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Phosphorylation tunes p62 condensates to drive autophagic degradation of ubiquitinated proteins.

Overview

Authors: Satoko Komatsu-Hirota1, Keisuke Tabata1, Yu-shin Sou2, Soichiro Kakuta3, Jun-ichi Sakamaki1, Hikaru Tsuchiya1,4, Jiachen Li1, Hiroyuki Kumeta5, Yuji Sakai6, Yuko Fujioka7, Daisuke Noshiro7, Shunsuke F Shimobayashi8, Tomo Kurimura8, Takashi Taniguchi9, Manabu Abe10, Masato Koike2, Hideaki Morishita11, Nobuo N Noda7, Masaaki Komatsu1,4
  1. Department of Physiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
  2. Department of Cell Biology and Neuroscience, Juntendo University Graduate School of Medicine, Tokyo, Japan
  3. Laboratory of Morphology and Image Analysis, Biomedical Research Core Facilities, Juntendo University Graduate School of Medicine, Tokyo, Japan
  4. Autophagy Research Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
  5. Frontier Research Center for Advanced Material and Life Science, Graduate School of Life Science and Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
  6. Graduate School of Nanobioscience, Yokohama City University, Yokohama, Japan
  7. Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
  8. Department of Life Science Frontiers Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
  9. Graduate School of Engineering, Department of Chemical Engineering, Kyoto University, Kyoto, Japan
  10. Department of Animal Model Development, Brain Research Institute, Niigata University, Niigata, Japan
  11. Department of Molecular Cell Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
Journal: The EMBO journal, volume 45, issue 12, pages 4061-4093
Dates: received 22 December 2025; accepted 2 April 2026; published online 5 May 2026; in print June 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1038/s44318-026-00785-1 · PMID 42086857 · PMCID PMC13270050 · OpenAlex W7160232610
Open access: gold, a free copy (OpenAlex)
Status: data only
Categories: human (organism), mouse (organism), cellular / molecular (subfield)
Methods: Spectral & time-frequency, Statistics, Evoked potentials, fMRI & imaging, Physiology & signal measures
Keywords: Organelles, Post-translational Modifications & Proteolysis
MeSH: Autophagy*, Sequestosome-1 Protein*, Ubiquitinated Proteins*, Animals, Humans, Mice, Phosphorylation, Protein Serine-Threonine Kinases, Proteolysis (* major topic)
Topic: Autophagy in Disease and Therapy (Epidemiology, Medicine), according to OpenAlex
Funding: MEXT | Japan Society for the Promotion of Science (JSPS) (JP25H00315, JP23K27134, JP24H01901, JP25H01328, JP23K06065, JP23K20044, JP25H00966, JP25H01320, JP25H01323, JP25H01419, JP23H04923, JP25K09567, JP22H04926, JP24H00060, JP25H0132); MEXT | JST | Core Research for Evolutional Science and Technology (CREST) (JPMJCR20E3); Takeda Medical Research Foundation; Kobayashi Foundation for Cancer Research; Uehara Memorial Foundation; Japan Agency for Medical Research and Development (AMED) (JP22gm1410004h0003, 21gm6410019h0001); Mitsubishi Foundation
Citations: cited by 1 paper (Europe PMC); 62 references in the paper
Research resources: Anti-FLAG M2 affinity agarose gel RRID:AB_10063035, Rabbit monoclonal anti-TBK1BP1 RRID:AB_10839270, Mouse monoclonal anti-DDDDK-tag RRID:AB_11123930, Rabbit monoclonal anti-TAX1BP1 RRID:AB_11178939, Chicken polyclonal anti-NeuN RRID:AB_11205760, Rabbit polyclonal anti-p62 RRID:AB_1279301, Mouse polyclonal anti-PPP2R5A RRID:AB_2042675, Rabbit polyclonal anti-KEAP1 RRID:AB_2132625, Mouse monoclonal anti-NBR1 RRID:AB_2149402, Rat monoclonal anti-Nestin RRID:AB_2151130, Mouse polyclonal anti-PPP2CA RRID:AB_2169495, Rabbit polyclonal anti-LC3 RRID:AB_2274121, RRID:AB_2307391, Cy3-conjugated Streptavidin RRID:AB_2337244, RRID:AB_2337402, HRP-conjugated goat Anti-Mouse IgG RRID:AB_2338511, RRID:AB_2535805, Goat polyclonal anti-MAP2 RRID:AB_2571793, RRID:AB_2687531, Mouse monoclonal anti-Ubiquitin (P4D1) RRID:AB_2762364, Rabbit monoclonal anti-TBK1 RRID:AB_2827657, Rabbit polyclonal anti-p62 (pSer403) RRID:AB_2885723, Anti-mouse STAR RED RRID:AB_3068620, Anti-Rabbit STAR ORANGE RRID:AB_3068622, Rabbit polyclonal anti-AZI2 RRID:AB_3672616, Rabbit monoclonal anti-PPP2R5E RRID:AB_3676292, Rabbit monoclonal anti-pTBK1 (pS172) RRID:AB_3695654, Mouse monoclonal anti-p62 Ick ligand RRID:AB_398152, Rat monoclonal anti-PPP2R5B RRID:AB_785345, pCMV-PE2-P2A-GFP RRID:Addgene_132776, pX330-U6-Chimeric_BB-CBh-hSpCas9 RRID:Addgene_42230, Huh-1 RRID:CVCL_2956, Fiji software RRID:SCR_002285, GraphPad Prism 9 RRID:SCR_002798, ImageJ software RRID:SCR_003070, Photoshop 2021v25.0 RRID:SCR_014199, Proteome Discoverer™ 3.2 RRID:SCR_014477

Abstract

p62/SQSTM1 self-assembles with polyubiquitin into liquid-like condensates (“p62 bodies”) that function as stress-signaling hubs and selective autophagy cargo. We show that TBK1-dependent phosphorylation at Ser403 acts as a threshold-dependent modulator of a condensate’s physical properties and promotes their rapid autophagic clearance. Phosphorylation within p62 bodies drives a transition from large, fluid droplets to compact, gel-like condensates that efficiently capture LC3-positive isolation membranes and accelerate the autophagic removal of ubiquitinated proteins. PP2A holoenzymes containing PPP2R5A/B/E, recruited via a KEAP1 bridge, counteract TBK1 by dephosphorylating Ser403. Homozygous p62S403E/S403E knock-in embryonic stem cells differentiate into post-mitotic neurons enriched in miniaturized, gel-like p62 bodies. Consistently, phosphorylation-mimetic knock-in mice show similar remodeling of p62 condensates in vivo, demonstrating that this phosphorylation-driven mechanism maintains proteostasis across scales. We propose that Ser403 phosphorylation functions as a molecular switch that couples the material state of p62 condensates to their stability and serves as a central control point for p62-mediated protein degradation.

Reproduced under the paper's license (CC BY), from the paper cited above.

Code

The paper links to its data, not to its authors' code: see the Data section.

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Data

Data links

Data availability

The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD074538 (https://www.ebi.ac.uk/pride/archive/projects/PXD074538) (https://www.ebi.ac.uk/pride/archive/projects/PXD074538). NMR chemical shift assignments have been deposited in the Biological Magnetic Resonance Data Bank (BMRB) under accession number 53579 (http://bmrb.io/data_library/summary/index.php?bmrbId= 53579). All data supporting the findings of this study are provided within the paper.

The source data of this paper are collected in the following database record: biostudies:S-SCDT-10_1038-S44318-026-00785-1 (https://www.ebi.ac.uk/biostudies/sourcedata/studies/S-SCDT-10_1038-S44318-026-00785-1).

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 19 authors, 2 keywords, 9 MeSH terms, 7 funders, 61 references, 37 RRIDs.

Cite

This paper

Komatsu-Hirota, S., Tabata, K., Sou, Y.-s., Kakuta, S., Sakamaki, J.-i., Tsuchiya, H., Li, J., Kumeta, H., Sakai, Y., Fujioka, Y., Noshiro, D., Shimobayashi, S. F., Kurimura, T., Taniguchi, T., Abe, M., Koike, M., Morishita, H., Noda, N. N., & Komatsu, M. (2026). Phosphorylation tunes p62 condensates to drive autophagic degradation of ubiquitinated proteins. The EMBO journal, 45(12), 4061-4093. https://doi.org/10.1038/s44318-026-00785-1

BibTeX

@article{komatsuhirota2026phosphorylation,
author = {Komatsu-Hirota, Satoko and Tabata, Keisuke and Sou, Yu-shin and Kakuta, Soichiro and Sakamaki, Jun-ichi and Tsuchiya, Hikaru and Li, Jiachen and Kumeta, Hiroyuki and Sakai, Yuji and Fujioka, Yuko and Noshiro, Daisuke and Shimobayashi, Shunsuke F and Kurimura, Tomo and Taniguchi, Takashi and Abe, Manabu and Koike, Masato and Morishita, Hideaki and Noda, Nobuo N and Komatsu, Masaaki},
title = {{Phosphorylation tunes p62 condensates to drive autophagic degradation of ubiquitinated proteins}},
journal = {The EMBO journal},
year = {2026},
month = may,
volume = {45},
number = {12},
pages = {4061--4093},
publisher = {Nature Publishing Group},
issn = {0261-4189},
doi = {10.1038/s44318-026-00785-1},
url = {https://doi.org/10.1038/s44318-026-00785-1},
pmid = {42086857},
pmcid = {PMC13270050}
}

RIS

TY - JOUR
AU - Komatsu-Hirota, Satoko
AU - Tabata, Keisuke
AU - Sou, Yu-shin
AU - Kakuta, Soichiro
AU - Sakamaki, Jun-ichi
AU - Tsuchiya, Hikaru
AU - Li, Jiachen
AU - Kumeta, Hiroyuki
AU - Sakai, Yuji
AU - Fujioka, Yuko
AU - Noshiro, Daisuke
AU - Shimobayashi, Shunsuke F
AU - Kurimura, Tomo
AU - Taniguchi, Takashi
AU - Abe, Manabu
AU - Koike, Masato
AU - Morishita, Hideaki
AU - Noda, Nobuo N
AU - Komatsu, Masaaki
TI - Phosphorylation tunes p62 condensates to drive autophagic degradation of ubiquitinated proteins
T2 - The EMBO journal
J2 - EMBO J
PY - 2026
DA - 2026/05/05
VL - 45
IS - 12
SP - 4061
EP - 4093
SN - 0261-4189
PB - Nature Publishing Group
DO - 10.1038/s44318-026-00785-1
UR - https://doi.org/10.1038/s44318-026-00785-1
LA - en
ER -

CSL-JSON

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