Structural basis of p62/SQSTM1 helical filaments and their role in cellular cargo uptake.

Arabidopsis Proteins / chemistry Arginine / chemistry Autophagy / physiology Carrier Proteins / chemistry Cryoelectron Microscopy Crystallography, X-Ray HeLa Cells Humans Kelch-Like ECH-Associated Protein 1 / genetics Lysosomes / metabolism Polymerization Protein Conformation Protein Domains Sequestosome-1 Protein / chemistry

Journal

Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555

Informations de publication

Date de publication:
23 01 2020
Historique:
received: 28 05 2019
accepted: 02 01 2020
entrez: 25 1 2020
pubmed: 25 1 2020
medline: 25 4 2020
Statut: epublish

Résumé

p62/SQSTM1 is an autophagy receptor and signaling adaptor with an N-terminal PB1 domain that forms the scaffold of phase-separated p62 bodies in the cell. The molecular determinants that govern PB1 domain filament formation in vitro remain to be determined and the role of p62 filaments inside the cell is currently unclear. We here determine four high-resolution cryo-EM structures of different human and Arabidopsis PB1 domain assemblies and observed a filamentous ultrastructure of p62/SQSTM1 bodies using correlative cellular EM. We show that oligomerization or polymerization, driven by a double arginine finger in the PB1 domain, is a general requirement for lysosomal targeting of p62. Furthermore, the filamentous assembly state of p62 is required for autophagosomal processing of the p62-specific cargo KEAP1. Our results show that using such mechanisms, p62 filaments can be critical for cargo uptake in autophagy and are an integral part of phase-separated p62 bodies.

Identifiants

DOI: 10.1038/s41467-020-14343-8 PMID: 31974402 PMC: PMC6978347
pubmed: 31974402
doi: 10.1038/s41467-020-14343-8
pii: 10.1038/s41467-020-14343-8
pmc: PMC6978347
doi:

Substances chimiques

Arabidopsis Proteins 0
Carrier Proteins 0
KEAP1 protein, human 0
Kelch-Like ECH-Associated Protein 1 0
NBR1 protein, Arabidopsis 0
SQSTM1 protein, human 0
Sequestosome-1 Protein 0
Arginine 94ZLA3W45F

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

440

Références

Katsuragi, Y., Ichimura, Y. & Komatsu, M. p62/SQSTM1 functions as a signaling hub and an autophagy adaptor. FEBS J. 282, 4672–4678 (2015).
pubmed: 26432171 doi: 10.1111/febs.13540
Lamark, T. et al. Interaction codes within the family of mammalian Phox and Bem1p domain-containing proteins. J. Biol. Chem. 278, 34568–34581 (2003).
pubmed: 12813044 doi: 10.1074/jbc.M303221200
Moscat, J., Diaz-Meco, M. T., Albert, A. & Campuzano, S. Cell signaling and function organized by PB1 domain interactions. Mol. Cell 23, 631–640 (2006).
pubmed: 16949360 doi: 10.1016/j.molcel.2006.08.002
Korasick, D. A. et al. Molecular basis for AUXIN RESPONSE FACTOR protein interaction and the control of auxin response repression. Proc. Natl Acad. Sci. USA 111, 5427–5432 (2014).
pubmed: 24706860 doi: 10.1073/pnas.1400074111
Wilson, M. I., Gill, D. J., Perisic, O., Quinn, M. T. & Williams, R. L. PB1 domain-mediated heterodimerization in NADPH oxidase and signaling complexes of atypical protein kinase C with Par6 and p62. Mol. Cell 12, 39–50 (2003).
pubmed: 12887891 doi: 10.1016/S1097-2765(03)00246-6
Sumimoto, H., Kamakura, S. & Ito, T. Structure and function of the PB1 domain, a protein interaction module conserved in animals, fungi, amoebas, and plants. Sci. STKE 2007, re6 (2007).
pubmed: 17726178 doi: 10.1126/stke.4012007re6
Paine, M. G., Babu, J. R., Seibenhener, M. L. & Wooten, M. W. Evidence for p62 aggregate formation: role in cell survival. FEBS Lett. 579, 5029–5034 (2005).
pubmed: 16129434 doi: 10.1016/j.febslet.2005.08.010
Ciuffa, R. et al. The selective autophagy receptor p62 forms a flexible filamentous helical scaffold. Cell Rep. 11, 748–758 (2015).
pubmed: 25921531 doi: 10.1016/j.celrep.2015.03.062
Mizushima, N. & Komatsu, M. Autophagy: renovation of cells and tissues. Cell 147, 728–741 (2011).
pubmed: 22078875 doi: 10.1016/j.cell.2011.10.026
Johansen, T. & Lamark, T. Selective autophagy mediated by autophagic adapter proteins. Autophagy 7, 279–296 (2011).
pubmed: 21189453 pmcid: 3060413 doi: 10.4161/auto.7.3.14487
Kraft, C., Peter, M. & Hofmann, K. Selective autophagy: ubiquitin-mediated recognition and beyond. Nat. Cell Biol. 12, 836–841 (2010).
pubmed: 20811356 doi: 10.1038/ncb0910-836
Itakura, E. & Mizushima, N. p62 Targeting to the autophagosome formation site requires self-oligomerization but not LC3 binding. J. Cell Biol. 192, 17–27 (2011).
pubmed: 21220506 pmcid: 3019556 doi: 10.1083/jcb.201009067
Wurzer, B. et al. Oligomerization of p62 allows for selection of ubiquitinated cargo and isolation membrane during selective autophagy. eLife 4, 1687 (2015).
doi: 10.7554/eLife.08941
Bjørkøy, G. et al. p62/SQSTM1 forms protein aggregates degraded by autophagy and has a protective effect on huntingtin-induced cell death. J. Cell Biol. 171, 603–614 (2005).
pubmed: 16286508 pmcid: 2171557 doi: 10.1083/jcb.200507002
Pankiv, S. et al. p62/SQSTM1 binds directly to Atg8/LC3 to facilitate degradation of ubiquitinated protein aggregates by autophagy. J. Biol. Chem. 282, 24131–24145 (2007).
pubmed: 17580304 doi: 10.1074/jbc.M702824200
Jain, A. et al. p62/SQSTM1 is a target gene for transcription factor NRF2 and creates a positive feedback loop by inducing antioxidant response element-driven gene transcription. J. Biol. Chem. 285, 22576–22591 (2010).
pubmed: 20452972 pmcid: 2903417 doi: 10.1074/jbc.M110.118976
Komatsu, M. et al. The selective autophagy substrate p62 activates the stress responsive transcription factor Nrf2 through inactivation of Keap1. Nat. Cell Biol. 12, 213–223 (2010).
pubmed: 20173742 doi: 10.1038/ncb2021
Duran, A. et al. The signaling adaptor p62 is an important NF-kappaB mediator in tumorigenesis. Cancer Cell 13, 343–354 (2008).
pubmed: 18394557 doi: 10.1016/j.ccr.2008.02.001
Carroll, B. et al. Oxidation of SQSTM1/p62 mediates the link between redox state and protein homeostasis. Nat. Commun. 9, 256–11 (2018).
pubmed: 29343728 pmcid: 5772351 doi: 10.1038/s41467-017-02746-z
Sukseree, S. et al. Filamentous aggregation of sequestosome-1/p62 in brain neurons and neuroepithelial cells upon Tyr-Cre-mediated deletion of the autophagy gene Atg7. Mol. Neurobiol. 55, 8425–8437 (2018).
pubmed: 29550918 pmcid: 6153718 doi: 10.1007/s12035-018-0996-x
Zaffagnini, G. et al. p62 filaments capture and present ubiquitinated cargos for autophagy. EMBO J. 37, e98308 (2018).
Sun, D., Wu, R., Zheng, J., Li, P. & Yu, L. Polyubiquitin chain-induced p62 phase separation drives autophagic cargo segregation. Cell Res. 28, 405–415 (2018).
pubmed: 29507397 pmcid: 5939046 doi: 10.1038/s41422-018-0017-7
Svenning, S., Lamark, T., Krause, K. & Johansen, T. Plant NBR1 is a selective autophagy substrate and a functional hybrid of the mammalian autophagic adapters NBR1 and p62/SQSTM1. Autophagy 7, 993–1010 (2011).
pubmed: 21606687 pmcid: 3210314 doi: 10.4161/auto.7.9.16389
Saio, T., Yokochi, M. & Inagaki, F. The NMR structure of the p62 PB1 domain, a key protein in autophagy and NF-kappaB signaling pathway. J. Biomol. NMR 45, 335–341 (2009).
pubmed: 19728111 doi: 10.1007/s10858-009-9370-7
Saio, T., Yokochi, M., Kumeta, H. & Inagaki, F. PCS-based structure determination of protein-protein complexes. J. Biomol. NMR 46, 271–280 (2010).
pubmed: 20300805 pmcid: 2844537 doi: 10.1007/s10858-010-9401-4
Krissinel, E. & Henrick, K. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372, 774–797 (2007).
pubmed: 17681537 doi: 10.1016/j.jmb.2007.05.022
Ren, J., Wang, J., Wang, Z. & Wu, J. Structural and biochemical insights into the homotypic PB1-PB1 complex between PKCζ and p62. Sci. China Life Sci. 57, 69–80 (2014).
pubmed: 24369353 doi: 10.1007/s11427-013-4592-z
Egelman, E. H. et al. Structural plasticity of helical nanotubes based on coiled-coil assemblies. Structure 23, 280–289 (2015).
pubmed: 25620001 pmcid: 4318749 doi: 10.1016/j.str.2014.12.008
Kirkin, V. et al. A role for NBR1 in autophagosomal degradation of ubiquitinated substrates. Mol. Cell 33, 505–516 (2009).
pubmed: 19250911 doi: 10.1016/j.molcel.2009.01.020
Studier, F. W. Protein production by auto-induction in high density shaking cultures. Protein Expr. Purif. 41, 207–234 (2005).
pubmed: 15915565 doi: 10.1016/j.pep.2005.01.016
Jakobi, A. J., Mashaghi, A., Tans, S. J. & Huizinga, E. G. Calcium modulates force sensing by the von Willebrand factor A2 domain. Nat. Commun. 2, 385 (2011).
pubmed: 21750539 pmcid: 3144584 doi: 10.1038/ncomms1385
Scheuermann, T. H. & Brautigam, C. A. High-precision, automated integration of multiple isothermal titration calorimetric thermograms: new features of NITPIC. Methods 76, 87–98 (2015).
pubmed: 25524420 doi: 10.1016/j.ymeth.2014.11.024
Zhao, H., Piszczek, G. & Schuck, P. SEDPHAT-a platform for global ITC analysis and global multi-method analysis of molecular interactions. Methods 76, 137–148 (2015).
pubmed: 25477226 doi: 10.1016/j.ymeth.2014.11.012
Brautigam, C. A., Zhao, H., Vargas, C., Keller, S. & Schuck, P. Integration and global analysis of isothermal titration calorimetry data for studying macromolecular interactions. Nat. Protoc. 11, 882–894 (2016).
pubmed: 27055097 doi: 10.1038/nprot.2016.044
Ohi, M., Li, Y., Cheng, Y. & Walz, T. Negative staining and image classification—powerful tools in modern electron microscopy. Biol. Proc. Online 6, 23–34 (2004).
doi: 10.1251/bpo70
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).
pubmed: 22743772 pmcid: 22743772 doi: 10.1038/nmeth.2019
Li, X. et al. Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat. Methods 10, 584–590 (2013).
pubmed: 23644547 pmcid: 3684049 doi: 10.1038/nmeth.2472
Rohou, A. & Grigorieff, N. CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015).
pubmed: 26278980 pmcid: 6760662 doi: 10.1016/j.jsb.2015.08.008
Tang, G. et al. EMAN2: an extensible image processing suite for electron microscopy. J. Struct. Biol. 157, 38–46 (2007).
pubmed: 16859925 doi: 10.1016/j.jsb.2006.05.009
Desfosses, A., Ciuffa, R., Gutsche, I. & Sachse, C. SPRING—an image processing package for single-particle based helical reconstruction from electron cryomicrographs. J. Struct. Biol. 185, 15–26 (2014).
pubmed: 24269218 doi: 10.1016/j.jsb.2013.11.003
Hohn, M. et al. SPARX, a new environment for Cryo-EM image processing. J. Struct. Biol. 157, 47–55 (2007).
pubmed: 16931051 doi: 10.1016/j.jsb.2006.07.003
Rosenthal, P. B. & Henderson, R. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 333, 721–745 (2003).
pubmed: 14568533 doi: 10.1016/j.jmb.2003.07.013 pmcid: 14568533
Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 7, 163 (2018).
doi: 10.7554/eLife.42166
Zhang, K. Gctf: real-time CTF determination and correction. J. Struct. Biol. 193, 1–12 (2016).
pubmed: 26592709 pmcid: 4711343 doi: 10.1016/j.jsb.2015.11.003
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D. Biol. Crystallogr. 60, 2126–2132 (2004).
pubmed: 15572765 doi: 10.1107/S0907444904019158
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D. Biol. Crystallogr. 66, 213–221 (2010).
pubmed: 20124702 pmcid: 2815670 doi: 10.1107/S0907444909052925
Jakobi, A. J., Wilmanns, M. & Sachse, C. Model-based local density sharpening of cryo-EM maps. eLife 6, e27131 (2017).
pubmed: 29058676 pmcid: 5679758 doi: 10.7554/eLife.27131
Kabsch, W. Integration, scaling, space-group assignment and post-refinement. Acta Crystallogr. D. Biol. Crystallogr. 66, 133–144 (2010).
pubmed: 20124693 pmcid: 2815666 doi: 10.1107/S0907444909047374
Evans, P. R. & Murshudov, G. N. How good are my data and what is the resolution? Acta Crystallogr. D. Biol. Crystallogr. 69, 1204–1214 (2013).
pubmed: 23793146 pmcid: 3689523 doi: 10.1107/S0907444913000061
Grosse-Kunstleve, R. W., Sauter, N. K., Moriarty, N. W. & Adams, P. D. The Computational Crystallography Toolbox: crystallographic algorithms in a reusable software framework. J. Appl. Crystallogr. 35, 126–136 (2002).
doi: 10.1107/S0021889801017824
Mccoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).
pubmed: 19461840 pmcid: 2483472 doi: 10.1107/S0021889807021206
Terwilliger, T. C. et al. Model morphing and sequence assignment after molecular replacement. Acta Crystallogr. D. Biol. Crystallogr. 69, 2244–2250 (2013).
pubmed: 24189236 pmcid: 3817698 doi: 10.1107/S0907444913017770
Langer, G., Cohen, S. X., Lamzin, V. S. & Perrakis, A. Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat. Protoc. 3, 1171–1179 (2008).
pubmed: 18600222 pmcid: 2582149 doi: 10.1038/nprot.2008.91
Kremer, J. R., Mastronarde, D. N. & McIntosh, J. R. Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116, 71–76 (1996).
pubmed: 8742726 doi: 10.1006/jsbi.1996.0013
Overå, K. et al. TRIM32, but not its muscular dystrophy-associated mutant, positively regulates and is targeted to autophagic degradation by p62/SQSTM1. J. Cell Sci. 132, jcs236596 (2019).
pubmed: 31685529 doi: 10.1242/jcs.236596
Alemu, E. A. et al. ATG8 family proteins act as scaffolds for assembly of the ULK complex: sequence requirements for LC3-interacting region (LIR) motifs. J. Biol. Chem. 287, 39275–39290 (2012).
pubmed: 23043107 doi: 10.1074/jbc.M112.378109
Larsen, K. B. et al. A reporter cell system to monitor autophagy based on p62/SQSTM1. Autophagy 6, 784–793 (2010).
pubmed: 20574168 doi: 10.4161/auto.6.6.12510
Bhujabal, Z. et al. FKBP8 recruits LC3A to mediate Parkin-independent mitophagy. EMBO Rep. 18, 947–961 (2017).

Auteurs

Arjen J Jakobi (AJ)

European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstraße 1, 69117, Heidelberg, Germany.
European Molecular Biology Laboratory (EMBL), Hamburg Unit c/o DESY, Notkestraße 85, 22607, Hamburg, Germany.
The Hamburg Centre for Ultrafast Imaging (CUI), Luruper Chaussee 149, 22761, Hamburg, Germany.
Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629, HZ Delft, The Netherlands.
ORCID: 0000-0002-7761-2027

Stefan T Huber (ST)

European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstraße 1, 69117, Heidelberg, Germany.
Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629, HZ Delft, The Netherlands.
ORCID: 0000-0003-3721-5104

Simon A Mortensen (SA)

European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstraße 1, 69117, Heidelberg, Germany.
Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons (ER-C-3/Structural Biology), Forschungszentrum Jülich, 52425, Jülich, Germany.
JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425, Jülich, Germany.

Sebastian W Schultz (SW)

Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Montebello, N-0379, Oslo, Norway.

Anthimi Palara (A)

Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø - The Arctic University of Norway, 9037, Tromsø, Norway.

Tanja Kuhm (T)

European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstraße 1, 69117, Heidelberg, Germany.
Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629, HZ Delft, The Netherlands.

Birendra Kumar Shrestha (BK)

Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø - The Arctic University of Norway, 9037, Tromsø, Norway.

Trond Lamark (T)

Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø - The Arctic University of Norway, 9037, Tromsø, Norway.
ORCID: 0000-0001-6338-3342

Wim J H Hagen (WJH)

European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstraße 1, 69117, Heidelberg, Germany.

Matthias Wilmanns (M)

European Molecular Biology Laboratory (EMBL), Hamburg Unit c/o DESY, Notkestraße 85, 22607, Hamburg, Germany.
The Hamburg Centre for Ultrafast Imaging (CUI), Luruper Chaussee 149, 22761, Hamburg, Germany.
ORCID: 0000-0002-4643-5435

Terje Johansen (T)

Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø - The Arctic University of Norway, 9037, Tromsø, Norway.
ORCID: 0000-0003-1451-9578

Andreas Brech (A)

Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Montebello, N-0379, Oslo, Norway.

Carsten Sachse (C)

European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstraße 1, 69117, Heidelberg, Germany. c.sachse@fz-juelich.de.
Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons (ER-C-3/Structural Biology), Forschungszentrum Jülich, 52425, Jülich, Germany. c.sachse@fz-juelich.de.
JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425, Jülich, Germany. c.sachse@fz-juelich.de.
ORCID: 0000-0002-1168-5143

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Classifications MeSH

questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéines végétales › Protéines d'Arabidopsis › Structural basis of p62/SQSTM1 helical...
questionsmedicales.fr › Acides aminés, peptides et protéines › Acides aminés › Acides aminés essentiels › Arginine › Structural basis of p62/SQSTM1 helical...
questionsmedicales.fr › Phénomènes physiologiques cellulaires › Autophagie › Structural basis of p62/SQSTM1 helical...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéines de transport › Structural basis of p62/SQSTM1 helical...
questionsmedicales.fr › Techniques d'investigation › Microscopie électronique › Cryomicroscopie électronique › Structural basis of p62/SQSTM1 helical...
questionsmedicales.fr › Techniques d'investigation › Techniques de chimie analytique › Cristallographie aux rayons X › Structural basis of p62/SQSTM1 helical...
questionsmedicales.fr › Cellules › Cellules épithéliales › Cellules HeLa › Structural basis of p62/SQSTM1 helical...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Structural basis of p62/SQSTM1 helical...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéines et peptides de signalisation intracellulaire › Protéines adaptatrices de la transduction du signal › Protéine-1 de type kelch associée à ECH › Structural basis of p62/SQSTM1 helical...
questionsmedicales.fr › Cellules › Structures cellulaires › Espace intracellulaire › Cytoplasme › Structures cytoplasmiques › Organites › Vésicules cytoplasmiques › Lysosomes › Structural basis of p62/SQSTM1 helical...
questionsmedicales.fr › Phénomènes chimiques › Polymérisation › Structural basis of p62/SQSTM1 helical...
questionsmedicales.fr › Phénomènes chimiques › Phénomènes biochimiques › Conformation moléculaire › Conformation des protéines › Structural basis of p62/SQSTM1 helical...
questionsmedicales.fr › Phénomènes chimiques › Phénomènes biochimiques › Conformation moléculaire › Conformation des protéines › Structure tertiaire des protéines › Domaines protéiques › Structural basis of p62/SQSTM1 helical...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéines et peptides de signalisation intracellulaire › Protéines adaptatrices de la transduction du signal › Séquestosome-1 › Structural basis of p62/SQSTM1 helical...