Showing papers in "Journal of Cell Biology in 2022"
TL;DR: Eskandari and Eaves review evidence of caspase-3-regulated protein quality, proliferation, differentiation, and tumorigenic activity in viable cells.
Abstract: Eskandari and Eaves review evidence of caspase-3-regulated protein quality, proliferation, differentiation, and tumorigenic activity in viable cells.
35 citations
TL;DR: Secretory autophagy via EVPs functions as an alternate route to clear sequestered material and maintain proteostasis during endolysosomal dysfunction or impaired autophagosome maturation.
Abstract: Solvik et al. reveal that the autophagy machinery facilitates the secretion of autophagy cargo receptors and other cellular components via extracellular vesicles and particles in response to lysosome inhibition or impaired autophagosome maturation.
35 citations
TL;DR: In this article , Hooper et al. reveal new insights into how V-ATPase V0-V1 engagement recruits the autophagy protein ATG16L1 to direct the conjugation of ATG8.
Abstract: Hooper et al. report on the role and regulation of V-ATPase in the activation of non-canonical autophagy, including LC3-associated phagocytosis. They reveal new insights into how V-ATPase V0-V1 engagement recruits the autophagy protein ATG16L1 to direct the conjugation of ATG8 to single membranes.
31 citations
TL;DR: In this paper, a novel lipid exchange at ER-endosome MCSs was proposed as a nonenzymatic PI4P-to-PS conversion mechanism that organizes membrane remodeling during retrograde membrane trafficking.
Abstract: Membrane contact sites (MCSs) serve as a zone for nonvesicular lipid transport by oxysterol-binding protein (OSBP)-related proteins (ORPs). ORPs mediate lipid countertransport, in which two distinct lipids are transported counterdirectionally. How such lipid countertransport controls specific biological functions, however, remains elusive. We report that lipid countertransport by ORP10 at ER-endosome MCSs regulates retrograde membrane trafficking. ORP10, together with ORP9 and VAP, formed ER-endosome MCSs in a phosphatidylinositol 4-phosphate (PI4P)-dependent manner. ORP10 exhibited a lipid exchange activity toward its ligands, PI4P and phosphatidylserine (PS), between liposomes in vitro, and between the ER and endosomes in situ. Cell biological analysis demonstrated that ORP10 supplies a pool of PS from the ER, in exchange for PI4P, to endosomes where the PS-binding protein EHD1 is recruited to facilitate endosome fission. Our study highlights a novel lipid exchange at ER-endosome MCSs as a nonenzymatic PI4P-to-PS conversion mechanism that organizes membrane remodeling during retrograde membrane trafficking.
23 citations
TL;DR: It is found that calcium flashes regulate epithelial barrier function, and mechanosensitive channel-dependent calcium flashes promote sustained local activation of RhoA, allowing cells to repair tight junction leaks induced by mechanical stimuli.
Abstract: Varadarajan et al. find that calcium flashes regulate epithelial barrier function. Using live imaging, optogenetics, and laser-induced tight junction injury, they show that mechanosensitive channel-dependent calcium flashes promote sustained local activation of RhoA, allowing cells to repair tight junction leaks induced by mechanical stimuli.
23 citations
TL;DR: In this paper , the crystal structure of VPS13s adaptor binding domain (VAB) complexed with a Pro-X-Pro peptide recognition motif present in one such receptor, the integral membrane protein Mcp1p, was presented.
Abstract: VPS13 proteins are proposed to function at contact sites between organelles as bridges for lipids to move directionally and in bulk between organellar membranes. VPS13s are anchored between membranes via interactions with receptors, including both peripheral and integral membrane proteins. Here we present the crystal structure of VPS13s adaptor binding domain (VAB) complexed with a Pro-X-Pro peptide recognition motif present in one such receptor, the integral membrane protein Mcp1p, and show biochemically that other Pro-X-Pro motifs bind the VAB in the same site. We further demonstrate that Mcp1p and another integral membrane protein that interacts directly with human VPS13A, XK, are scramblases. This finding supports an emerging paradigm of a partnership between bulk lipid transport proteins and scramblases. Scramblases can re-equilibrate lipids between membrane leaflets as lipids are removed from or inserted into the cytosolic leaflet of donor and acceptor organelles, respectively, in the course of protein-mediated transport.
22 citations
TL;DR: In this paper, a similar process takes place in the photosynthetic prokaryote Synechocystis sp. PCC 6803 in response to heat stress.
Abstract: Ferroptosis is an oxidative and iron-dependent form of regulated cell death (RCD) recently described in eukaryotic organisms like animals, plants, and parasites. Here, we report that a similar process takes place in the photosynthetic prokaryote Synechocystis sp. PCC 6803 in response to heat stress. After a heat shock, Synechocystis sp. PCC 6803 cells undergo a cell death pathway that can be suppressed by the canonical ferroptosis inhibitors, CPX, vitamin E, Fer-1, liproxstatin-1, glutathione (GSH), or ascorbic acid (AsA). Moreover, as described for eukaryotic ferroptosis, this pathway is characterized by an early depletion of the antioxidants GSH and AsA, and by lipid peroxidation. These results indicate that all of the hallmarks described for eukaryotic ferroptosis are conserved in photosynthetic prokaryotes and suggest that ferroptosis might be an ancient cell death program.
22 citations
TL;DR: Glycosylphosphatidylinositol anchors attach many proteins to the extracellular surface of the plasma membrane and tubelike lipid transport proteins bring PE to the ER to support GPI anchor production.
Abstract: Glycosylphosphatidylinositol (GPI) anchors attach many proteins to the extracellular surface of the plasma membrane. Anchor synthesis occurs in the ER and requires phosphatidylethanolamine (PE). Toulmay et al. show that tubelike lipid transport proteins bring PE to the ER to support GPI anchor production.
21 citations
TL;DR: It is demonstrated that cytolinker protein plectin is essential for the formation of the circumferential keratin rim, organization of radial keratin spokes, and desmosomal patterning and controls cell cohesion and maintenance of epithelial stability.
Abstract: Prechova et al. demonstrate that cytolinker protein plectin is essential for the formation of the circumferential keratin rim, organization of radial keratin spokes, and desmosomal patterning. Thus, plectin controls cell cohesion and maintenance of epithelial stability.
20 citations
TL;DR: In this paper , a link between ER-lysosome lipid transfer and innate immune activation in a model human cell line and place VPS13C in pathways relevant to PD pathogenesis.
Abstract: Mutations in VPS13C cause early-onset, autosomal recessive Parkinson’s disease (PD). We have established that VPS13C encodes a lipid transfer protein localized to contact sites between the ER and late endosomes/lysosomes. In the current study, we demonstrate that depleting VPS13C in HeLa cells causes an accumulation of lysosomes with an altered lipid profile, including an accumulation of di-22:6-BMP, a biomarker of the PD-associated leucine-rich repeat kinase 2 (LRRK2) G2019S mutation. In addition, the DNA-sensing cGAS-STING pathway, which was recently implicated in PD pathogenesis, is activated in these cells. This activation results from a combination of elevated mitochondrial DNA in the cytosol and a defect in the degradation of activated STING, a lysosome-dependent process. These results suggest a link between ER-lysosome lipid transfer and innate immune activation in a model human cell line and place VPS13C in pathways relevant to PD pathogenesis.
19 citations
TL;DR: In this article , the role of the import machinery when the UPRmt was induced was analyzed, and it was found that mitochondrial import increases when the unfolded protein response was activated in an ATFS-1-dependent manner, despite reduced mitochondrial membrane potential.
Abstract: The mitochondrial unfolded protein response (UPRmt) is dedicated to promoting mitochondrial proteostasis and is linked to extreme longevity. The key regulator of this process is the transcription factor ATFS-1, which, upon UPRmt activation, is excluded from the mitochondria and enters the nucleus to regulate UPRmt genes. However, the repair proteins synthesized as a direct result of UPRmt activation must be transported into damaged mitochondria that had previously excluded ATFS-1 owing to reduced import efficiency. To address this conundrum, we analyzed the role of the import machinery when the UPRmt was induced. Using in vitro and in vivo analysis of mitochondrial proteins, we surprisingly find that mitochondrial import increases when the UPRmt is activated in an ATFS-1–dependent manner, despite reduced mitochondrial membrane potential. The import machinery is upregulated, and an intact import machinery is essential for UPRmt-mediated lifespan extension. ATFS-1 has a weak mitochondrial targeting sequence (MTS), allowing for dynamic subcellular localization during the initial stages of UPRmt activation.
TL;DR: In this article , the authors reveal that peroxisome-ER associations via the ACBD5-VAPB tether are regulated by phosphorylation, which reveals for the first time a molecular mechanism for the regulation of peroxysomes-ER contacts in mammalian cells and expand the current model of FFAT motifs and VAP interaction.
Abstract: Peroxisomes and the endoplasmic reticulum (ER) cooperate in cellular lipid metabolism. They form membrane contacts through interaction of the peroxisomal membrane protein ACBD5 (acyl-coenzyme A-binding domain protein 5) and the ER-resident protein VAPB (vesicle-associated membrane protein-associated protein B). ACBD5 binds to the major sperm protein domain of VAPB via its FFAT-like (two phenylalanines [FF] in an acidic tract) motif. However, molecular mechanisms, which regulate formation of these membrane contact sites, are unknown. Here, we reveal that peroxisome-ER associations via the ACBD5-VAPB tether are regulated by phosphorylation. We show that ACBD5-VAPB binding is phosphatase-sensitive and identify phosphorylation sites in the flanking regions and core of the FFAT-like motif, which alter interaction with VAPB-and thus peroxisome-ER contact sites-differently. Moreover, we demonstrate that GSK3β (glycogen synthase kinase-3 β) regulates this interaction. Our findings reveal for the first time a molecular mechanism for the regulation of peroxisome-ER contacts in mammalian cells and expand the current model of FFAT motifs and VAP interaction.
TL;DR: In this paper, the authors used a proximity tagging system, PUP-IT, to identify new interacting proteins of MARCH5, which is a dual-organelle locating protein that interacts with several peroxisomal proteins.
Abstract: Mitochondria and peroxisomes are independent but functionally closely related organelles. A few proteins have been characterized as dual-organelle locating proteins with distinct or similar roles on mitochondria and peroxisomes. MARCH5 is a mitochondria-associated ubiquitin ligase best known for its regulatory role in mitochondria quality control, fission, and fusion. Here, we used a proximity tagging system, PUP-IT, and identified new interacting proteins of MARCH5. Our data uncover that MARCH5 is a dual-organelle locating protein that interacts with several peroxisomal proteins. PEX19 binds the transmembrane region on MARCH5 and targets it to peroxisomes. On peroxisomes, MARCH5 binds and mediates the ubiquitination of PMP70. Furthermore, we find PMP70 ubiquitination and pexophagy induced by mTOR inhibition are blocked in the absence of MARCH5. Our study suggests novel roles of MARCH5 on peroxisomes.
TL;DR: Fan et al. quantitatively dissect the decisive regulation of migration paradigm (persistence and velocity) to the formation of the migrasome, a cellular organelle with vesicle-like morphology that mediates migracytosis.
Abstract: Fan et al. quantitatively dissect the decisive regulation of migration paradigm (persistence and velocity) to the formation of the migrasome, a cellular organelle with vesicle-like morphology that mediates migracytosis. Their work adds up our current understanding of the role of cell behavior in migrasome studies.
TL;DR: It is demonstrated that DMV biogenesis, induced by virus infection or expression of nsp3/4, is impaired in the V MP1 KO or TMEM41B KO cells, and VMP1 was shown to regulate cross-membrane phosphatidylserine (PS) distribution, suggesting that PS participates in DMV formation.
Abstract: Ji et al. show that the autophagy proteins VMP1 and TMEM41B are required for β-coronavirus infection, and they function at different steps during DMV biogenesis. TMEM41B is involved in nsp3/4 binding and ER zippering, while VMP1 is essential for bending the paired ER into DMVs.
TL;DR: Deretic and Lazarou conceptualize atg8ylation as a membrane stress and remodeling response, with autophagy and nonautophagic processes as its outputs.
Abstract: Deretic and Lazarou conceptualize atg8ylation as a membrane stress and remodeling response, with autophagy and nonautophagic processes as its outputs.
TL;DR: Optogenetically controlled cell death effectors (optoCDEs) are reported, a novel class of optogenetic tools that enables light-mediated induction of three types of programmed cell death (PCD)-apoptosis, pyroptosis, and necroptosis-using Arabidopsis thaliana photosensitive protein Cryptochrome-2.
Abstract: Shkarina et al. report the development and characterization of a new optogenetic toolset for apoptosis, necroptosis, and pyroptosis induction in humans, mice, and zebrafish. They demonstrate its application for studying the extrusion and efferocytosis of dead cells in 2D, 3D cultures, and in vivo.
TL;DR: The stress-responsive signaling pathways that regulate the activity and composition of the extracellular proteostasis network are described and the mechanisms responsible for this regulation are described.
Abstract: Mesgarzadeh et al. describe the stress-responsive signaling pathways that regulate the activity and composition of the extracellular proteostasis network.
TL;DR: Wang et al. as discussed by the authors reported that the SARS-CoV-2 ORF10 promotes IFT46 degradation via stimulating CUL2ZYG11B activity, thereby impairing both cilia biogenesis and maintenance.
Abstract: Wang et al. report that the SARS-CoV-2 ORF10 promotes IFT46 degradation via stimulating CUL2ZYG11B activity, thereby impairing both cilia biogenesis and maintenance. The study provides a pathological mechanism connecting COVID-19 symptoms with cilia dysfunction.
TL;DR: In this paper, a quantitative, on-section correlative light and electron microscopy (CLEM) approach is presented to label hundreds of organelles that are subsequently visualized by EM and classified by ultrastructure.
Abstract: The key endosomal regulators Rab5, EEA1, and APPL1 are frequently applied in fluorescence microscopy to mark early endosomes, whereas Rab7 is used as a marker for late endosomes and lysosomes. However, endogenous levels of these proteins localize poorly in immuno-EM, and systematic studies on their native ultrastructural distributions are lacking. To address this gap, we here present a quantitative, on-section correlative light and electron microscopy (CLEM) approach. Using the sensitivity of fluorescence microscopy, we label hundreds of organelles that are subsequently visualized by EM and classified by ultrastructure. We show that Rab5 predominantly marks small, endocytic vesicles and early endosomes. EEA1 colocalizes with Rab5 on early endosomes, but unexpectedly also labels Rab5-negative late endosomes, which are positive for PI(3)P but lack Rab7. APPL1 is restricted to small Rab5-positive, tubulo-vesicular profiles. Rab7 primarily labels late endosomes and lysosomes. These data increase our understanding of the structural-functional organization of the endosomal system and introduce quantitative CLEM as a sensitive alternative for immuno-EM.
TL;DR: It is shown that human dynein light intermediate chain binds the N-terminal RH1 domain of JIP3, its paralog JIP4, and the lysosomal adaptor RILP, and this results highlight that RH1 domains are interaction hubs for cytoskeletal motors and suggest that Jip3-bound dyne in and kinesin-1 participate in bidirectional organelle transport.
Abstract: Celestino, Gama, Castro-Rodrigues et al. characterize how the retrograde motor dynein interacts with cargo adaptors of the RILP/JIP3 superfamily and selectively uncouple dynein and the opposing motor kinesin-1 from JIP3/UNC-16 in Caenorhabditis elegans, which reveals that JIP3 drives bidirectional organelle transport in neurons.
TL;DR: Wenzel et al. review how the endoplasmic reticulum controls the positioning, dynamics, and functions of other organelles via membrane contact sites via membranes contact sites.
Abstract: Wenzel et al. review how the endoplasmic reticulum controls the positioning, dynamics, and functions of other organelles via membrane contact sites.
TL;DR: In this paper , the lipid transfer proteins ORP5 and ORP8 control LD biogenesis at mitochondria-associated ER membrane (MAM) subdomains, enriched in phosphatidic acid.
Abstract: Lipid droplets (LDs) are the primary organelles of lipid storage, buffering energy fluctuations of the cell. They store neutral lipids in their core that is surrounded by a protein-decorated phospholipid monolayer. LDs arise from the endoplasmic reticulum (ER). The ER protein seipin, localizing at ER-LD junctions, controls LD nucleation and growth. However, how LD biogenesis is spatially and temporally coordinated remains elusive. Here, we show that the lipid transfer proteins ORP5 and ORP8 control LD biogenesis at mitochondria-associated ER membrane (MAM) subdomains, enriched in phosphatidic acid. We found that ORP5/8 regulates seipin recruitment to these MAM–LD contacts, and their loss impairs LD biogenesis. Importantly, the integrity of ER–mitochondria contact sites is crucial for ORP5/8 function in regulating seipin-mediated LD biogenesis. Our study uncovers an unprecedented ORP5/8 role in orchestrating LD biogenesis and maturation at MAMs and brings novel insights into the metabolic crosstalk between mitochondria, ER, and LDs at the membrane contact sites.
TL;DR: In this article, Carvalho, Gassmann, Abreu, and Dantas were supported by the FCT through the COMPETE 2020 Operacional Programme for Competitiveness and Internationalisation (POCI), Portugal 2020.
Abstract: This work was financed by Fundo Europeu de Desenvolvimento Regional (FEDER) through the COMPETE 2020 Operacional Programme for Competitiveness and Internationalisation (POCI), Portugal 2020, and Portuguese funds through Fundacao para a Ciencia e a Tecnologia (FCT)/Minist´erio da Ciencia, Tecnologia e Ensino Superior in the framework of the project POCI-01-0145-FEDER-029471 (PTDC/BIA-BID/29471/2017) to T.J. Dantas. A.X. Carvalho, R. Gassmann, C.M.C. Abreu, and T.J. Dantas were supported by the FCT: CEECIND/01967/2017, CEECIND/00333/2017, CEECIND/01985/2018, and CEECIND/00771/2017, respectively. N. Vieira is a Junior Researcher under the scope of the FCT Transitional Rule DL57/2016, and her work was supported by a 2016 NARSAD Young Investigator Grant (#24929) from the Brain and Behavior Research Foundation. D.R.M. Rodrigues received a PhD fellowship from FCT (SFRH/BD/143985/2019) and support fromthe Biomedical Sciences PhD program at Instituto de Ciencias Biom´edicas Abel Salazar (ICBAS). Some strains were provided by the National Bioresource Project for C. elegans and by the Caenorhabditis Genetics Center (CGC), which is funded by the National Institutes of Health Office of Research Infrastructure Programs (P40 OD010440).
TL;DR: In this paper , Atg39 is anchored to the outer nuclear membrane via its transmembrane domain and also associated with the inner nuclear membrane through membrane-binding amphipathic helices (APHs) in its perinuclear space region, thereby linking these membranes.
Abstract: In selective autophagy of the nucleus (hereafter nucleophagy), nucleus-derived double-membrane vesicles (NDVs) are formed, sequestered within autophagosomes, and delivered to lysosomes or vacuoles for degradation. In Saccharomyces cerevisiae, the nuclear envelope (NE) protein Atg39 acts as a nucleophagy receptor, which interacts with Atg8 to target NDVs to the forming autophagosomal membranes. In this study, we revealed that Atg39 is anchored to the outer nuclear membrane via its transmembrane domain and also associated with the inner nuclear membrane via membrane-binding amphipathic helices (APHs) in its perinuclear space region, thereby linking these membranes. We also revealed that autophagosome formation-coupled Atg39 crowding causes the NE to protrude toward the cytoplasm, and the tips of the protrusions are pinched off to generate NDVs. The APHs of Atg39 are crucial for Atg39 crowding in the NE and subsequent NE protrusion. These findings suggest that the nucleophagy receptor Atg39 plays pivotal roles in NE deformation during the generation of NDVs to be degraded by nucleophagy.
TL;DR: A connection between metabolism and vascular inflammation that provides a new framework for understanding and developing treatments for vascular disease is defined.
Abstract: Coon et al. identify an anti-inflammatory signaling pathway mediated by laminar shear stress stimulation of endothelial cells, whereby mitochondrial signaling and the adaptor protein, p62, promote ERK5 activation and enhance KLF2 expression. This accounts for relatively high KLF2 expression in laminar shear stimulated conditions compared to disturbed shear stimulation.
TL;DR: In this review, Braschi et al. provide an updated consensus nomenclature for components of dynein motors and their assembly factors.
Abstract: In this review, Braschi et al. provide an updated consensus nomenclature for components of dynein motors and their assembly factors.
TL;DR: This work identifies a novel protein that forms multiple contact sites and supports a role of lysosomal contacts in sphingolipid homeostasis and shows that changes in Cvm1 levels affect sphingOLipidHomeostasis, altering the levels of multiple sphingoipid classes and the response of sphingosomal-sensing signaling pathways.
Abstract: Membrane contact sites allow organelles to communicate with each other. Bisinski et al. show that Cvm1 is a novel component of three different contacts involving the yeast lysosome-like vacuole. These contacts both control and are regulated by the levels of sphingolipids in the cell.
TL;DR: This study reveals that the signaling adaptor TOM1L1 recruits Fyn to a specialized subset of clathrin-coated pits and is required for SHIP2 recruitment and regulation of Akt signaling by EGFR.
Abstract: Ligand binding to EGF receptor (EGFR) triggers signaling and concomitant receptor recruitment to clathrin-coated pits. This study reveals that the signaling adaptor TOM1L1 recruits Fyn to a specialized subset of clathrin-coated pits and is required for SHIP2 recruitment and regulation of Akt signaling by EGFR.
TL;DR: In this paper , the authors investigated what happens to misaligned chromosomes localized beyond the exclusion zone and showed that such chromosomes become ensheathed in multiple layers of endomembranes, which increases the frequency of chromosome missegregation and micronucleus formation.
Abstract: Errors in mitosis that cause chromosome missegregation lead to aneuploidy and micronucleus formation, which are associated with cancer. Accurate segregation requires the alignment of all chromosomes by the mitotic spindle at the metaphase plate, and any misalignment must be corrected before anaphase is triggered. The spindle is situated in a membrane-free "exclusion zone"; beyond this zone, endomembranes (mainly endoplasmic reticulum) are densely packed. We investigated what happens to misaligned chromosomes localized beyond the exclusion zone. Here we show that such chromosomes become ensheathed in multiple layers of endomembranes. Chromosome ensheathing delays mitosis and increases the frequency of chromosome missegregation and micronucleus formation. We use an induced organelle relocalization strategy in live cells to show that clearance of endomembranes allows for the rescue of chromosomes that were destined for missegregation. Our findings indicate that endomembranes promote the missegregation of misaligned chromosomes that are outside the exclusion zone and therefore constitute a risk factor for aneuploidy.