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Biochimica Et Biophysica Acta.... Dec 2021Autophagy is an essential process in cell self-repair and survival. The centre of the autophagic event is the generation of the so-called autophagosome (AP), a vesicle... (Review)
Review
Autophagy is an essential process in cell self-repair and survival. The centre of the autophagic event is the generation of the so-called autophagosome (AP), a vesicle surrounded by a double membrane (two bilayers). The AP delivers its cargo to a lysosome, for degradation and re-use of the hydrolysis products as new building blocks. AP formation is a very complex event, requiring dozens of specific proteins, and involving numerous instances of membrane biogenesis and architecture, including membrane fusion and fission. Many stages of AP generation can be rationalised in terms of curvature, both the molecular geometry of lipids interpreted in terms of 'intrinsic curvature', and the overall mesoscopic curvature of the whole membrane, as observed with microscopy techniques. The present contribution intends to bring together the worlds of biophysics and cell biology of autophagy, in the hope that the resulting cross-pollination will generate abundant fruit.
Topics: Autophagosomes; Autophagy; Biophysics; Cell Communication; Lipid Bilayers; Lysosomes; Membrane Fusion; Phagocytosis
PubMed: 34419487
DOI: 10.1016/j.bbamem.2021.183731 -
Molecular Biology of the Cell Aug 2022We report on how the endoplasmic reticulum (ER)-associated-autophagy pathway (ERAA) delivers P23H-rhodopsin (P23H-R) to the lysosome. P23H-R accumulates in an...
We report on how the endoplasmic reticulum (ER)-associated-autophagy pathway (ERAA) delivers P23H-rhodopsin (P23H-R) to the lysosome. P23H-R accumulates in an ERAD-resistant conformation that is stabilized in a detergent-soluble state by DNAJB12 and Hsp70. P23H-R, DNAJB12, and FIP200 colocalize in discrete foci that punctuate the rim of omegasome rings coated by WIPI1. Loss of DNAJB12 function prevents the association of P23H-R containing ER tubules with omegasomes. P23H-R tubules thread through the wall of WIPI1 rings into their central cavity. Transfer of P23H-R from ER-connected phagophores to lysosomes requires GABARAP and is associated with the transient docking of lysosomes to WIPI1 rings. After departure from WIPI1 rings, new patches of P23H-R are seen in the membranes of lysosomes. The absence of GABARAP prevents transfer of P23H-R from phagophores to lysosomes without interfering with docking. These data identify lysosome docking to omegasomes as an important step in the DNAJB12- and GABARAP-dependent autophagic disposal of dominantly toxic P23H-R.
Topics: Autophagosomes; Autophagy; Endoplasmic Reticulum; Lysosomes; Rhodopsin
PubMed: 35704470
DOI: 10.1091/mbc.E21-10-0505 -
Autophagy Jun 2021In eukaryotes, ATG4/Atg4 is a critical regulator of macroautophagy/autophagy. The protease activity of Atg4/ATG4, involved in conjugation and deconjugation of...
In eukaryotes, ATG4/Atg4 is a critical regulator of macroautophagy/autophagy. The protease activity of Atg4/ATG4, involved in conjugation and deconjugation of Atg8-family proteins, was so far regarded as its sole functional contribution. However, the role of individual ATG4-family proteins during mammalian autophagy had previously not been examined . During their recent investigation, Nguyen et al. discovered a hitherto unexplored role for mammalian ATG4s during mitophagy - the recruitment of ATG9A-containing vesicles. Their article, highlighted here, discusses the finding, which uses a novel artificial intelligence (AI)-directed analysis technique for focused ion beam-scanning electron microscopy (FIB-SEM) imaging to demonstrate the role of ATG4s in promoting phagophore growth and establishing phagophore-ER contacts.
Topics: Animals; Apoptosis Regulatory Proteins; Artificial Intelligence; Autophagosomes; Autophagy; Autophagy-Related Proteins; Humans; Microtubule-Associated Proteins; Mitophagy
PubMed: 34011239
DOI: 10.1080/15548627.2021.1917284 -
Cells Aug 2022Autophagy is an evolutionally conserved degradation mechanism for maintaining cell homeostasis whereby cytoplasmic components are wrapped in autophagosomes and... (Review)
Review
Autophagy is an evolutionally conserved degradation mechanism for maintaining cell homeostasis whereby cytoplasmic components are wrapped in autophagosomes and subsequently delivered to lysosomes for degradation. This process requires the concerted actions of multiple autophagy-related proteins and accessory regulators. In neurons, autophagy is dynamically regulated in different compartments including soma, axons, and dendrites. It determines the turnover of selected materials in a spatiotemporal control manner, which facilitates the formation of specialized neuronal functions. It is not surprising, therefore, that dysfunctional autophagy occurs in epilepsy, mainly caused by an imbalance between excitation and inhibition in the brain. In recent years, much attention has been focused on how autophagy may cause the development of epilepsy. In this article, we overview the historical landmarks and distinct types of autophagy, recent progress in the core machinery and regulation of autophagy, and biological roles of autophagy in homeostatic maintenance of neuronal structures and functions, with a particular focus on synaptic plasticity. We also discuss the relevance of autophagy mechanisms to the pathophysiology of epileptogenesis.
Topics: Autophagosomes; Autophagy; Axons; Epilepsy; Humans; Neurons
PubMed: 36078029
DOI: 10.3390/cells11172621 -
Proceedings of the National Academy of... Mar 2023Selective macroautophagy (hereafter referred to as autophagy) describes a process in which cytosolic material is engulfed in a double membrane organelle called an...
Selective macroautophagy (hereafter referred to as autophagy) describes a process in which cytosolic material is engulfed in a double membrane organelle called an autophagosome. Autophagosomes are carriers responsible for delivering their content to a lytic compartment for destruction. The cargo can be of diverse origin, ranging from macromolecular complexes to protein aggregates, organelles, and even invading pathogens. Each cargo is unique in composition and size, presenting different challenges to autophagosome biogenesis. Among the largest cargoes targeted by the autophagy machinery are intracellular bacteria, which can, in the case of range from 2 to 5 μm in length and 0.5 to 1.5 μm in width. How phagophores form and expand on such a large cargo remains mechanistically unclear. Here, we used HeLa cells infected with an auxotrophic to study the process of phagophore biogenesis using in situ correlative cryo-ET. We show that host cells generate multiple phagophores at the site of damaged -containing vacuoles (SCVs). The observed double membrane structures range from disk-shaped to expanded cup-shaped phagophores, which have a thin intermembrane lumen with a dilating rim region and expand using the SCV, the outer membrane of , or existing phagophores as templates. Phagophore rims establish different forms of contact with the endoplasmic reticulum (ER) via structurally distinct molecular entities for membrane formation and expansion. Early omegasomes correlated with the marker Double-FYVE domain-Containing Protein 1 (DFCP1) are observed in close association with the ER without apparent membrane continuity. Our study provides insights into the formation of phagophores around one of the largest selective cargoes.
Topics: Humans; Autophagosomes; Autophagy; Endoplasmic Reticulum; HeLa Cells; Macroautophagy
PubMed: 36917659
DOI: 10.1073/pnas.2221712120 -
Trends in Cell Biology Mar 2017Contact sites are places where two organelles join together to carry out a shared activity requiring nonvesicular communication. A large number of contact sites have... (Review)
Review
Contact sites are places where two organelles join together to carry out a shared activity requiring nonvesicular communication. A large number of contact sites have been discovered, and almost any two organelles can contact each other. General rules about contacts include constraints on bridging proteins, with only a minority of bridges physically creating contacts by acting as 'tethers'. The downstream effects of contacts include changing the physical behaviour of organelles, and also forming biochemically heterogeneous subdomains. However, some functions typically localized to contact sites, such as lipid transfer, have no absolute requirement to be situated there. Therefore, the key aspect of contacts is the directness of communication, which allows metabolic channelling and collective regulation.
Topics: Animals; Autophagosomes; Humans; Intracellular Membranes; Models, Biological; Organelles
PubMed: 27717534
DOI: 10.1016/j.tcb.2016.08.010 -
Quantitative 3D correlative light and electron microscopy of organelle association during autophagy.Cell Structure and Function Dec 2022In macroautophagy, disk-shaped double-membrane structures called phagophores elongate to form cup-shaped structures, becoming autophagosomes upon closure. These...
In macroautophagy, disk-shaped double-membrane structures called phagophores elongate to form cup-shaped structures, becoming autophagosomes upon closure. These autophagosomes then fuse with lysosomes to become autolysosomes and degrade engulfed material. Autophagosome formation is reported to involve other organelles, including the endoplasmic reticulum (ER) and mitochondria. Organelles are also taken up by autophagosomes as autophagy cargos. However, few studies have performed systematic spatiotemporal analysis of inter-organelle relationships during macroautophagy. Here, we investigated the organelles in contact with phagophores, autophagosomes, and autolysosomes by using three-dimensional correlative light and electron microscopy with array tomography in cells starved 30 min. As previously reported, all phagophores associate with the ER. The surface area of phagophores in contact with the ER decreases gradually as they mature into autophagosomes and autolysosomes. However, the ER still associates with 92% of autophagosomes and 79% of autolysosomes, suggesting that most autophagosomes remain on the ER after closure and even when they fuse with lysosomes. In addition, we found that phagophores form frequently near other autophagic structures, suggesting the presence of potential hot spots for autophagosome formation. We also analyzed the contents of phagophores and autophagosomes and found that the ER is the most frequently engulfed organelle (detected in 65% of total phagophores and autophagosomes). These quantitative three-dimensional ultrastructural data provide insights into autophagosome-organelle relationships during macroautophagy.Key words: 3D-CLEM, autophagosome, electron microscopy, endoplasmic reticulum, lysosome.
Topics: Autophagy; Autophagosomes; Endoplasmic Reticulum; Macroautophagy; Lysosomes; Microscopy, Electron
PubMed: 36418108
DOI: 10.1247/csf.22071 -
Autophagy Mar 2023Macroautophagy/autophagy, a cellular process that sequesters and breaks down cellular components in the lysosome/vacuole, is important in various events where cell...
Macroautophagy/autophagy, a cellular process that sequesters and breaks down cellular components in the lysosome/vacuole, is important in various events where cell composition undergoes changes. Broadly, autophagy is involved in T cell regulation including maintaining cell homeostasis. One process where a cell alters its composition is in the activation of helper T cells in the immune system. When helper (CD4) T cells are activated by antigens, they both grow and alter their cellular components to become effector T cells. Autophagy is the process that facilitates the breakdown of these cellular components and is therefore hypothesized to have a role in CD4 T cell activation. Previous research has concluded that CD4 T cell activation induces autophagy, providing an avenue for further research aimed at examining the ways in which this induced autophagy affects CD4 T cell proliferation and function. Toward this end, Zhou et al. researched the autophagosomal cargo present within CD4 T cells and the impact this cargo has on CD4 T cell proliferation.
Topics: Autophagosomes; Autophagy; T-Lymphocytes; Proteomics; CD4-Positive T-Lymphocytes
PubMed: 36576209
DOI: 10.1080/15548627.2022.2161154 -
International Journal of Molecular... Sep 2017Cell death is the last fate of the life cycle of cells. Different pathways involved in cell death are known to date, and are mostly represented by apoptosis, necrosis,... (Review)
Review
Cell death is the last fate of the life cycle of cells. Different pathways involved in cell death are known to date, and are mostly represented by apoptosis, necrosis, and autophagy. Autophagy is one of the most preserved cell death pathways, characterized by the elimination of large parts of cytoplasmic components after being consumed by a double-membraned vesicle called an autophagosome. The formed autophagosome then fuses with a lysosome containing degrading enzymes and leads to the digestion of the autophagosome content. Autophagy is triggered by stress-related inducers, and is partially dependent on apoptotic proteins. It plays a major role in cancer, particularly in the tumor microenvironment where it has a paradoxical function in acting as a tumor suppressor and also as a tumor promoter. In the tumor microenvironment, autophagy regulates the differentiation of macrophages into tumor-associated macrophages (TAMs) and fibroblasts into cancer-associated fibroblasts (CAFs). TAMs and CAFs are abundantly present in the tumor microenvironment, and participate actively in tumor growth, tumor invasiveness, and tumor resistance to chemotherapy.
Topics: Apoptosis; Autophagosomes; Autophagy; Cytokines; Humans; Inflammation; Lysosomes; Macrophages; Neoplasms; Tumor Microenvironment
PubMed: 28930154
DOI: 10.3390/ijms18092016 -
Frontiers in Immunology 2018Cellular responses to stress can be defined by the overwhelming number of changes that cells go through upon contact with and stressful conditions such as infection and... (Review)
Review
Cellular responses to stress can be defined by the overwhelming number of changes that cells go through upon contact with and stressful conditions such as infection and modifications in nutritional status. One of the main cellular responses to stress is autophagy. Much progress has been made in the understanding of the mechanisms involved in the induction of autophagy during infection by intracellular bacteria. This review aims to discuss recent findings on the role of autophagy as a cellular response to intracellular bacterial pathogens such as, , how the autophagic machinery senses these bacteria directly or indirectly (through the detection of bacteria-induced nutritional stress), and how some of these bacterial pathogens manage to escape from autophagy.
Topics: AMP-Activated Protein Kinases; Amino Acids; Animals; Autophagosomes; Autophagy; Bacterial Infections; Bacterial Physiological Phenomena; Biological Transport; Biomarkers; Host-Pathogen Interactions; Humans; Intracellular Space; Signal Transduction
PubMed: 29875765
DOI: 10.3389/fimmu.2018.00935