Evidence map›Paper›PMID 40728716›Full record

ArticleThe Journal of cell biology2025

The p97 ATPase and its adaptor UBXD8 maintain peroxisome pools by preventing pexophagy.

Iris D Montes, Suganthan Amirthagunanathan, Rakesh Ganji, Joao A Paulo, Brittany A Ahlstedt, Ly Nguyen, Amit S Joshi, Malavika Raman

Abstract read
In one paragraph

Article in The Journal of cell biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Review
  2. 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

8 authors.

Iris D MontesDepartment of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA.ORCID 0000-0002-9272-7308
Suganthan AmirthagunanathanDepartment of Biochemistry and Cell and Molecular Biology, University of Tennessee, Knoxville, TN, USA.ORCID 0009-0008-9560-1963
Rakesh GanjiDepartment of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA.ORCID 0000-0003-2874-5007
Joao A PauloDepartment of Cell Biology Harvard Medical School , Boston, MA, USA.ORCID 0000-0002-4291-413X
Brittany A AhlstedtDepartment of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA.
Ly NguyenDepartment of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA.ORCID 0009-0007-2367-7398
Amit S JoshiDepartment of Biochemistry and Cell and Molecular Biology, University of Tennessee, Knoxville, TN, USA.ORCID 0000-0003-3321-0744
Malavika RamanDepartment of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA.ORCID 0000-0002-4773-8673

Funding

“Regulation of Protein Quality Control by the VCP AAA-ATPase”R01GM127557 · NIGMS · TUFTS UNIVERSITY BOSTON · PI Malavika Raman · 2018 to 2026
$3.5M
MECHANISMS OF ORGANELLE BIOGENESIS AT THE ENDOPLASMIC RETICULUM SUBDOMAINSR35GM147189 · NIGMS · UNIVERSITY OF TENNESSEE KNOXVILLE · PI Amit Joshi · 2022 to 2026
$2.1M
Advancing Multiplexed Isobaric Tag-based Strategies for Proteome ProfilingR01GM132129 · NIGMS · HARVARD MEDICAL SCHOOL · PI PAULO, JOAO A · 2019 to 2023
$1.7M
Developing proteomics pipelines to improve depth, throughput, and accuracyR35GM156406 · NIGMS · HARVARD MEDICAL SCHOOL · PI Joao A Paulo · 2025 to 2026
$878k
Investigating the impact of p97 mutation in Amyotrophic Lateral SclerosisR21NS123631 · NINDS · TUFTS UNIVERSITY BOSTON · PI RAMAN, MALAVIKA · 2022 to 2023
$454k
Determining the Role of p97 Adaptor UBXD8 in Peroxisome FunctionF31GM148057 · NIGMS · TUFTS UNIVERSITY BOSTON · PI MONTES, IRIS · 2022 to 2024
$131k
Israel National Road Safety Authority F31 GM148057-01NIGMS NIH HHS F31 GM148057NIGMS NIH HHS R01 GM127557NIGMS NIH HHS R01 GM132129NIGMS NIH HHS R35 GM147189NIGMS NIH HHS R35 GM156406NIH HHS R01 GM127557NIH HHS R01 XXNIH HHS R21 NS123631NIH HHS R35 GM147189NINDS NIH HHS R21 NS123631
6 · The paper itself

Abstract

Peroxisomes perform key metabolic functions in eukaryotic cells. Loss of peroxisome function causes peroxisome biogenesis disorders and severe childhood diseases with disrupted lipid metabolism. One mechanism regulating peroxisome abundance is degradation via selective autophagy (pexophagy). However, the mechanisms regulating pexophagy remain poorly understood in mammalian cells. Here, we find that the evolutionarily conserved AAA-ATPase p97/VCP and its adaptor UBXD8/FAF2 are essential for maintaining peroxisome abundance. From quantitative proteomics studies, we show that loss of UBXD8 affects the abundance of many peroxisomal proteins and that the depletion of UBXD8 results in a loss of peroxisomes. Loss of p97-UBXD8 and inhibition of p97 catalytic activity increase peroxisomal turnover through autophagy and can be rescued by depleting key autophagy proteins and E3 ligases or overexpressing the deubiquitylase USP30. We find increased ubiquitylation of PMP70 and PEX5 in cells lacking UBXD8 or p97. Our findings identify a new role of the p97-UBXD8 in regulating peroxisome abundance by removing ubiquitylated peroxisome membrane proteins to prevent pexophagy.

Indexed as

Adaptor Proteins, Signal TransducingAdenosine TriphosphatasesAutophagyPeroxisomesValosin Containing ProteinAnimalsHEK293 CellsHeLa CellsHumansMembrane ProteinsNuclear ProteinsPeroxisome-Targeting Signal 1 ReceptorUbiquitinationAdaptor Proteins, Signal TransducingAdenosine TriphosphatasesMembrane ProteinsNuclear Proteinsp97 ATPasePeroxisome-Targeting Signal 1 ReceptorPEX5 protein, humanValosin Containing ProteinVCP protein, human

Identifiers

PMID40728716
PMCPMC12306898

What OpenQuestion holds

Textmetadata
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.