ATPase activity of DFCP1 controls selective autophagy

Autophagy, 2012

Initially described as a nonspecific degradation process induced upon starvation, autophagy is now known also to be involved in the degradation of specific ubiquitinated substrates such as mitochondria, bacteria and aggregated proteins, ensuring crucial functions in cell physiology and immunity. We report here that the deubiquitinating enzyme USP36 controls selective autophagy activation in Drosophila and in human cells. We show that dUsp36 loss of function autonomously inhibits cell growth while activating autophagy. Despite the phenotypic similarity, dUSP36 is not part of the TOR signaling pathway. Autophagy induced by dUsp36 loss of function depends on p62/SQSTM1, an adaptor for delivering cargo marked by polyubiquitin to autophagosomes. Consistent with p62 requirement, dUsp36 mutant cells display nuclear aggregates of ubiquitinated proteins, including Histone H2B, and cytoplasmic ubiquitinated proteins; the latter are eliminated by autophagy. Importantly, USP36 function in p62-dependent selective autophagy is conserved in human cells. Our work identifies a novel, crucial role for a deubiquitinating enzyme in selective autophagy.

Autophagy, 2011

IAA Journal of Scientific Research, 2024

Autophagy, an evolutionarily conserved cellular process, intricately regulates the degradation and recycling of cellular components, ensuring cellular homeostasis. The molecular orchestration of autophagy involves a sophisticated network of signaling pathways and key molecular players. Key initiation steps involve nutrient-sensing pathways, including mTOR and AMPK, converging on the ULK1 complex, triggering autophagosome formation. Subsequent stages encompass the role of the PI3K complex, recruitment of ATGs, and autophagosome expansion, leading to cargo recognition and closure. The selectivity in autophagy is achieved through cargo-specific adaptors and receptors like p62/SQSTM1, NIX/BNIP3L, and NDP52, ensuring targeted degradation of damaged organelles, misfolded proteins, and pathogens. Upon fusion with lysosomes, autolysosomes are formed, culminating in the breakdown of engulfed cargo via lysosomal hydrolases. Autophagy's intricate interplay with cellular processes, including metabolism, immunity, and cell death pathways, underscores its multifaceted roles in physiological and pathological conditions. Dysregulated autophagy is implicated in neurodegenerative disorders, cancer, metabolic diseases, and infections, highlighting its clinical relevance. Understanding the molecular mechanisms of autophagy offers promising prospects for therapeutic interventions by targeting autophagic pathways. This overview provides insights into the molecular intricacies of autophagy, offering potential avenues for therapeutic modulation in various disease contexts.

Journal of Biological Chemistry, 2007

Protein degradation by basal constitutive autophagy is important to avoid accumulation of polyubiquitinated protein aggregates and development of neurodegenerative diseases. The polyubiquitin-binding protein p62/SQSTM1 is degraded by autophagy. It is found in cellular inclusion bodies together with polyubiquitinated proteins and in cytosolic protein aggregates that accumulate in various chronic, toxic, and degenerative diseases. Here we show for the first time a direct interaction between p62 and the autophagic effector proteins LC3A and -B and the related ␥-aminobutyrate receptor-associated protein and ␥-aminobutyrate receptor-associated-like proteins. The binding is mediated by a 22-residue sequence of p62 containing an evolutionarily conserved motif. To monitor the autophagic sequestration of p62-and LC3-positive bodies, we developed a novel pH-sensitive fluorescent tag consisting of a tandem fusion of the red, acid-insensitive mCherry and the acid-sensitive green fluorescent proteins. This approach revealed that p62-and LC3-positive bodies are degraded in autolysosomes. Strikingly, even rather large p62-positive inclusion bodies (2 m diameter) become degraded by autophagy. The specific interaction between p62 and LC3, requiring the motif we have mapped, is instrumental in mediating autophagic degradation of the p62-positive bodies. We also demonstrate that the previously reported aggresome-like induced structures containing ubiquitinated proteins in cytosolic bodies are dependent on p62 for their formation. In fact, p62 bodies and these structures are indistinguishable. Taken together, our results clearly suggest that p62 is required both for the formation and the degradation of polyubiquitin-containing bodies by autophagy.

Trends in Biochemical Sciences, 2017

Developmental Cell, 2019

Highlights d Mitophagy requires coordination of machineries for target recognition and engulfment d IVM-induced mitophagy depends on TRAF2/CIAP1/CIAP2 for ubiquitination of mitochondria d Ubiquitinated mitochondria within ER regions facilitate targeting and autophagy d ULK complex is required, but not for initiation, with FIP200 acting before ATG13

Nature Cell Biology, 2011

A plethora of cellular processes, including apoptosis, depend on regulated changes in mitochondrial shape and ultrastructure. The role of mitochondria and of their morphology during autophagy, a bulk degradation and recycling process of eukaryotic cells' constituents, is not well understood. Here we show that mitochondrial morphology determines the cellular response to macroautophagy. When autophagy is triggered, mitochondria elongate in vitro and in vivo. During starvation, cellular cyclic AMP levels increase and protein kinase A (PKA) is activated. PKA in turn phosphorylates the pro-fission dynamin-related protein 1 (DRP1), which is therefore retained in the cytoplasm, leading to unopposed mitochondrial fusion. Elongated mitochondria are spared from autophagic degradation, possess more cristae, increased levels of dimerization and activity of ATP synthase, and maintain ATP production. Conversely, when elongation is genetically or pharmacologically blocked, mitochondria consume ATP, precipitating starvation-induced death. Thus, regulated changes in mitochondrial morphology determine the fate of the cell during autophagy.

EMBO reports, 2013

Autophagy and autophagy-related processes are fundamentally important in human health and disease. These processes are viewed primarily as cellular degradative pathways that recycle macromolecules and dysfunctional or redundant organelles into amino acids, sugars and lipids, especially during starvation. However, the ubiquitin-like autophagy proteins and other components of the autophagic machinery additionally participate in cellular reprogramming. We highlight these non-autophagic roles of autophagy proteins with the aim of drawing attention to this growing, but unexplored, research topic. We focus on the non-autophagic functions of autophagy proteins in cell survival and apoptosis, modulation of cellular traffic, protein secretion, cell signalling, transcription, translation and membrane reorganization.

Nature, 2015

The endoplasmic reticulum (ER) is the largest intracellular endomembrane system, enabling protein and lipid synthesis, ion homeostasis, quality control of newly synthesized proteins and organelle communication 1 . Constant ER turnover and modulation is needed to meet different cellular requirements and autophagy has an important role in this process 2-8 . However, its underlying regulatory mechanisms remain unexplained. Here we show that members of the FAM134 reticulon protein family are ER-resident receptors that bind to autophagy modifiers LC3 and GABARAP, and facilitate ER degradation by autophagy ('ER-phagy'). Downregulation of FAM134B protein in human cells causes an expansion of the ER, while FAM134B overexpression results in ER fragmentation and lysosomal degradation. Mutant FAM134B proteins that cause sensory neuropathy in humans 9 are unable to act as ER-phagy receptors. Consistently, disruption of Fam134b in mice causes expansion of the ER, inhibits ER turnover, sensitizes cells to stress-induced apoptotic cell death and leads to degeneration of sensory neurons. Therefore, selective ER-phagy via FAM134 proteins is indispensable for mammalian cell homeostasis and controls ER morphology and turnover in mice and humans.

Nature Reviews Molecular Cell Biology

Autophagy is a process that targets intracellular elements for degradation by sequestering them in double-membrane autophagosomes which then fuse with late endosomes/lysosomes forming degradative autolysomes. Autophagy can be associated with the engulfment of bulk cytosolic components, thereby being non-selective, which occurs for instance in response to starvation and is commonly referred to as bulk or non-selective autophagy. By contrast, selective autophagy has specific targets, such as damaged organelles (mitophagy, lysophagy, ER-phagy, ribophagy), aggregate proteins (aggrephagy) or invading bacteria (xenophagy), thereby being importantly involved in cellular quality control. Hence, not surprisingly, insufficiency of selective autophagy pathways has been associated with various human pathologies, prominently including neurodegeneration and infection. Determination of cargo specificity has been attributed to selective autophagy receptors such as p62, NBR1, OPTN, NDP52, which can both bind the cargo and ubiquitin simultaneously to initiate pathways leading to autophagosome membrane recruitment. In recent years a considerable progress has been made in understanding mechanisms governing selective cargo engulfment, which opens up the possibilities of enhancing selective autophagy pathways to boost cellular quality control capabilities and alleviate pathology.