bims-lypmec 2023-11-12 papers

Issue of 2023‒11‒12
seven papers selected by
Satoru Kobayashi, New York Institute of Technology

EMBO J. 2023 Nov 06. e114272

TOLLIP acts as a cargo adaptor to promote lysosomal degradation of aberrant ER membrane proteins.

Yuki Hayashi, Sho Takatori, Waleed Y Warsame, Taisuke Tomita, Takao Fujisawa, Hidenori Ichijo.

Endoplasmic reticulum (ER) proteostasis is maintained by various catabolic pathways. Lysosomes clear entire ER portions by ER-phagy, while proteasomes selectively clear misfolded or surplus aberrant proteins by ER-associated degradation (ERAD). Recently, lysosomes have also been implicated in the selective clearance of aberrant ER proteins, but the molecular basis remains unclear. Here, we show that the phosphatidylinositol-3-phosphate (PI3P)-binding protein TOLLIP promotes selective lysosomal degradation of aberrant membrane proteins, including an artificial substrate and motoneuron disease-causing mutants of VAPB and Seipin. These cargos are recognized by TOLLIP through its misfolding-sensing intrinsically disordered region (IDR) and ubiquitin-binding CUE domain. In contrast to ER-phagy receptors, which clear both native and aberrant proteins by ER-phagy, TOLLIP selectively clears aberrant cargos by coupling them with the PI3P-dependent lysosomal trafficking without promoting bulk ER turnover. Moreover, TOLLIP depletion augments ER stress after ERAD inhibition, indicating that TOLLIP and ERAD cooperatively safeguard ER proteostasis. Our study identifies TOLLIP as a unique type of cargo-specific adaptor dedicated to the clearance of aberrant ER cargos and provides insights into molecular mechanisms underlying lysosome-mediated quality control of membrane proteins.

Keywords: ER-phagy; TOLLIP; cargo adaptor; intrinsically disordered region; lysosome

DOI: https://doi.org/10.15252/embj.2023114272

Autophagy. 2023 Nov 09. 1-17

A conserved requirement for RME-8/DNAJC13 in neuronal autophagic lysosome reformation.

Sierra B Swords, Nuo Jia, Anne Norris, Jil Modi, Qian Cai, Barth D Grant.

Autophagosomes fuse with lysosomes, forming autolysosomes that degrade engulfed cargo. To maintain lysosomal capacity, autophagic lysosome reformation (ALR) must regenerate lysosomes from autolysosomes using a membrane tubule-based process. Maintaining lysosomal capacity is required to maintain cellular health, especially in neurons where lysosomal dysfunction has been repeatedly implicated in neurodegenerative disease. The DNA-J domain HSC70 co-chaperone RME-8/DNAJC13 has been linked to endosomal coat protein regulation and to neurological disease. We report new analysis of the requirements for the RME-8/DNAJC13 protein in neurons, focusing on intact C. elegans mechanosensory neurons, and primary mouse cortical neurons in culture. Loss of RME-8/DNAJC13 in both systems results in accumulation of grossly elongated autolysosomal tubules. Further C. elegans analysis revealed a similar autolysosome tubule accumulation defect in mutants known to be required for ALR in mammals, including mutants lacking bec-1/BECN1/Beclin1 and vps-15/PIK3R4/p150 that regulate the class III phosphatidylinositol 3-kinase (PtdIns3K) VPS-34, and dyn-1/dynamin that severs ALR tubules. Clathrin is also an important ALR regulator implicated in autolysosome tubule formation and release. In C. elegans we found that loss of RME-8 causes severe depletion of clathrin from neuronal autolysosomes, a phenotype shared with bec-1 and vps-15 mutants. We conclude that RME-8/DNAJC13 plays a previously unrecognized role in ALR, likely affecting autolysosome tubule severing. Additionally, in both systems, loss of RME-8/DNAJC13 reduced macroautophagic/autophagic flux, suggesting feedback regulation from ALR to autophagy. Our results connecting RME-8/DNAJC13 to ALR and autophagy provide a potential mechanism by which RME-8/DNAJC13 could influence neuronal health and the progression of neurodegenerative disease.Abbreviation: ALR, autophagic lysosome reformation; ATG-13/EPG-1, AuTophaGy (yeast Atg homolog)-13; ATG-18, AuTophaGy (yeast Atg homolog)-18; AV, autophagic vacuole; CLIC-1, Clathrin Light Chain-1; EPG-3, Ectopic P Granules-3; EPG-6, Ectopic P Granules-6; LGG-1, LC3, GABARAP and GATE-16 family-1; MAP1LC3/LC3, microtubule-associated protein 1 light chain 3; PD, Parkinson disease; PtdIns3P, phosphatidylinositol-3-phosphate; PtdIns(4,5)P2, phosphatidylinositol-4,5-bisphosphate; RME-8, Receptor Mediated Endocytosis-8; SNX-1, Sorting NeXin-1; VPS-34, related to yeast Vacuolar Protein Sorting factor-34.

Keywords: Autophagy; clathrin; endocytosis; lysosomes; neurodegeneration; trafficking

DOI: https://doi.org/10.1080/15548627.2023.2269028

Exploration (Beijing). 2023 Oct;3(5): 20230002

Burst of hopping trafficking correlated reversible dynamic interactions between lipid droplets and mitochondria under starvation.

Zhongju Ye, Chengyuan Hu, Junli Wang, Hua Liu, Luping Li, Jie Yuan, Ji Won Ha, Zhaohui Li, Lehui Xiao.

Dynamic membrane contacts between lipid droplets (LDs) and mitochondria play key roles in lipid metabolism and energy homeostasis. Understanding the dynamics of LDs under energy stimulation is thereby crucial to disclosing the metabolic mechanism. Here, the reversible interactions between LDs and mitochondria are tracked in real-time using a robust LDs-specific fluorescent probe (LDs-Tags). Through tracking the dynamics of LDs at the single-particle level, spatiotemporal heterogeneity is revealed. LDs in starved cells communicate and integrate their activities (i.e., lipid exchange) through a membrane contact site-mediated mechanism. Thus the diffusion is intermittently alternated between active and confined states. Statistical analysis shows that the translocation of LDs in response to starvation stress is non-Gaussian, and obeys nonergodic-like behavior. These results provide deep understanding of the anomalous diffusion of LDs in living cells, and also afford guidance for rationally designing efficient transporter.

Keywords: dynamic contact; fluorescence imaging; lipid droplet; mitochondrion; single‐particle tracking

DOI: https://doi.org/10.1002/EXP.20230002

J Biochem. 2023 Nov 08. pii: mvad089. [Epub ahead of print]

p62 bodies: cytosolic zoning by phase separation.

Reo Kurusu, Hideaki Morishita, Masaaki Komatsu.

Cellular zoning or partitioning is critical in preventing macromolecules from random diffusion and in orchestrating the spatiotemporal dynamics of biochemical reactions. Along with membranous organelles, membrane-less organelles contribute to the precise regulation of biochemical reactions inside cells. In response to environmental cues, membrane-less organelles rapidly form through liquid-liquid phase separation, sequester certain proteins and RNAs, mediate specific reactions, and dissociate. Among membrane-less organelles, ubiquitin-positive condensates, namely, p62 bodies, maintain cellular homeostasis through selective autophagy of themselves to contribute to intracellular quality control. p62 bodies also activate the anti-oxidative stress response regulated by the KEAP1-NRF2 system. In this review, we present an overview of recent advancements in cellular and molecular biology related to p62 bodies, highlighting their dynamic nature and functions.

Keywords: Autophagy; KEAP1-NRF2 system; intracellular quality control; liquid-liquid phase separation; p62 body

DOI: https://doi.org/10.1093/jb/mvad089

RSC Adv. 2023 Oct 31. 13(46): 32276-32281

Structural features localizing the ferroptosis inhibitor GIF-2197-r to lysosomes.

Yoko Hirata, Tomohiro Hashimoto, Kaori Ando, Yuji O Kamatari, Hiroshi Takemori, Kyoji Furuta.

We previously reported that N,N-dimethylaniline derivatives are potent ferroptosis inhibitors. Among them, the novel aminoindan derivative GIF-2197-r (the racemate of GIF-2115 (R-form) and GIF-2196 (S-form)) is effective at a concentration of 0.01 μM due to its localization to lysosomes and ferrous ion coordination capacity. The current study demonstrates that the aliphatic tertiary amine moiety of GIF-2197-r is responsible for lysosomal localization. Although N,N-dimethylaniline derivatives cannot form chelate structures with Fe2+, density functional theory computation demonstrates that they can form stable monodentate complexes with a hydrated ferrous ion, likely due to the highly electron-rich nature of the (dialkylamino)phenyl ring. Furthermore, the results suggest that the aliphatic tertiary amine moiety contributes to stabilizing the complexation. These findings could prove useful for developing improved lysosomotropic ferroptosis inhibitors for neurodegenerative diseases.

DOI: https://doi.org/10.1039/d3ra06611h

Biomed Pharmacother. 2023 Nov 06. pii: S0753-3322(23)01641-4. [Epub ahead of print]168 115843

The current state of preclinical modeling of human diabetic cardiomyopathy using rodents.

Magdalena Jasińska-Stroschein.

The prevalence of diabetic cardiomyopathy (DCM), a specific cardiovascular complication of diabetes mellitus, has recently increased. Its pathogenesis is not fully understood, and no consensus regarding therapeutic options has been reached. Experimental studies on rodents are expected to yield further data at the preclinical stage. The present paper describes and quantitatively compares the experimental protocols intended to mimic human DCM. Experimental articles (conducted between 1990 and 2022) were identified from online electronic databases according to the PRISMA Protocol. The Cochrane Q-test was used to estimate study heterogeneity; the quality of each individual study was assessed using SYRCLE's risk of bias tool for animal studies. Sensitivity analysis was performed according to the leave-one-out method. Publication bias across studies was assessed using Egger's weighted regression and Duval and Tweedie 'trim and fill' method. A wide spectrum of protocols - from 651 papers, was examined (type 1 or 2 diabetes mellitus, as well as obesity models). They were found to vary in their presentation of DCM according to a variety of hemodynamic, echocardiographic, histopathologic and metabolic parameters. Particular attention was paid to comorbid conditions, and cardiac performance featured as systolic, diastolic dysfunction, or refractory heart failure. The majority of models displayed diastolic dysfunction, as well as myocardial fibrosis and left ventricle hypertrophy, which mimics early stage DCM. Unlike in humans, animal DCM rarely progressed to the symptomatic heart failure with reduced ejection fraction (HFrEF). The ability of individual procedures to reflect refractory heart failure or biventricular dysfunction - in the end-stage DCM has remained unclear.

Keywords: Diabetes; Diabetic cardiomyopathy; Heart failure; Meta-research; Rodents

DOI: https://doi.org/10.1016/j.biopha.2023.115843

Autophagy. 2023 Nov 07.

Synthetic autophagy receptor.

Ziwen Jiang, Yu-Hsuan Kuo, Michelle R Arkin.

Macroautophagy/autophagy receptors target their substrates to phagophores for subsequent sequestration within autophagosomes. During phagophore membrane expansion in mammalian cells, autophagy receptors simultaneously interact with the ubiquitinated substrates and the LC3/GABARAP proteins on the expanding membrane. In this punctum, we summarize and discuss our recent research progress on synthetic autophagy receptors (AceTACs). The series of AceTACs were designed by engineering the essential interacting domains and motifs of SQSTM1/p62 (sequestosome 1), a major mammalian autophagy receptor. Particularly, we replaced the ubiquitin-associated domain of SQSTM1 with a target-specific antibody, redirecting the bifunctional interactions of wild-type SQSTM1 and directing the degradation target into the autophagy process. We successfully demonstrated the targeted degradation of aggregation-prone proteins using the AceTAC degraders. Moreover, we presented a model system with a guideline to induce targeted degradation of organelles through the autophagy machinery.

Keywords: Antibody-fusion protein; autophagy receptor; targeted organelle degradation; targeted protein degradation

DOI: https://doi.org/10.1080/15548627.2023.2278954