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Article ; Online: Mouse oocytes sequester aggregated proteins in degradative super-organelles.

Zaffagnini, Gabriele / Cheng, Shiya / Salzer, Marion C / Pernaute, Barbara / Duran, Juan Manuel / Irimia, Manuel / Schuh, Melina / Böke, Elvan

Cell

2024 Volume 187, Issue 5, Page(s) 1109–1126.e21

Abstract: Oocytes are among the longest-lived cells in the body and need to preserve their cytoplasm to support proper embryonic development. Protein aggregation is a major threat for intracellular homeostasis in long-lived cells. How oocytes cope with protein ... ...

Abstract	Oocytes are among the longest-lived cells in the body and need to preserve their cytoplasm to support proper embryonic development. Protein aggregation is a major threat for intracellular homeostasis in long-lived cells. How oocytes cope with protein aggregation during their extended life is unknown. Here, we find that mouse oocytes accumulate protein aggregates in specialized compartments that we named endolysosomal vesicular assemblies (ELVAs). Combining live-cell imaging, electron microscopy, and proteomics, we found that ELVAs are non-membrane-bound compartments composed of endolysosomes, autophagosomes, and proteasomes held together by a protein matrix formed by RUFY1. Functional assays revealed that in immature oocytes, ELVAs sequester aggregated proteins, including TDP-43, and degrade them upon oocyte maturation. Inhibiting degradative activity in ELVAs leads to the accumulation of protein aggregates in the embryo and is detrimental for embryo survival. Thus, ELVAs represent a strategy to safeguard protein homeostasis in long-lived cells.
MeSH term(s)	Animals ; Female ; Mice ; Autophagosomes ; Cytoplasmic Vesicles/metabolism ; Lysosomes/metabolism ; Oocytes/cytology ; Oocytes/metabolism ; Proteasome Endopeptidase Complex ; Protein Aggregates ; Proteolysis
Chemical Substances	Proteasome Endopeptidase Complex (EC 3.4.25.1) ; Protein Aggregates
Language	English
Publishing date	2024-02-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2024.01.031
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Article ; Online: A mathematical model of p62-ubiquitin aggregates in autophagy.

Delacour, Julia / Doumic, Marie / Martens, Sascha / Schmeiser, Christian / Zaffagnini, Gabriele

Journal of mathematical biology

2021 Volume 84, Issue 1-2, Page(s) 3

Abstract: Aggregation of ubiquitinated cargo by oligomers of the protein p62 is an important preparatory step in cellular autophagy. In this work a mathematical model for the dynamics of these heterogeneous aggregates in the form of a system of ordinary ... ...

Abstract	Aggregation of ubiquitinated cargo by oligomers of the protein p62 is an important preparatory step in cellular autophagy. In this work a mathematical model for the dynamics of these heterogeneous aggregates in the form of a system of ordinary differential equations is derived and analyzed. Three different parameter regimes are identified, where either aggregates are unstable, or their size saturates at a finite value, or their size grows indefinitely as long as free particles are abundant. The boundaries of these regimes as well as the finite size in the second case can be computed explicitly. The growth in the third case (quadratic in time) can also be made explicit by formal asymptotic methods. In the absence of rigorous results the dynamic stability of these structures has been investigated by numerical simulations. A comparison with recent experimental results permits a partial parametrization of the model.
MeSH term(s)	Autophagy ; Models, Theoretical ; Proteins ; Sequestosome-1 Protein/metabolism ; Ubiquitin/metabolism
Chemical Substances	Proteins ; Sequestosome-1 Protein ; Ubiquitin
Language	English
Publishing date	2021-12-14
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	187101-8
ISSN	1432-1416 ; 0303-6812
ISSN (online)	1432-1416
ISSN	0303-6812
DOI	10.1007/s00285-021-01659-2
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Article ; Online: Mechanisms of Selective Autophagy.

Zaffagnini, Gabriele / Martens, Sascha

Journal of molecular biology

2016 Volume 428, Issue 9 Pt A, Page(s) 1714–1724

Abstract: Selective autophagy contributes to intracellular homeostasis by mediating the degradation of cytoplasmic material such as aggregated proteins, damaged or over-abundant organelles, and invading pathogens. The molecular machinery for selective autophagy ... ...

Abstract	Selective autophagy contributes to intracellular homeostasis by mediating the degradation of cytoplasmic material such as aggregated proteins, damaged or over-abundant organelles, and invading pathogens. The molecular machinery for selective autophagy must ensure efficient recognition and sequestration of the cargo within autophagosomes. Cargo specificity can be mediated by autophagic cargo receptors that specifically bind the cargo material and the autophagosomal membrane. Here we review the recent insights into the mechanisms that enable cargo receptors to confer selectivity and exclusivity to the autophagic process. We also discuss their different roles during starvation-induced and selective autophagy. We propose to classify autophagic events into cargo-independent and cargo-induced autophagosome formation events.
MeSH term(s)	Autophagosomes/metabolism ; Autophagy ; Homeostasis
Language	English
Publishing date	2016--08
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2016.02.004
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Article: Mechanisms of Selective Autophagy

Zaffagnini, Gabriele / Martens, Sascha

Journal of Molecular Biology. 2016 May 08, v. 428

2016

Abstract	Selective autophagy contributes to intracellular homeostasis by mediating the degradation of cytoplasmic material such as aggregated proteins, damaged or over-abundant organelles, and invading pathogens. The molecular machinery for selective autophagy must ensure efficient recognition and sequestration of the cargo within autophagosomes. Cargo specificity can be mediated by autophagic cargo receptors that specifically bind the cargo material and the autophagosomal membrane. Here we review the recent insights into the mechanisms that enable cargo receptors to confer selectivity and exclusivity to the autophagic process. We also discuss their different roles during starvation-induced and selective autophagy. We propose to classify autophagic events into cargo-independent and cargo-induced autophagosome formation events.
Keywords	autophagy ; homeostasis ; organelles ; pathogens ; receptors
Language	English
Dates of publication	2016-0508
Size	p. 1714-1724.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2016.02.004
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Article ; Online: Comparative analysis of vertebrates reveals that mouse primordial oocytes do not contain a Balbiani body.

Dhandapani, Laasya / Salzer, Marion C / Duran, Juan M / Zaffagnini, Gabriele / De Guirior, Cristian / Martínez-Zamora, Maria Angeles / Böke, Elvan

Journal of cell science

2022 Volume 135, Issue 1

Abstract: Oocytes spend the majority of their lifetime in a primordial state. The cellular and molecular biology of primordial oocytes is largely unexplored; yet, it is necessary to study them to understand the mechanisms through which oocytes maintain cellular ... ...

Abstract	Oocytes spend the majority of their lifetime in a primordial state. The cellular and molecular biology of primordial oocytes is largely unexplored; yet, it is necessary to study them to understand the mechanisms through which oocytes maintain cellular fitness for decades, and why they eventually fail with age. Here, we develop enabling methods for live-imaging-based comparative characterization of Xenopus, mouse and human primordial oocytes. We show that primordial oocytes in all three vertebrate species contain active mitochondria, Golgi and lysosomes. We further demonstrate that human and Xenopus oocytes have a Balbiani body characterized by a dense accumulation of mitochondria in their cytoplasm. However, despite previous reports, we did not find a Balbiani body in mouse oocytes. Instead, we demonstrate that what was previously used as a marker for the Balbiani body in mouse primordial oocytes is in fact a ring-shaped Golgi that is not functionally associated with oocyte dormancy. This study provides the first insights into the organization of the cytoplasm in mammalian primordial oocytes, and clarifies the relative advantages and limitations of choosing different model organisms for studying oocyte dormancy.
MeSH term(s)	Animals ; Cytoplasm ; Mice ; Mitochondria ; Oocytes/metabolism ; Organelles ; Xenopus laevis
Language	English
Publishing date	2022-01-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2993-2
ISSN	1477-9137 ; 0021-9533
ISSN (online)	1477-9137
ISSN	0021-9533
DOI	10.1242/jcs.259394
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Zs.A 1200: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Oligomerization of p62 allows for selection of ubiquitinated cargo and isolation membrane during selective autophagy.

Wurzer, Bettina / Zaffagnini, Gabriele / Fracchiolla, Dorotea / Turco, Eleonora / Abert, Christine / Romanov, Julia / Martens, Sascha

eLife

2015 Volume 4, Page(s) e08941

Abstract: Autophagy is a major pathway for the clearance of harmful material from the cytoplasm. During autophagy, cytoplasmic material is delivered into the lysosomal system by organelles called autophagosomes. Autophagosomes form in a de novo manner and, in the ... ...

Abstract	Autophagy is a major pathway for the clearance of harmful material from the cytoplasm. During autophagy, cytoplasmic material is delivered into the lysosomal system by organelles called autophagosomes. Autophagosomes form in a de novo manner and, in the course of their formation, isolate cargo material from the rest of the cytoplasm. Cargo specificity is conferred by autophagic cargo receptors that selectively link the cargo to the autophagosomal membrane decorated with ATG8 family proteins such as LC3B. Here we show that the human cargo receptor p62/SQSTM-1 employs oligomerization to stabilize its interaction with LC3B and linear ubiquitin when they are clustered on surfaces. Thus, oligomerization enables p62 to simultaneously select for the isolation membrane and the ubiquitinated cargo. We further show in a fully reconstituted system that the interaction of p62 with ubiquitin and LC3B is sufficient to bend the membrane around the cargo.
MeSH term(s)	Adaptor Proteins, Signal Transducing/metabolism ; Autophagy ; Humans ; Intracellular Membranes/metabolism ; Microtubule-Associated Proteins/metabolism ; Protein Binding ; Protein Multimerization ; Sequestosome-1 Protein ; Ubiquitin/metabolism
Chemical Substances	Adaptor Proteins, Signal Transducing ; MAP1LC3B protein, human ; Microtubule-Associated Proteins ; SQSTM1 protein, human ; Sequestosome-1 Protein ; Ubiquitin
Language	English
Publishing date	2015-09-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.08941
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Article ; Online: p62 filaments capture and present ubiquitinated cargos for autophagy.

Zaffagnini, Gabriele / Savova, Adriana / Danieli, Alberto / Romanov, Julia / Tremel, Shirley / Ebner, Michael / Peterbauer, Thomas / Sztacho, Martin / Trapannone, Riccardo / Tarafder, Abul K / Sachse, Carsten / Martens, Sascha

The EMBO journal

2018 Volume 37, Issue 5

Abstract: The removal of misfolded, ubiquitinated proteins is an essential part of the protein quality control. The ubiquitin-proteasome system (UPS) and autophagy are two interconnected pathways that mediate the degradation of such proteins. During autophagy, ... ...

Abstract	The removal of misfolded, ubiquitinated proteins is an essential part of the protein quality control. The ubiquitin-proteasome system (UPS) and autophagy are two interconnected pathways that mediate the degradation of such proteins. During autophagy, ubiquitinated proteins are clustered in a p62-dependent manner and are subsequently engulfed by autophagosomes. However, the nature of the protein substrates targeted for autophagy is unclear. Here, we developed a reconstituted system using purified components and show that p62 and ubiquitinated proteins spontaneously coalesce into larger clusters. Efficient cluster formation requires substrates modified with at least two ubiquitin chains longer than three moieties and is based on p62 filaments cross-linked by the substrates. The reaction is inhibited by free ubiquitin, K48-, and K63-linked ubiquitin chains, as well as by the autophagosomal marker LC3B, suggesting a tight cross talk with general proteostasis and autophagosome formation. Our study provides mechanistic insights on how substrates are channeled into autophagy.
MeSH term(s)	Autophagosomes/physiology ; Autophagy/physiology ; Cell Line, Tumor ; Humans ; Microtubule-Associated Proteins/metabolism ; Protein Aggregation, Pathological/pathology ; Protein Aggregation, Pathological/prevention & control ; Protein Folding ; RNA-Binding Proteins/metabolism ; Ubiquitin/metabolism ; Ubiquitinated Proteins/metabolism
Chemical Substances	MAP1LC3B protein, human ; Microtubule-Associated Proteins ; P62 protein, human ; RNA-Binding Proteins ; Ubiquitin ; Ubiquitinated Proteins
Language	English
Publishing date	2018-01-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	586044-1
ISSN	1460-2075 ; 0261-4189
ISSN (online)	1460-2075
ISSN	0261-4189
DOI	10.15252/embj.201798308
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Article ; Online: Phasing out the bad-How SQSTM1/p62 sequesters ubiquitinated proteins for degradation by autophagy.

Autophagy

2018 Volume 14, Issue 7, Page(s) 1280–1282

Abstract: The degradation of misfolded, ubiquitinated proteins is essential for cellular homeostasis. These proteins are primarily degraded by the ubiquitin-proteasome system (UPS) and macroautophagy/autophagy serves as a backup mechanism when the UPS is ... ...

Abstract	The degradation of misfolded, ubiquitinated proteins is essential for cellular homeostasis. These proteins are primarily degraded by the ubiquitin-proteasome system (UPS) and macroautophagy/autophagy serves as a backup mechanism when the UPS is overloaded. How autophagy and the UPS are coordinated is not fully understood. During the autophagy of misfolded, ubiquitinated proteins, referred to as aggrephagy, substrate proteins are clustered into larger structures in a SQSTM1/p62-dependent manner before they are sequestered by phagophores, the precursors to autophagosomes. We have recently shown that SQSTM1/p62 and ubiquitinated proteins spontaneously phase separate into micrometer-sized clusters in vitro. This enabled us to characterize the properties of the ubiquitin-positive substrates that are necessary for the SQSTM1/p62-mediated cluster formation. Our results suggest that aggrephagy is triggered by the accumulation of substrates with multiple ubiquitin chains and that the process can be inhibited by active proteasomes.
MeSH term(s)	Autophagy ; Humans ; Models, Biological ; Proteasome Endopeptidase Complex/metabolism ; Sequestosome-1 Protein/metabolism ; Ubiquitin/metabolism ; Ubiquitinated Proteins/metabolism
Chemical Substances	Sequestosome-1 Protein ; Ubiquitin ; Ubiquitinated Proteins ; Proteasome Endopeptidase Complex (EC 3.4.25.1)
Language	English
Publishing date	2018-07-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2454135-7
ISSN	1554-8635 ; 1554-8627
ISSN (online)	1554-8635
ISSN	1554-8627
DOI	10.1080/15548627.2018.1462079
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Article ; Online: FIP200 Claw Domain Binding to p62 Promotes Autophagosome Formation at Ubiquitin Condensates.

Turco, Eleonora / Witt, Marie / Abert, Christine / Bock-Bierbaum, Tobias / Su, Ming-Yuan / Trapannone, Riccardo / Sztacho, Martin / Danieli, Alberto / Shi, Xiaoshan / Zaffagnini, Gabriele / Gamper, Annamaria / Schuschnig, Martina / Fracchiolla, Dorotea / Bernklau, Daniel / Romanov, Julia / Hartl, Markus / Hurley, James H / Daumke, Oliver / Martens, Sascha

Molecular cell

2019 Volume 74, Issue 2, Page(s) 330–346.e11

Abstract: The autophagy cargo receptor p62 facilitates the condensation of misfolded, ubiquitin-positive proteins and their degradation by autophagy, but the molecular mechanism of p62 signaling to the core autophagy machinery is unclear. Here, we show that ... ...

Abstract	The autophagy cargo receptor p62 facilitates the condensation of misfolded, ubiquitin-positive proteins and their degradation by autophagy, but the molecular mechanism of p62 signaling to the core autophagy machinery is unclear. Here, we show that disordered residues 326-380 of p62 directly interact with the C-terminal region (CTR) of FIP200. Crystal structure determination shows that the FIP200 CTR contains a dimeric globular domain that we designated the "Claw" for its shape. The interaction of p62 with FIP200 is mediated by a positively charged pocket in the Claw, enhanced by p62 phosphorylation, mutually exclusive with the binding of p62 to LC3B, and it promotes degradation of ubiquitinated cargo by autophagy. Furthermore, the recruitment of the FIP200 CTR slows the phase separation of ubiquitinated proteins by p62 in a reconstituted system. Our data provide the molecular basis for a crosstalk between cargo condensation and autophagosome formation.
MeSH term(s)	Autophagosomes/chemistry ; Autophagosomes/metabolism ; Autophagy/genetics ; Autophagy-Related Proteins ; Crystallography, X-Ray ; Humans ; Microtubule-Associated Proteins/chemistry ; Microtubule-Associated Proteins/genetics ; Protein Conformation ; Protein Interaction Maps/genetics ; Protein-Tyrosine Kinases/chemistry ; Protein-Tyrosine Kinases/genetics ; Proteolysis ; Sequestosome-1 Protein/chemistry ; Sequestosome-1 Protein/genetics ; Signal Transduction/genetics ; Ubiquitin/chemistry ; Ubiquitin/genetics
Chemical Substances	Autophagy-Related Proteins ; MAP1LC3B protein, human ; Microtubule-Associated Proteins ; RB1CC1 protein, human ; SQSTM1 protein, human ; Sequestosome-1 Protein ; Ubiquitin ; Protein-Tyrosine Kinases (EC 2.7.10.1)
Language	English
Publishing date	2019-03-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2019.01.035
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Article ; Online: How RB1CC1/FIP200 claws its way to autophagic engulfment of SQSTM1/p62-ubiquitin condensates.

Autophagy

2019 Volume 15, Issue 8, Page(s) 1475–1477

Abstract: Macroautophagy/autophagy mediates the degradation of ubiquitinated aggregated proteins within lysosomes in a process known as aggrephagy. The cargo receptor SQSTM1/p62 condenses aggregated proteins into larger structures and links them to the nascent ... ...

Abstract	Macroautophagy/autophagy mediates the degradation of ubiquitinated aggregated proteins within lysosomes in a process known as aggrephagy. The cargo receptor SQSTM1/p62 condenses aggregated proteins into larger structures and links them to the nascent autophagosomal membrane (phagophore). How the condensation reaction and autophagosome formation are coupled is unclear. We recently discovered that a region of SQSTM1 containing its LIR motif directly interacts with RB1CC1/FIP200, a protein acting at early stages of autophagosome formation. Determination of the structure of the C-terminal region of RB1CC1 revealed a claw-shaped domain. Using a structure-function approach, we show that the interaction of SQSTM1 with the RB1CC1 claw domain is crucial for the productive recruitment of the autophagy machinery to ubiquitin-positive condensates and their subsequent degradation by autophagy. We also found that concentrated Atg8-family proteins on the phagophore displace RB1CC1 from SQSTM1, suggesting an intrinsic directionality in the process of autophagosome formation. Ultimately, our study reveals how the interplay of SQSTM1 and RB1CC1 couples cargo condensation to autophagosome formation.
MeSH term(s)	Animals ; Autophagosomes/metabolism ; Autophagy ; Autophagy-Related Proteins/metabolism ; Humans ; Models, Biological ; Protein Binding ; Sequestosome-1 Protein/metabolism ; Ubiquitin/metabolism
Chemical Substances	Autophagy-Related Proteins ; Sequestosome-1 Protein ; Ubiquitin
Language	English
Publishing date	2019-05-22
Publishing country	United States
Document type	Journal Article
ZDB-ID	2454135-7
ISSN	1554-8635 ; 1554-8627
ISSN (online)	1554-8635
ISSN	1554-8627
DOI	10.1080/15548627.2019.1615306
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