Biology subjects

Tooze, S.

Publications and source records attributed to Tooze, S..

9 recordsLinked to original sources

bioRxiv2025

Chaperone AIP Couples mTORC1 Activation and Catabolic Metabolism During Neonatal Development

To grow and divide cells must tightly coordinate anabolic programs with the availability of nutrients and growth factors. This balance is especially critical during postnatal development, when biosynthetic and energetic demands are high, and nutrient supply and neonates have to adapt to periods of fasting. These conditions place acute stress on the proteostasis network, making autophagy essential for nutrient recycling. We found that the chaperone aryl hydrocarbon receptor-interacting protein (AIP) supports both arms of this metabolic balance: promoting anabolic PI3K-AKT signaling for mTORC1 activation and enabling catabolic processes such as proteasomal degradation and autophagy. Loss of AIP causes a severe neonatal metabolic disorder, where affected infants fail to thrive postnatally. Our findings establish AIP as a central regulator of neonatal metabolic adaptation and cellular homeostasis. One Sentence SummaryAIP integrates nutrient sensing and protein recycling to sustain neonatal survival.

developmental biology↗

bioRxiv2024

Mechanistic studies of autophagic cargo recruitment and membrane expansion through in vitro reconstitution

Autophagy is a highly conserved catabolic pathway to remove deleterious cytosolic material to maintain cellular homeostasis and cell survival. Upon autophagy induction, a unique double-membraned structure, called a phagophore, forms and expands into a cup shape to engulf these cytosolic substrates. ATG8 proteins are covalently conjugated to autophagic membranes by lipidation of phosphatidylethanolamine (PE) and are thought to localise on both sides of the phagophore membrane. ATG8 conjugated on the inner membrane of the phagophore recruits autophagy cargo receptors, such as p62. To recapitulate events on the inner membrane, we used giant unilamellar vesicles (GUVs) as a model membrane and encapsulated proteins of interest inside GUVs, thus generating a membrane platform to which ATG8 proteins could be localised on the inner leaflet of the vesicles. We reconstituted WIPI2b-directed and cargo-directed ATG8 lipidation inside the GUVs and revealed distinct roles of WIPI2b and p62 in initiating the ATG conjugation cascade. Furthermore, we showed that p62 or p62 droplets were recruited to the inner membrane of the GUVs though interaction with membrane-bound ATG8s. Using a bead-based membrane expansion assay, we demonstrated a redistribution and local enrichment of membrane-bound ATG8s across the membrane upon interaction with p62 and p62 droplets. Our study provides novel model systems to investigate the interactions on the inner membrane of the phagophore and reveals fundamental molecular insights into phagophore membrane bending. This process is directed by ATG8-cargo interaction, during which cargo receptors concentrate ATG8 proteins on the inner surface of the phagophore membrane.

biochemistry↗

bioRxiv2024

Biallelic Loss of Molecular Chaperone Molecule AIP Results in a Novel Severe Multisystem Disease Defined by Defective Proteostasis

Children born with deleterious biallelic variants of the chaperone aryl hydrocarbon receptor interacting protein (AIP) have a novel pediatric metabolic disease presenting a severe, complex clinical phenotype characterized by failure to develop following birth. Analysis of Aip knockout mouse embryonic fibroblasts and patient-derived dermal fibroblasts revealed that AIP was required to support proteostasis; including proteasome activity, induction of autophagy and lysosome function. aip knockout zebrafish, recapitulated the phenotype of the children; dying at an early stage of development when autophagy is required to adapt to periods of starvation. Our results demonstrate that AIP plays a crucial role in initiating autophagy and maintaining proteostasis in vitro and in vivo. One Sentence SummaryHomozygous loss of the chaperone AIP results in a novel pediatric disease exhibiting multiple features of a lysosomal storage disease.

molecular biology↗

bioRxiv2024

ATG9A and ARFIP2 cooperate to regulate PI4P levels for lysosomal repair

Lysosome damage activates multiple pathways to prevent lysosome-dependent cell death, including a repair mechanism involving ER-lysosome membrane contact sites, phosphatidylinositol 4-kinase- 2a (PI4K2A), phosphatidylinositol-4 phosphate (PI4P) and oxysterol-binding protein-related proteins (ORPs), lipid transfer proteins. PI4K2A localizes to trans-Golgi network and endosomes yet how it is delivered to damaged lysosomes remains unknown. During acute sterile damage, and damage caused by intracellular bacteria, we show that ATG9A-containing vesicles perform a critical role in delivering PI4K2A to damaged lysosomes. ADP ribosylation factor interacting protein 2 (ARFIP2), a component of ATG9A vesicles, binds and sequesters PI4P on lysosomes, balancing ORP- dependent lipid transfer and promoting retrieval of ATG9A vesicles through recruitment of the adaptor protein complex-3 (AP-3). Our results reveal a role for mobilized ATG9A vesicles and ARFIP2 in lysosome homeostasis after damage and bacterial infection.

cell biology↗

bioRxiv2023

Unique Amphipathic α-helix Drives Membrane Insertion and Enzymatic Activity of ATG3

AbstractAutophagosome biogenesis requires a localized perturbation of lipid membrane dynamics and a unique protein-lipid conjugate. Autophagy-related (ATG) proteins catalyze this biogenesis on cellular membranes, but the underlying molecular mechanism remains unclear. Focusing on the final step of the protein-lipid conjugation reaction, ATG8/LC3 lipidation, we show how membrane association of the conjugation machinery is organized and fine-tuned at the atomistic level. Amphipathic -helices in ATG3 proteins (AHATG3) are found to have low hydrophobicity and to be less bulky. Molecular dynamics simulations reveal that AHATG3 regulates the dynamics and accessibility of the thioester bond of the ATG3[~]LC3 conjugate to lipids, allowing covalent lipidation of LC3. Live cell imaging shows that the transient membrane association of ATG3 with autophagic membranes is governed by the less bulky- hydrophobic feature of AHATG3. Collectively, the unique properties of AHATG3 facilitate protein- lipid bilayer association leading to the remodeling of the lipid bilayer required for the formation of autophagosomes. TeaserWe uncover the unique biophysical property of amphipathic -helix essential for autophagy

cell biology↗

bioRxiv2022

Intracellular calcium elevations drive the nucleation of FIP200- and ATG13-containing pre-autophagosomal structures that become omegasomes

Ca2+ modulates autophagy at multiple steps including the induction and maturation of autophagosomes, but the magnitude and spatiotemporal properties of this calcium signal and its ultimate effect on the autophagic machinery are unclear. Focusing on the induction step leading to omegasome formation, we report that low but sustained elevations in cytosolic calcium levels induce omegasome formation but treatments that only transiently elevate calcium do not. The calcium-induced structures are early intermediates that mature into omegasomes but do not constitute full autophagosomes because they are partially devoid of late autophagy proteins ATG16 and LC3. In addition to omegasomes, all four components of the ULK complex (ULK1, FIP200, ATG13, ATG101) respond to calcium modulation: they translocate to early autophagy puncta in complete medium upon calcium elevation, and are inhibited from translocation during starvation by calcium chelation with BAPTA-2 AM. The principal early step affected by calcium lies downstream of mTORC1 inactivation and upstream of VPS34 activation, coinciding biochemically with phosphorylation of ATG13 at serine 318, which is known to require ULK1 activity. However, although the calcium-mediated step requires ATG9, FIP200 and ATG13, it does not require ULK1/2, suggesting that calcium does not directly regulate ULK1 activity but rather it regulates the mechanism by which the ULK complex components ATG13 and FIP200, together with ATG9, nucleate pre-autophagosomal precursors. This calcium-induced nucleation is sufficient to drive autophagy induction up to the omegasome step, but not beyond it.

cell biology↗

bioRxiv2022

Cis-membrane association of human ATG8 proteins N-terminus mediates autophagy

Autophagy is an essential catabolic pathway which sequesters and engulfs cytosolic substrates via autophagosomes, unique double-membraned structures. ATG8 proteins are ubiquitin-like proteins recruited to autophagosome membranes by lipidation at the C-terminus. ATG8s recruit substrates, such as p62, and play an important role in mediating autophagosome membrane expansion. However, the precise function of lipidated ATG8 in expansion remains obscure. Using a real-time in vitro lipidation assay, we revealed that the N-termini of lipidated human ATG8s (LC3B and GABARAP) are highly dynamic and interact with the membrane. Moreover, atomistic MD simulation and FRET assays indicate that N-termini of LC3B and GABARAP associate in cis on the membrane. The cis-membrane association of the N-terminus is critical to maintain membrane expansion and the size of autophagosomes in cells, consequently, mediating the efficient degradation of p62. Our study provides fundamental molecular insights into autophagosome membrane expansion, revealing the critical and unique function of lipidated ATG8.

cell biology↗

bioRxiv2022

Unraveling membrane properties at the organelle-level with LipidDyn

Cellular membranes are formed from many different lipids in various amounts and proportions depending on the subcellular localization. The lipid composition of membranes is sensitive to changes in the cellular environment, and their alterations are linked to several diseases, including cancer. Lipids not only form lipid-lipid interactions but also interact with other biomolecules, including proteins, profoundly impacting each other. Molecular dynamics (MD) simulations are a powerful tool to study the properties of cellular membranes and membrane-protein interactions on different timescales and at varying levels of resolution. Over the last few years, software and hardware for biomolecular simulations have been optimized to routinely run long simulations of large and complex biological systems. On the other hand, high-throughput techniques based on lipidomics provide accurate estimates of the composition of cellular membranes at the level of subcellular compartments. The community needs computational tools for lipidomics and simulation data effectively interacting to better understand how changes in lipid compositions impact membrane function and structure. Lipidomic data can be analyzed to design biologically relevant models of membranes for MD simulations. Similar applications easily result in a massive amount of simulation data where the bottleneck becomes the analysis of the data to understand how membrane properties and membrane-protein interactions are changing in the different conditions. In this context, we developed LipidDyn, an in silico pipeline to streamline the analyses of MD simulations of membranes of different compositions. Once the simulations are collected, LipidDyn provides average properties and time series for several membrane properties such as area per lipid, thickness, diffusion motions, the density of lipid bilayers, and lipid enrichment/depletion. The calculations exploit parallelization and the pipelines include graphical outputs in a publication-ready form. We applied LipidDyn to different case studies to illustrate its potential, including membranes from cellular compartments and transmembrane protein domains. LipidDyn is implemented in Python and relies on open-source libraries. LipidDyn is available free of charge under the GNU General Public License from https://github.com/ELELAB/LipidDyn.

bioinformatics↗

bioRxiv2020

The phosphatidylinositol 3-phosphate binding protein SNX4 controls ATG9A recycling and autophagy

Late endosomes and lysosomes (endolysosomes) receive proteins and cargo from the secretory, endocytic and autophagic pathways. Whereas these pathways and the degradative processes of endolysosomes are well characterized, less is understood about protein traffic from these organelles. In this study, we demonstrate the direct involvement of the phosphatidylinositol 3-phosphate (PI3P) binding SNX4 protein in membrane protein recycling from endolysosomes, and show that SNX4 is required for proper autophagic flux. We show that SNX4 mediates recycling of the transmembrane autophagy machinery protein ATG9A from endolysosomes to early endosomes, from where ATG9A is recycled to the trans-Golgi network in a retromer-dependent manner. Upon siRNA-mediated depletion of SNX4 or the retromer component VPS35, we observed accumulation of ATG9A on endolysosomes and early endosomes, respectively. Moreover, starvation-induced autophagosome biogenesis and autophagic flux were inhibited when SNX4 was downregulated. Altogether, we propose that proper ATG9A recycling by SNX4 sustains autophagy by preventing exhaustion of the available ATG9A pool.

cell biology↗