A Selective Autophagy Pathway for Phase-Separated Endocytic Protein Deposits

SummaryAutophagy eliminates cytoplasmic content selected by autophagy receptors, which link cargoes to the membrane bound autophagosomal ubiquitin-like protein Atg8/LC3. Here, we discover a selective autophagy pathway for protein condensates formed by endocytic proteins. In this pathway, the endocytic yeast protein Ede1 functions as a selective autophagy receptor. Distinct domains within Ede1 bind Atg8 and mediate phase separation into condensates. Both properties are necessary for an Ede1-dependent autophagy pathway for endocytic proteins, which differs from regular endocytosis, does not involve other known selective autophagy receptors, but requires the core autophagy machinery. Cryo-electron tomography of Ede1-containing condensates – at the plasma membrane and in autophagic bodies – shows a phase-separated compartment at the beginning and end of the Ede1-mediated selective autophagy pathway. Our data suggest a model for autophagic degradation of membraneless compartments by the action of intrinsic autophagy receptors.HighlightsEde1 is a selective autophagy receptor for aberrant CME protein assembliesAberrant CME assemblies form by liquid-liquid phase separationCore autophagy machinery and Ede1 are important for degradation of CME condensatesUltrastrucural view of a LLPS compartment at the PM and within autophagic bodies

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A Diversity of Selective Autophagy Receptors Determines the Specificity of the Autophagy Pathway

Molecular Cell ◽

10.1016/j.molcel.2019.09.005 ◽

2019 ◽

Vol 76 (2) ◽

pp. 268-285 ◽

Cited By ~ 66

Author(s):

Vladimir Kirkin ◽

Vladimir V. Rogov

Keyword(s):

Selective Autophagy ◽

Autophagy Pathway

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A selective autophagy pathway takes an unconventional route

Autophagy ◽

10.1080/15548627.2015.1110669 ◽

2015 ◽

Vol 11 (12) ◽

pp. 2381-2382 ◽

Cited By ~ 7

Author(s):

Xiao-Man Liu ◽

Li-Lin Du

Keyword(s):

Selective Autophagy ◽

Autophagy Pathway

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Evolving Concepts of Glycogen-Selective Autophagy

10.20944/preprints202106.0594.v1 ◽

2021 ◽

Author(s):

Parisa Koutsifeli ◽

Upasna Varma ◽

Lorna Daniels ◽

Marco Annandale ◽

Xun Li ◽

...

Keyword(s):

Degradation Pathway ◽

Specific Protein ◽

Current Evidence ◽

Evolutionary Stage ◽

Major Pathway ◽

Selective Autophagy ◽

Protein Partners ◽

Health And Disease ◽

Autophagy Pathway

Macro-autophagy is an essential cellular process involved in degradation of aberrant organelles and proteins. Initially proposed to be a ‘bulk’ degradation pathway, a more nuanced appreciation of selective autophagy pathways has emerged in recent years. The discovery of a glycogen-selective autophagy pathway (‘glycophagy’) has highlighted the importance of autophagy in regulating cellular metabolic homeostasis and identified a novel non-canonical major pathway of glycogen flux. The field of glycogen autophagy research is at an early evolutionary stage, but already it is clear that the implications of these discoveries are far-reaching and provide scope for multi-disciplinary investigations into the role of glycophagy in health and disease. With potential cognate protein partners identified, the opportunities for targeted intervention have become viable. Here we review the current evidence relating to specific protein mediators involved in glycophagy, and highlight areas of uncertainty that provide opportunity for further investigation.

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Galectin-8 senses phagosomal damage and recruits selective autophagy adapter TAX1BP1 to control Mycobacterium tuberculosis infection in macrophages

10.1101/2020.06.30.180877 ◽

2020 ◽

Author(s):

Samantha L. Bell ◽

Kayla L. Lopez ◽

Jeffery S. Cox ◽

Kristin L. Patrick ◽

Robert O. Watson

Keyword(s):

Mycobacterium Tuberculosis ◽

Specific Interaction ◽

Secretion System ◽

Autophagosome Formation ◽

Mycobacterium Tuberculosis Infection ◽

Selective Autophagy ◽

Galectin 3 ◽

Autophagy Pathway ◽

Sense And Respond ◽

Phagosomal Membrane

ABSTRACTMycobacterium tuberculosis (Mtb) infects a quarter of the world and causes the deadliest infectious disease worldwide. Upon infection, Mtb is phagocytosed by macrophages and uses its virulence-associated ESX-1 secretion system to modulate the host cell and establish a replicative niche. We have previously shown the ESX-1 secretion system permeabilizes the Mtb-containing phagosome and that a population (~30%) of intracellular Mtb are recognized within the cytosol, tagged with ubiquitin, and targeted to the selective autophagy pathway. Despite the importance of selective autophagy in controlling infection, the mechanisms through which macrophages sense and respond to damaged Mtb-containing phagosomes remains unclear. Here, we demonstrate that several cytosolic glycan-binding proteins, known as galectins, recognize Mtb-containing phagosomes. We found that galectins-3, -8, and -9 are all recruited to the same Mtb population that colocalizes with selective autophagy markers like ubiquitin, p62, and LC3, which indicates Mtb damages its phagosomal membrane such that cytosolic host sensors can recognize danger signals in the lumen. To determine which galectins are required for controlling Mtb replication in macrophages, we generated CRISPR/Cas9 knockout macrophages lacking individual or multiple galectins and found that galectin-8-/- and galectin-3/8/9-/- knockout macrophages were similarly defective in targeting Mtb to selective autophagy and controlling replication, suggesting galectin-8 plays a privileged role in anti-Mtb autophagy. In investigating this specificity, we identified a novel and specific interaction between galectin-8 and TAX1BP1, one of several autophagy adaptors that bridges cargo and LC3 during the course of autophagosome formation, and this galectin-8/TAX1BP1 interaction was necessary to efficiently target Mtb to selective autophagy. Remarkably, overexpressing individual galectins increased targeting of Mtb to antibacterial autophagy and limited Mtb replication. Taken together, these data imply that galectins recognize damaged Mtb-containing phagosomes, recruit downstream autophagy machinery, and may represent promising targets for host-directed therapeutics to treat Mtb.

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Molecular and structural mechanisms of ZZ domain-mediated cargo recognition by autophagy receptor Nbr1

10.1101/2021.02.07.430097 ◽

2021 ◽

Author(s):

Ying-Ying Wang ◽

Jianxiu Zhang ◽

Xiao-Man Liu ◽

Meng-Qiu Dong ◽

Keqiong Ye ◽

...

Keyword(s):

High Resolution ◽

Fission Yeast ◽

Protein Interactions ◽

Specific Protein ◽

Structural Basis ◽

Protein Protein Interactions ◽

Selective Autophagy ◽

Specific Manner ◽

Autophagy Pathway ◽

Structural Mechanisms

AbstractIn selective autophagy, cargo selectivity is determined by autophagy receptors. However, it remains scarcely understood how autophagy receptors recognize specific protein cargos. In the fission yeast Schizosaccharomyces pombe, a selective autophagy pathway termed Nbr1-mediated vacuolar targeting (NVT) employs Nbr1, an autophagy receptor conserved across eukaryotes including humans, to target cytosolic hydrolases into the vacuole. Here, we identify two new NVT cargos, the mannosidase Ams1 and the aminopeptidase Ape4, that bind competitively to the first ZZ domain of Nbr1 (Nbr1-ZZ1). High-resolution cryo-EM analyses reveal how a single ZZ domain recognizes two distinct protein cargos. Nbr1-ZZ1 not only recognizes the N-termini of cargos via a conserved acidic pocket, similar to other characterized ZZ domains, but also engages additional parts of cargos in a cargo-specific manner. Our findings unveil a single-domain bispecific mechanism of autophagy cargo recognition, elucidate its underlying structural basis, and expand the understanding of ZZ domain-mediated protein-protein interactions.

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Aberrant Stress Granule Dynamics and Aggrephagy in ALS Pathogenesis

Cells ◽

10.3390/cells10092247 ◽

2021 ◽

Vol 10 (9) ◽

pp. 2247

Author(s):

Yi Zhang ◽

Jiayu Gu ◽

Qiming Sun

Keyword(s):

Amyotrophic Lateral Sclerosis ◽

Phase Separation ◽

Gene Mutations ◽

Stress Granules ◽

Protein Aggregates ◽

Toxic Protein ◽

Selective Autophagy ◽

Dynamic Assembly ◽

Autophagy Pathway ◽

Lateral Sclerosis

Stress granules are conserved cytosolic ribonucleoprotein (RNP) compartments that undergo dynamic assembly and disassembly by phase separation in response to stressful conditions. Gene mutations may lead to aberrant phase separation of stress granules eliciting irreversible protein aggregations. A selective autophagy pathway called aggrephagy may partially alleviate the cytotoxicity mediated by these protein aggregates. Cells must perceive when and where the stress granules are transformed into toxic protein aggregates to initiate autophagosomal engulfment for subsequent autolysosomal degradation, therefore, maintaining cellular homeostasis. Indeed, defective aggrephagy has been causally linked to various neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). In this review, we discuss stress granules at the intersection of autophagy and ALS pathogenesis.

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Full length RTN3 regulates turnover of tubular endoplasmic reticulum via selective autophagy

eLife ◽

10.7554/elife.25555 ◽

2017 ◽

Vol 6 ◽

Cited By ~ 136

Author(s):

Paolo Grumati ◽

Giulio Morozzi ◽

Soraya Hölper ◽

Muriel Mari ◽

Marie-Lena IE Harwardt ◽

...

Keyword(s):

Endoplasmic Reticulum ◽

Biological Activity ◽

Mammalian Cells ◽

The Other ◽

Unique Function ◽

Specific Receptor ◽

Selective Autophagy ◽

Specific Receptors ◽

Autophagy Pathway ◽

Tubular Endoplasmic Reticulum

The turnover of endoplasmic reticulum (ER) ensures the correct biological activity of its distinct domains. In mammalian cells, the ER is degraded via a selective autophagy pathway (ER-phagy), mediated by two specific receptors: FAM134B, responsible for the turnover of ER sheets and SEC62 that regulates ER recovery following stress. Here, we identified reticulon 3 (RTN3) as a specific receptor for the degradation of ER tubules. Oligomerization of the long isoform of RTN3 is sufficient to trigger fragmentation of ER tubules. The long N-terminal region of RTN3 contains several newly identified LC3-interacting regions (LIR). Binding to LC3s/GABARAPs is essential for the fragmentation of ER tubules and their delivery to lysosomes. RTN3-mediated ER-phagy requires conventional autophagy components, but is independent of FAM134B. None of the other reticulon family members have the ability to induce fragmentation of ER tubules during starvation. Therefore, we assign a unique function to RTN3 during autophagy.

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