2022

The UFM1 system regulates ER-phagy through the ufmylation of CYB5R3.

Ryosuke Ishimura, Afnan H El-Gowily, Daisuke Noshiro, Satoko Komatsu-Hirota, Yasuko Ono, Mayumi Shindo, Tomohisa Hatta, Manabu Abe, Takefumi Uemura, Hyeon-Cheol Lee-Okada and 10 more

Open access · goldAbstract read
In one paragraph

Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.

0numbers the graph read from it
0cells of the map it votes in
64citing papers in PubMed
5.9field-weighted citation impact, top 2% 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

64 citing papers in PubMed, 84 citations in OpenAlex.

  1. Review
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  8. The mechanistic basis and cellular functions of UFMylation.Nature reviews. Molecular cell biology · 2026
    Review
  9. Article
  10. Article
  11. Article
  12. Article
  13. Article
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  16. UFMylation of Pyruvate Dehydrogenase Regulates Mitochondrial Metabolism.bioRxiv : the preprint server for biology · 2026
    Article
  17. Article
  18. Core principles of autophagy initiation mechanisms.Nature structural & molecular biology · 2026
    Review
  19. Ribosome-associated quality control and related mechanisms.Nature structural & molecular biology · 2026
    Review
  20. Review

4 more citing papers are in PubMed but not listed here.

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

20 authors at 8 institutions in 2 countries.

Ryosuke IshimuraDepartment of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan.
Afnan H El-GowilyDepartment of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan.ORCID 0000-0001-5290-7278
Daisuke NoshiroDivision of Biological Molecular Mechanisms, Institute for Genetic Medicine, Hokkaido University, Sapporo, 060-0815, Japan.ORCID 0000-0001-7024-2054
Satoko Komatsu-HirotaDepartment of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan.
Yasuko OnoCalpain Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, 156-8506, Japan.
Mayumi ShindoAdvanced Technical Support Department, Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, 156-8506, Japan.
Tomohisa HattaNational Institutes of Advanced Industrial Science and Technology, Biological Information Research Center (JBIRC), Kohtoh-ku, Tokyo, 135-0064, Japan.
Manabu AbeDepartment of Animal Model Development, Brain Research Institute, Niigata University, Chuo-ku, Niigata, 951-8585, Japan.ORCID 0000-0001-8534-2138
Takefumi UemuraDepartment of Anatomy and Histology, Fukushima Medical University School of Medicine, Hikarigaoka, Fukshima, 960-1295, Japan.
Hyeon-Cheol Lee-OkadaDepartment of Biochemistry, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan.ORCID 0000-0002-5493-8112
Tarek M MohamedBiochemistry Division, Chemistry Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt.
Takehiko YokomizoDepartment of Biochemistry, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan.
Takashi UenoLaboratory of Proteomics and Biomolecular Science, Biomedical Research Core Facilities, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan.
Kenji SakimuraDepartment of Animal Model Development, Brain Research Institute, Niigata University, Chuo-ku, Niigata, 951-8585, Japan.
Tohru NatsumeNational Institutes of Advanced Industrial Science and Technology, Biological Information Research Center (JBIRC), Kohtoh-ku, Tokyo, 135-0064, Japan.ORCID 0000-0002-1510-2582
Hiroyuki SorimachiCalpain Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, 156-8506, Japan.ORCID 0000-0001-9509-6727
Toshifumi InadaDivision of RNA and gene regulation, Institute of Medical Science, The University of Tokyo, Minato-Ku, 108-8639, Japan.ORCID 0000-0002-2695-588X
Satoshi WaguriDepartment of Anatomy and Histology, Fukushima Medical University School of Medicine, Hikarigaoka, Fukshima, 960-1295, Japan.ORCID 0000-0001-9919-7111
Nobuo N NodaDivision of Biological Molecular Mechanisms, Institute for Genetic Medicine, Hokkaido University, Sapporo, 060-0815, Japan.ORCID 0000-0002-6940-8069
Masaaki KomatsuDepartment of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, 113-8421, Japan. mkomatsu@juntendo.ac.jp.ORCID 0000-0001-7672-7722
Juntendo University · JPTokyo Metropolitan Institute of Medical Science · JPFukushima Medical University · JPHokkaido University · JPNational Institute of Advanced Industrial Science and Technology · JPNiigata University · JPTanta University · EGThe University of Tokyo · JP

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Protein modification by ubiquitin-like proteins (UBLs) amplifies limited genome information and regulates diverse cellular processes, including translation, autophagy and antiviral pathways. Ubiquitin-fold modifier 1 (UFM1) is a UBL covalently conjugated with intracellular proteins through ufmylation, a reaction analogous to ubiquitylation. Ufmylation is involved in processes such as endoplasmic reticulum (ER)-associated protein degradation, ribosome-associated protein quality control at the ER and ER-phagy. However, it remains unclear how ufmylation regulates such distinct ER-related functions. Here we identify a UFM1 substrate, NADH-cytochrome b5 reductase 3 (CYB5R3), that localizes on the ER membrane. Ufmylation of CYB5R3 depends on the E3 components UFL1 and UFBP1 on the ER, and converts CYB5R3 into its inactive form. Ufmylated CYB5R3 is recognized by UFBP1 through the UFM1-interacting motif, which plays an important role in the further uyfmylation of CYB5R3. Ufmylated CYB5R3 is degraded in lysosomes, which depends on the autophagy-related protein Atg7- and the autophagy-adaptor protein CDK5RAP3. Mutations of CYB5R3 and genes involved in the UFM1 system cause hereditary developmental disorders, and ufmylation-defective Cyb5r3 knock-in mice exhibit microcephaly. Our results indicate that CYB5R3 ufmylation induces ER-phagy, which is indispensable for brain development.

Indexed as

AutophagyCytochrome-B(5) ReductaseEndoplasmic ReticulumUbiquitinsAnimalsCell Cycle ProteinsMiceProtein Processing, Post-TranslationalProteinsTumor Suppressor ProteinsUbiquitinationCdk5rap3 protein, mouseCell Cycle ProteinsCyb5r3 protein, mouseCytochrome-B(5) ReductaseProteinsTumor Suppressor ProteinsUbiquitinsUfm1 protein, mouse

Identifiers

PMID36543799
PMCPMC9772183
OpenAlexW4313340002

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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.