bims-apauto 2022-04-10 papers

bims-apauto

Biomed News

on Apoptosis and autophagy

Issue of 2022–04–10
ten papers selected by
Su Hyun Lee, Seoul National University

CCT2 is an aggrephagy receptor for clearance of solid protein aggregates.
WIPI2 positively regulates mitophagy by promoting mitochondrial recruitment of VCP.
Endosomal-associated RFFL facilitates mitochondrial clearance by enhancing PRKN/parkin recruitment to mitochondria.
Autophagy and Skin Diseases.
A switch of chaperonin function regulates the clearance of solid protein aggregates.
Autophagopathies: from autophagy gene polymorphisms to precision medicine for human diseases.
Mitophagy and Neurodegeneration: Between the Knowns and the Unknowns.
Structural basis for the linkage specificity of ubiquitin-binding domain and deubiquitinase.
Local biogenesis of autophagic vesicles in neuronal dendrites facilitates long-term synaptic depression.
TMEM189 negatively regulates the stability of ULK1 protein and cell autophagy.

Cell. 2022 Mar 27. pii: S0092-8674(22)00265-3. [Epub ahead of print]

CCT2 is an aggrephagy receptor for clearance of solid protein aggregates.

Xinyu Ma, Caijing Lu, Yuting Chen, Shulin Li, Ningjia Ma, Xuan Tao, Ying Li, Jing Wang, Min Zhou, Yong-Bin Yan, Pilong Li, Kartoosh Heydari, Haiteng Deng, Min Zhang, Cong Yi, Liang Ge.

  Protein aggregation is a hallmark of multiple human pathologies. Autophagy selectively degrades protein aggregates via aggrephagy. How selectivity is achieved has been elusive. Here, we identify the chaperonin subunit CCT2 as an autophagy receptor regulating the clearance of aggregation-prone proteins in the cell and the mouse brain. CCT2 associates with aggregation-prone proteins independent of cargo ubiquitination and interacts with autophagosome marker ATG8s through a non-classical VLIR motif. In addition, CCT2 regulates aggrephagy independently of the ubiquitin-binding receptors (P62, NBR1, and TAX1BP1) or chaperone-mediated autophagy. Unlike P62, NBR1, and TAX1BP1, which facilitate the clearance of protein condensates with liquidity, CCT2 specifically promotes the autophagic degradation of protein aggregates with little liquidity (solid aggregates). Furthermore, aggregation-prone protein accumulation induces the functional switch of CCT2 from a chaperone subunit to an autophagy receptor by promoting CCT2 monomer formation, which exposes the VLIR to ATG8s interaction and, therefore, enables the autophagic function.

Keywords:  CCT2; FUS; GABARAP; Huntington’s disease; LC3; NBR1; P62; SOD1; TAX1BP1; TRiC; aggrephagy; autophagy; chaperone; chaperonin; huntingtin; neurodegeneration; phase separation; protein aggregates; protein aggregation; tau

DOI:  https://doi.org/10.1016/j.cell.2022.03.005
Autophagy. 2022 Apr 07. 1-15

WIPI2 positively regulates mitophagy by promoting mitochondrial recruitment of VCP.

Guang Lu, Hayden Weng Siong Tan, Tomas Schmauck-Medina, Liming Wang, Jiaqing Chen, Yik-Lam Cho, Kelie Chen, Jing-Zi Zhang, Weifeng He, Yihua Wu, Dajing Xia, Jing Zhou, Evandro F Fang, Lei Fang, Wei Liu, Han-Ming Shen.

  The mammalian Atg18 ortholog WIPI2 is a key regulator of LC3 lipidation to promote autophagosome biogenesis during nonselective macroautophagy, while its functions in selective autophagy such as mitophagy remain largely unexplored. In this study, we explored the role of WIPI2 in PINK1-PRKN/parkin-mediated mitophagy. First, we found that WIPI2 is recruited to damaged mitochondria upon mitophagy induction. Second, loss of WIPI2 impedes mitochondrial damaging agents-induced mitophagy. Third, at molecular level, WIPI2 binds to and promotes AAA-ATPase VCP/p97 (valosin containing protein) to damaged mitochondria; and WIPI2 depletion blunts the recruitment of VCP to damaged mitochondria, leading to reduction in degradation of outer mitochondrial membrane (OMM) proteins and mitophagy. Finally, WIPI2 is implicated in cell fate decision as cells deficient in WIPI2 are largely resistant to cell death induced by mitochondrial damage. In summary, our study reveals a critical regulatory role of WIPI2 in mitochondrial recruitment of VCP to promote OMM protein degradation and eventual mitophagy.Abbreviations: ATG, autophagy related; CALCOCO2/NDP52, calcium binding and coiled-coil domain 2; CCCP, carbonyl cyanide chlorophenylhydrazone; CYCS, cytochrome c, somatic; HSPD1/HSP60, heat shock protein family D (Hsp60) member 1; IMM, inner mitochondrial membrane; MAP1LC3/LC3, microtubule associated protein 1 light chain 3; NPLOC4, NPL4 homolog, ubiquitin recognition factor; OMM, outer mitochondrial membrane; OPTN, optineurin; PtdIns3P, phosphatidylinositol-3-phosphate; PINK1, PTEN induced kinase 1; PRKN/Parkin, parkin RBR E3 ubiquitin protein ligase; UBXN6/UBXD1, UBX domain protein 6; UFD1, ubiquitin recognition factor in ER associated degradation 1; VCP/p97, valosin containing protein; WIPI2, WD repeat domain, phosphoinositide interacting 2.

Keywords:  Autophagy; PINK1; PRKN; VCP; WIPI2; cell death; mitophagy

DOI:  https://doi.org/10.1080/15548627.2022.2052461
Autophagy. 2022 Apr 03. 1-14

Endosomal-associated RFFL facilitates mitochondrial clearance by enhancing PRKN/parkin recruitment to mitochondria.

Rishith Ravindran, Anoop Kumar G Velikkakath, Nikhil Dev Narendradev, Aneesh Chandrasekharan, T R Santhoshkumar, Srinivasa M Srinivasula.

  Mutations in the ubiquitin ligase PRKN (parkin RBR E3 ubiquitin protein ligase) are associated with Parkinson disease and defective mitophagy. Conceptually, PRKN-dependent mitophagy is classified into two phases: 1. PRKN recruits to and ubiquitinates mitochondrial proteins; 2. formation of phagophore membrane, sequestering mitochondria for degradation. Recently, endosomal machineries are reported to contribute to the later stage for membrane assembly. We reported a role for endosomes in the events upstream of phase 1. We demonstrate that the endosomal ubiquitin ligase RFFL (ring finger and FYVE like domain containing E3 ubiquitin protein ligase) associated with damaged mitochondria, and this association preceded that of PRKN. RFFL interacted with PRKN, and stable recruitment of PRKN to damaged mitochondria was substantially reduced in RFFL KO cells. Our study unraveled a novel role of endosomes in modulating upstream pathways of PRKN-dependent mitophagy initiation.Abbreviations CCCP: carbonyl cyanide 3-chlorophenylhydrazone; DMSO: dimethyl sulfoxide; EGFP: enhanced green fluorescence protein; KO: knockout; PRKN: parkin RBR E3 ubiquitin protein ligase; RFFL: ring finger and FYVE like domain containing E3 ubiquitin protein ligase; UQCRC1: ubiquinol-cytochrome c reductase core protein 1; WT: wild-type.

Keywords:  Endosomes; PRKN; RFFL; mitophagy; ubiquitin ligases

DOI:  https://doi.org/10.1080/15548627.2022.2052460
Front Pharmacol. 2022 ;13 844756

Autophagy and Skin Diseases.

Kim Klapan, Dagmar Simon, Alexander Karaulov, Marina Gomzikova, Albert Rizvanov, Shida Yousefi, Hans-Uwe Simon.

  Autophagy is a highly conserved lysosomal degradation system that involves the creation of autophagosomes, which eventually fuse with lysosomes and breakdown misfolded proteins and damaged organelles with their enzymes. Autophagy is widely known for its function in cellular homeostasis under physiological and pathological settings. Defects in autophagy have been implicated in the pathophysiology of a variety of human diseases. The new line of evidence suggests that autophagy is inextricably linked to skin disorders. This review summarizes the principles behind autophagy and highlights current findings of autophagy's role in skin disorders and strategies for therapeutic modulation.

Keywords:  atopic dermatitis; autophagy; inflammation; psoriasis; skin cancer

DOI:  https://doi.org/10.3389/fphar.2022.844756
Autophagy. 2022 Apr 05. 1-3

A switch of chaperonin function regulates the clearance of solid protein aggregates.

Xinyu Ma, Min Zhang, Liang Ge.

  Protein aggregation is related to many human diseases. Selective macroautophagy/autophagy is the major way to clear protein aggregates in eukaryotic cells. While multiple types of autophagy receptors have been reported to mediate autophagic clearance of protein condensates with liquidity, it has been unclear if and how solid aggregates could be degraded by autophagy. Our recent work identifies the chaperonin subunit CCT2 as a new type of aggrephagy receptor specifically facilitating the autophagic clearance of solid protein aggregates, and indicates that multiple aggrephagy pathways act in parallel to remove different types of protein aggregates. In addition, this work reveals a functional switch of the chaperonin system by showing that CCT2 acts both as a chaperonin component and an autophagy-receptor via complex and monomer formation.

Keywords:  Aggrephagy; CCT2; TRiC; autophagosome; autophagy; chaperone; chaperonin; phase separation; protein aggregation

DOI:  https://doi.org/10.1080/15548627.2022.2052581
Autophagy. 2022 Apr 06. 1-18

Autophagopathies: from autophagy gene polymorphisms to precision medicine for human diseases.

Iris Grosjean, Barnabé Roméo, Marie-Angela Domdom, Amine Belaid, Grégoire D'Andréa, Nicolas Guillot, Romain K Gherardi, Jocelyn Gal, Gérard Milano, Charles Hugo Marquette, Rayjean J Hung, Maria Teresa Landi, Younghun Han, Patrick Brest, Martin Von Bergen, Daniel J Klionsky, Christopher I Amos, Paul Hofman, Baharia Mograbi.

  At a time when complex diseases affect globally 280 million people and claim 14 million lives every year, there is an urgent need to rapidly increase our knowledge into their underlying etiologies. Though critical in identifying the people at risk, the causal environmental factors (microbiome and/or pollutants) and the affected pathophysiological mechanisms are not well understood. Herein, we consider the variations of autophagy-related (ATG) genes at the heart of mechanisms of increased susceptibility to environmental stress. A comprehensive autophagy genomic resource is presented with 263 single nucleotide polymorphisms (SNPs) for 69 autophagy-related genes associated with 117 autoimmune, inflammatory, infectious, cardiovascular, neurological, respiratory, and endocrine diseases. We thus propose the term 'autophagopathies' to group together a class of complex human diseases the etiology of which lies in a genetic defect of the autophagy machinery, whether directly related or not to an abnormal flux in autophagy, LC3-associated phagocytosis, or any associated trafficking. The future of precision medicine for common diseases will lie in our ability to exploit these ATG SNP x environment relationships to develop new polygenetic risk scores, new management guidelines, and optimal therapies for afflicted patients.Abbreviations: ATG, autophagy-related; ALS-FTD, amyotrophic lateral sclerosis-frontotemporal dementia; ccRCC, clear cell renal cell carcinoma; CD, Crohn disease; COPD, chronic obstructive pulmonary disease; eQTL, expression quantitative trait loci; HCC, hepatocellular carcinoma; HNSCC, head and neck squamous cell carcinoma; GTEx, genotype-tissue expression; GWAS, genome-wide association studies; LAP, LC3-associated phagocytosis; LC3-II, phosphatidylethanolamine conjugated form of LC3; LD, linkage disequilibrium; LUAD, lung adenocarcinoma; MAF, minor allele frequency; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; NSCLC, non-small cell lung cancer; OS, overall survival; PtdIns3K CIII, class III phosphatidylinositol 3 kinase; PtdIns3P, phosphatidylinositol-3-phosphate; SLE, systemic lupus erythematosus; SNPs, single-nucleotide polymorphisms; mQTL, methylation quantitative trait loci; ULK, unc-51 like autophagy activating kinase; UTRs, untranslated regions; WHO, World Health Organization.

Keywords:  Autophagy; cancers; diseases; eQTL; pollutants/exposomics; polymorphism; prognosis; risk; susceptibility; theragnosis

DOI:  https://doi.org/10.1080/15548627.2022.2039994
Front Cell Dev Biol. 2022 ;10 837337

Mitophagy and Neurodegeneration: Between the Knowns and the Unknowns.

Cuckoo Teresa Jetto, Akshaya Nambiar, Ravi Manjithaya.

  Macroautophagy (henceforth autophagy) an evolutionary conserved intracellular pathway, involves lysosomal degradation of damaged and superfluous cytosolic contents to maintain cellular homeostasis. While autophagy was initially perceived as a bulk degradation process, a surfeit of studies in the last 2 decades has revealed that it can also be selective in choosing intracellular constituents for degradation. In addition to the core autophagy machinery, these selective autophagy pathways comprise of distinct molecular players that are involved in the capture of specific cargoes. The diverse organelles that are degraded by selective autophagy pathways are endoplasmic reticulum (ERphagy), lysosomes (lysophagy), mitochondria (mitophagy), Golgi apparatus (Golgiphagy), peroxisomes (pexophagy) and nucleus (nucleophagy). Among these, the main focus of this review is on the selective autophagic pathway involved in mitochondrial turnover called mitophagy. The mitophagy pathway encompasses diverse mechanisms involving a complex interplay of a multitude of proteins that confers the selective recognition of damaged mitochondria and their targeting to degradation via autophagy. Mitophagy is triggered by cues that signal the mitochondrial damage such as disturbances in mitochondrial fission-fusion dynamics, mitochondrial membrane depolarisation, enhanced ROS production, mtDNA damage as well as developmental cues such as erythrocyte maturation, removal of paternal mitochondria, cardiomyocyte maturation and somatic cell reprogramming. As research on the mechanistic aspects of this complex pathway is progressing, emerging roles of new players such as the NIPSNAP proteins, Miro proteins and ER-Mitochondria contact sites (ERMES) are being explored. Although diverse aspects of this pathway are being investigated in depth, several outstanding questions such as distinct molecular players of basal mitophagy, selective dominance of a particular mitophagy adapter protein over the other in a given physiological condition, molecular mechanism of how specific disease mutations affect this pathway remain to be addressed. In this review, we aim to give an overview with special emphasis on molecular and signalling pathways of mitophagy and its dysregulation in neurodegenerative disorders.

Keywords:  mitochondrial dynamics; mitochondrial dysfunction; mitophagy; neurodegenaration; phosphorylation; ubiquitination

DOI:  https://doi.org/10.3389/fcell.2022.837337
J Biochem. 2022 Apr 08. pii: mvac031. [Epub ahead of print]

Structural basis for the linkage specificity of ubiquitin-binding domain and deubiquitinase.

Yusuke Sato.

  Ubiquitination is a post-translational modification system essential for regulating a wide variety of biological processes in eukaryotes. Ubiquitin (Ub) itself undergoes post-translational modifications, including ubiquitination. All seven lysine residues and one N-terminal amino group of Ub can act as acceptors for further ubiquitination, producing eight types of Ub chains. Ub chains of different linkage types have different cellular functions and are referred to as the 'ubiquitin code'. Decoder molecules that contain linkage-specific Ub-binding domains (UBDs) recognize the Ub chains to regulate different cellular functions. On the other hand, deubiquitinases (DUBs) cleave Ub chains to reverse ubiquitin signals. This review discusses the molecular mechanisms of linkage-specific recognitions of Ub chains by UBDs and DUBs, which have been revealed by structural studies.

Keywords:  deubiquitinase; linkage specificity; ubiquitin binding domain; ubiquitin chain; ubiquitin code

DOI:  https://doi.org/10.1093/jb/mvac031
Autophagy. 2022 Apr 07. 1-2

Local biogenesis of autophagic vesicles in neuronal dendrites facilitates long-term synaptic depression.

Akrivi-Dimitra Daskalaki, Emmanouela Kallergi, Angeliki Kolaxi, Vassiliki Nikoletopoulou.

  Neurons are highly polarized and functionally compartmentalized cells. Under basal conditions, the biogenesis of autophagic vesicles (AVs) was previously shown to take place in the axon tip. As the sequestration of autophagic cargo occurs during the formation of nascent AVs, this would mean that only axonal proteins can be degraded via macroautophagy/autophagy, unless AV biogenesis can also take place on demand, in other neuronal compartments. Our work shows that indeed, activation of NMDA or group I metabotropic glutamate receptors during long-term synaptic depression (LTD) triggers the biogenesis of AVs locally in dendrites. Under these conditions, nascent dendritic AVs are required for synaptic plasticity, as they sequester postsynaptic proteins, whose removal from the postsynapse is necessary for LTD.

Keywords:  Atg5; ULK1 complex; autophagic vesicle biogenesis; cognitive flexibility; dendrites; excitatory neurons; hippocampus; synaptic plasticity

DOI:  https://doi.org/10.1080/15548627.2022.2061757
Cell Death Dis. 2022 Apr 07. 13(4): 316

TMEM189 negatively regulates the stability of ULK1 protein and cell autophagy.

Jiahong Yu, Liujing Qu, Yan Xia, Xuan Zhang, Jinqiu Feng, Mengyuan Duan, Pengli Guo, Yaxin Lou, Ping Lv, Wenping Lu, Yingyu Chen.

ULK1 is crucial for initiating autophagosome formation and its activity is tightly regulated by post-translational modifications and protein-protein interactions. In the present study, we demonstrate that TMEM189 (Transmembrane protein 189), also known as plasmanylethanolamine desaturase 1 (PEDS1), negatively regulates the proteostasis of ULK1 and autophagy activity. In TMEM189-overexpressed cells, the formation of autophagesome is impaired, while TMEM189 knockdown increases cell autophagy. Further investigation reveals that TMEM189 interacts with and increases the instability of ULK1, as well as decreases its kinase activities. The TMEM189 N-terminal domain is required for the interaction with ULK1. Additionally, TMEM189 overexpression can disrupt the interaction between ULK1 and TRAF6, profoundly impairs K63-linked polyubiquitination of ULK1 and self-association, leading to the decrease of ULK1 stability. Moreover, in vitro and in vivo experiments suggest that TMEM189 deficiency results in the inhibition of tumorigenicity of gastric cancer. Our findings provide a new insight into the molecular regulation of autophagy and laboratory evidence for investigating the physiological and pathological roles of TMEM189.

DOI: https://doi.org/10.1038/s41419-022-04722-y