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Wilson A, McCormick C. Reticulophagy and viral infection. Autophagy 2024. [PMID: 39394962 DOI: 10.1080/15548627.2024.2414424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 10/03/2024] [Accepted: 10/06/2024] [Indexed: 10/14/2024] Open
Abstract
All viruses are obligate intracellular parasites that use host machinery to synthesize viral proteins. In infected eukaryotes, viral secreted and transmembrane proteins are synthesized at the endoplasmic reticulum (ER). Many viruses refashion ER membranes into bespoke factories where viral products accumulate while evading host pattern recognition receptors. ER processes are tightly regulated to maintain cellular homeostasis, so viruses must either conform to ER regulatory mechanisms or subvert them to ensure efficient viral replication. Reticulophagy is a catabolic process that directs lysosomal degradation of ER components. There is accumulating evidence that reticulophagy serves as a form of antiviral defense; we call this defense "xERophagy" to acknowledge its relationship to xenophagy, the catabolic degradation of microorganisms by macroautophagy/autophagy. In turn, viruses can subvert reticulophagy to suppress host antiviral responses and support efficient viral replication. Here, we review the evidence for functional interplay between viruses and the host reticulophagy machinery.
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Affiliation(s)
- Alexa Wilson
- Department of Microbiology & Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Craig McCormick
- Department of Microbiology & Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
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2
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Leytens A, Benítez-Fernández R, Jiménez-García C, Roubaty C, Stumpe M, Boya P, Dengjel J. Targeted proteomics addresses selectivity and complexity of protein degradation by autophagy. Autophagy 2024:1-16. [PMID: 39245437 DOI: 10.1080/15548627.2024.2396792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 08/21/2024] [Accepted: 08/22/2024] [Indexed: 09/10/2024] Open
Abstract
Macroautophagy/autophagy is a constitutively active catabolic lysosomal degradation pathway, often found dysregulated in human diseases. It is often considered to act in a cytoprotective manner and is commonly upregulated in cells undergoing stress. Its initiation is regulated at the protein level and does not require de novo protein synthesis. Historically, autophagy has been regarded as nonselective; however, it is now clear that different stimuli can lead to the selective degradation of cellular components via selective autophagy receptors (SARs). Due to its selective nature and the existence of multiple degradation pathways potentially acting in concert, monitoring of autophagy flux, i.e. selective autophagy-dependent protein degradation, should address this complexity. Here, we introduce a targeted proteomics approach monitoring abundance changes of 37 autophagy-related proteins covering process-relevant proteins such as the initiation complex and the Atg8-family protein lipidation machinery, as well as most known SARs. We show that proteins involved in autophagosome biogenesis are upregulated and spared from degradation under autophagy-inducing conditions in contrast to SARs, in a cell-line dependent manner. Classical bulk stimuli such as nutrient starvation mainly induce degradation of ubiquitin-dependent soluble SARs and not of ubiquitin-independent, membrane-bound SARs. In contrast, treatment with the iron chelator deferiprone leads to the degradation of ubiquitin-dependent and -independent SARs linked to mitophagy and reticulophagy/ER-phagy. Our approach is automatable and supports large-scale screening assays paving the way to (pre)clinical applications and monitoring of specific autophagy flux.Abbreviation: AMBRA1: autophagy and beclin 1 regulator 1; ATG: autophagy related; BafA1: bafilomycin A1; BNIP1: BCL2 interacting protein 1; BNIP3: BCL2 interacting protein 3; BNIP3L/NIX: BCL2 interacting protein 3-like; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; CCPG1: cell cycle progression 1; CV: coefficients of variations; CCCP: carbonyl cyanide m-chlorophenyl hydrazone; DFP: deferiprone; ER: endoplasmic reticulum; FKBP8: FKBP prolyl isomerase 8; GABARAPL: GABA type A receptor associated protein like; LC: liquid chromatography; LOD: limit of detection; LOQ: limit of quantification; MAP1LC3: microtubule associated protein 1 light chain 3; MS: mass spectrometry; NCOA4: nuclear receptor coactivator 4; NBR1: NBR1 autophagy cargo receptor; NUFIP1: nuclear FMR1 interacting protein 1; OPTN: optineurin; PHB2: prohibitin 2; PNPLA2/ATGL: patatin like phospholipase domain containing 2; POI: protein of interest; PTM: posttranslational modification; PRM: parallel reaction monitoring; RB1CC1/FIP200: RB1 inducible coiled-coil 1; RETREG1/FAM134B: reticulophagy regulator 1; RPS6KB1: ribosomal protein S6 kinase B1; RTN3: reticulon 3; SARs: selective autophagy receptors; SQSTM1/p62: sequestosome 1; STBD1: starch binding domain 1; TAX1BP1: Tax1 binding protein 1; TFEB: transcription factor EB; TNIP1: TNFAIP3 interacting protein 1; TOLLIP: toll interacting protein; ULK1: unc-51 like autophagy activating kinase 1; WBP2: WW domain binding protein 2; WDFY3/Alfy: WD repeat and FYVE domain containing 3; WIPI2: WD repeat domain, phosphoinositide interacting 2.
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Affiliation(s)
- Alexandre Leytens
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Rocío Benítez-Fernández
- Department of Neuroscience and Movement Science, University of Fribourg, Fribourg, Switzerland
| | - Carlos Jiménez-García
- Department of Neuroscience and Movement Science, University of Fribourg, Fribourg, Switzerland
| | - Carole Roubaty
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Michael Stumpe
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Patricia Boya
- Department of Neuroscience and Movement Science, University of Fribourg, Fribourg, Switzerland
| | - Jörn Dengjel
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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3
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Zhang Y, Sun Y, Shi J, Xu P, Wang Y, Liu J, Gong X, Wang Y, Tang Y, Liu H, Zhou X, Lin Z, Baba O, Morita T, Yu B, Pan L. Decoding the molecular mechanism of selective autophagy of glycogen mediated by autophagy receptor STBD1. Proc Natl Acad Sci U S A 2024; 121:e2402817121. [PMID: 39236246 PMCID: PMC11406230 DOI: 10.1073/pnas.2402817121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 07/20/2024] [Indexed: 09/07/2024] Open
Abstract
Autophagy of glycogen (glycophagy) is crucial for the maintenance of cellular glucose homeostasis and physiology in mammals. STBD1 can serve as an autophagy receptor to mediate glycophagy by specifically recognizing glycogen and relevant key autophagic factors, but with poorly understood mechanisms. Here, we systematically characterize the interactions of STBD1 with glycogen and related saccharides, and determine the crystal structure of the STBD1 CBM20 domain with maltotetraose, uncovering a unique binding mode involving two different oligosaccharide-binding sites adopted by STBD1 CBM20 for recognizing glycogen. In addition, we demonstrate that the LC3-interacting region (LIR) motif of STBD1 can selectively bind to six mammalian ATG8 family members. We elucidate the detailed molecular mechanism underlying the selective interactions of STBD1 with ATG8 family proteins by solving the STBD1 LIR/GABARAPL1 complex structure. Importantly, our cell-based assays reveal that both the STBD1 LIR/GABARAPL1 interaction and the intact two oligosaccharide binding sites of STBD1 CBM20 are essential for the effective association of STBD1, GABARAPL1, and glycogen in cells. Finally, through mass spectrometry, biochemical, and structural modeling analyses, we unveil that STBD1 can directly bind to the Claw domain of RB1CC1 through its LIR, thereby recruiting the key autophagy initiation factor RB1CC1. In all, our findings provide mechanistic insights into the recognitions of glycogen, ATG8 family proteins, and RB1CC1 by STBD1 and shed light on the potential working mechanism of STBD1-mediated glycophagy.
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Affiliation(s)
- Yuchao Zhang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Yishan Sun
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200032, China
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jungang Shi
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200032, China
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Peng Xu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200032, China
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Yingli Wang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Jianping Liu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Xinyu Gong
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Yaru Wang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200032, China
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Yubin Tang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Haobo Liu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Xindi Zhou
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhiqiao Lin
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Otto Baba
- Oral and Maxillofacial Anatomy, Tokushima University Graduate School, Tokushima 770-8504, Japan
| | - Tsuyoshi Morita
- Oral and Maxillofacial Anatomy, Tokushima University Graduate School, Tokushima 770-8504, Japan
| | - Biao Yu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200032, China
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Lifeng Pan
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200032, China
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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4
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White J, Choi YB, Zhang J, Vo MT, He C, Shaikh K, Harhaj EW. Phosphorylation of the selective autophagy receptor TAX1BP1 by TBK1 and IKBKE/IKKi promotes ATG8-family protein-dependent clearance of MAVS aggregates. Autophagy 2024:1-18. [PMID: 39193925 DOI: 10.1080/15548627.2024.2394306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 08/12/2024] [Accepted: 08/15/2024] [Indexed: 08/29/2024] Open
Abstract
TAX1BP1 is a selective macroautophagy/autophagy receptor that inhibits NFKB and RIGI-like receptor (RLR) signaling to prevent excessive inflammation and maintain homeostasis. Selective autophagy receptors such as SQSTM1/p62 and OPTN are phosphorylated by the kinase TBK1 to stimulate their selective autophagy function. However, it is unknown if TAX1BP1 is regulated by TBK1 or other kinases under basal conditions or during RNA virus infection. Here, we found that TBK1 and IKBKE/IKKi function redundantly to phosphorylate TAX1BP1 and regulate its autophagic turnover through canonical macroautophagy. TAX1BP1 phosphorylation promotes its localization to lysosomes, resulting in its degradation. Additionally, we found that during vesicular stomatitis virus infection, TAX1BP1 is targeted to lysosomes in an ATG8-family protein-independent manner. Furthermore, TAX1BP1 plays a critical role in the clearance of MAVS aggregates, and phosphorylation of TAX1BP1 controls its MAVS aggrephagy function. Together, our data support a model whereby TBK1 and IKBKE license TAX1BP1-selective autophagy function to inhibit MAVS and RLR signaling.Abbreviations: ATG: autophagy related; BafA1: bafilomycin A1; CALCOCO2: calcium binding and coiled-coil domain 2; GFP: green fluorescent protein; IFA: indirect immunofluorescence assay; IFN: interferon; IκB: inhibitor of nuclear factor kappa B; IKK: IκB kinase; IRF: interferon regulatory factor; KO: knockout; LAMP1: lysosomal associated membrane protein 1; LIR: LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MAVS: mitochondrial antiviral signaling protein; MEF: mouse embryonic fibroblast; MOI: multiplicity of infection; IKBKG/NEMO: inhibitor of nuclear factor kappa B kinase regulatory subunit gamma; NFKB: nuclear factor kappa B; OPTN: optineurin; Poly(I:C): polyinosinic-polycytidylic acid; RB1CC1/FIP200: RB1 inducible coiled-coil 1; RIGI: RNA sensor RIG-I; RLR: RIGI-like receptor; SDD-AGE: semi-denaturing detergent-agarose gel electrophoresis; SeV: Sendai virus; SLR: SQSTM1-like receptor; SQSTM1: sequestosome 1; TAX1BP1: Tax1 binding protein 1; TBK1: TANK binding kinase 1; TNF: tumor necrosis factor; TRAF: TNF receptor associated factor; VSV: vesicular stomatitis virus; ZnF: zinc finger.
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Affiliation(s)
- Jesse White
- Department of Microbiology and Immunology, Penn State College of Medicine, Hershey, PA, USA
| | - Young Bong Choi
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jiawen Zhang
- Department of Microbiology and Immunology, Penn State College of Medicine, Hershey, PA, USA
| | - Mai Tram Vo
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Chaoxia He
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Kashif Shaikh
- Department of Microbiology and Immunology, Penn State College of Medicine, Hershey, PA, USA
| | - Edward W Harhaj
- Department of Microbiology and Immunology, Penn State College of Medicine, Hershey, PA, USA
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Wen W, Ertas YN, Erdem A, Zhang Y. Dysregulation of autophagy in gastric carcinoma: Pathways to tumor progression and resistance to therapy. Cancer Lett 2024; 591:216857. [PMID: 38583648 DOI: 10.1016/j.canlet.2024.216857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/22/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024]
Abstract
The considerable death rates and lack of symptoms in early stages of gastric cancer (GC) make it a major health problem worldwide. One of the most prominent risk factors is infection with Helicobacter pylori. Many biological processes, including those linked with cell death, are disrupted in GC. The cellular "self-digestion" mechanism necessary for regular balance maintenance, autophagy, is at the center of this disturbance. Misregulation of autophagy, however, plays a role in the development of GC. In this review, we will examine how autophagy interacts with other cell death processes, such as apoptosis and ferroptosis, and how it affects the progression of GC. In addition to wonderful its role in the epithelial-mesenchymal transition, it is engaged in GC metastasis. The role of autophagy in GC in promoting drug resistance stands out. There is growing interest in modulating autophagy for GC treatment, with research focusing on natural compounds, small-molecule inhibitors, and nanoparticles. These approaches could lead to breakthroughs in GC therapy, offering new hope in the fight against this challenging disease.
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Affiliation(s)
- Wen Wen
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Liaoning Clinical Research Center for Laboratory Medicine, Shenyang, China
| | - Yavuz Nuri Ertas
- Department of Biomedical Engineering, Erciyes University, Kayseri, Turkey; ERNAM-Nanotechnology Research and Application Center, Erciyes University, Kayseri, Turkey.
| | - Ahmet Erdem
- Institute for Quantitative Health Science and Engineering (IQ), Department of Biomedical Engineering, College of Engineering and Human Medicine, Michigan State University, East Lansing, MI, 48824, USA; Department of Biomedical Engineering, Kocaeli University, Umuttepe Campus, Kocaeli, 41001 Turkey.
| | - Yao Zhang
- Department of Gynaecology, Shengjing Hospital of China Medical University, Shenyang, China.
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North BJ, Ohnstad AE, Ragusa MJ, Shoemaker CJ. The LC3-interacting region of NBR1 is a protein interaction hub enabling optimal flux. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593318. [PMID: 38766171 PMCID: PMC11100792 DOI: 10.1101/2024.05.09.593318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
During autophagy, potentially toxic cargo is enveloped by a newly formed autophagosome and trafficked to the lysosome for degradation. Ubiquitinated protein aggregates, a key target for autophagy, are identified by multiple autophagy receptors. NBR1 is an archetypal autophagy receptor and an excellent model for deciphering the role of the multivalent, heterotypic interactions made by cargo-bound receptors. Using NBR1 as a model, we find that three critical binding partners - ATG8-family proteins, FIP200, and TAX1BP1 - each bind to a short linear interaction motif (SLiM) within NBR1. Mutational peptide arrays indicate that these binding events are mediated by distinct overlapping determinants, rather than a single, convergent, SLiM. AlphaFold modeling underlines the need for conformational flexibility within the NBR1 SLiM, as distinct conformations mediate each binding event. To test the extent to which overlapping SLiMs exist beyond NBR1, we performed peptide binding arrays on >100 established LC3-interacting regions (LIRs), revealing that FIP200 and/or TAX1BP1 binding to LIRs is a common phenomenon and suggesting LIRs as protein interaction hotspots. Comparative analysis of phosphomimetic peptides highlights that while FIP200 and Atg8-family binding are generally augmented by phosphorylation, TAX1BP1 binding is nonresponsive, suggesting differential regulation of these binding events. In vivo studies confirm that LIR-mediated interactions with TAX1BP1 enhance NBR1 activity, increasing autophagosomal delivery by leveraging an additional LIR from TAX1BP1. In sum, these results reveal a one-to-many binding modality in NBR1, providing key insights into the cooperative mechanisms among autophagy receptors. Furthermore, these findings underscore the pervasive role of multifunctional SLiMs in autophagy, offering substantial avenues for further exploration into their regulatory functions.
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Affiliation(s)
- Brian J North
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Amelia E Ohnstad
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | | | - Christopher J Shoemaker
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
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Degli Esposti M. Did mitophagy follow the origin of mitochondria? Autophagy 2024; 20:985-993. [PMID: 38361280 PMCID: PMC11135861 DOI: 10.1080/15548627.2024.2307215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/30/2023] [Accepted: 01/13/2024] [Indexed: 02/17/2024] Open
Abstract
Mitophagy is the process of selective autophagy that removes superfluous and dysfunctional mitochondria. Mitophagy was first characterized in mammalian cells and is now recognized to follow several pathways including basal forms in specific organs. Mitophagy pathways are regulated by multiple, often interconnected factors. The present review aims to streamline this complexity and evaluate common elements that may define the evolutionary origin of mitophagy. Key issues surrounding mitophagy signaling at the mitochondrial surface may fundamentally derive from mitochondrial membrane dynamics. Elements of such membrane dynamics likely originated during the endosymbiosis of the alphaproteobacterial ancestor of our mitochondria but underwent an evolutionary leap forward in basal metazoa that determined the currently known variations in mitophagy signaling.Abbreviations: AGPAT, 1-acylglycerol-3-phosphate O-acyltransferase; ATG, autophagy related; BCL2L13, BCL2 like 13; BNIP3, BCL2 interacting protein 3; BNIP3L, BCL2 interacting protein 3 like; CALCOCO, calcium binding and coiled-coil domain; CL, cardiolipin; ER, endoplasmic reticulum; ERMES, ER-mitochondria encounter structure; FBXL4, F-box and leucine rich repeat protein 4; FUNDC1, FUN14 domain containing 1; GABARAPL1, GABA type A receptor associated protein like 1; HIF, hypoxia inducible factor; IMM, inner mitochondrial membrane; LBPA/BMP, lysobisphosphatidic acid; LIR, LC3-interacting region; LPA, lysophosphatidic acid; MAM, mitochondria-associated membranes; MAP1LC3/LC3, microtubule associated protein 1 light chain 3; MCL, monolysocardiolipin; ML, maximum likelihood; NBR1, NBR1 autophagy cargo receptor; OMM, outer mitochondrial membrane; PA, phosphatidic acid; PACS2, phosphofurin acidic cluster sorting protein 2; PC/PLC, phosphatidylcholine; PE, phosphatidylethanolamine; PHB2, prohibitin 2; PINK1, PTEN induced kinase 1; PtdIns, phosphatidylinositol; SAR, Stramenopiles, Apicomplexa and Rhizaria; TAX1BP1, Tax1 binding protein 1; ULK1, unc-51 like autophagy activating kinase 1; VDAC/porin, voltage dependent anion channel.
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Affiliation(s)
- Mauro Degli Esposti
- Center for Genomic Sciences, UNAM Campus de Morelos, Cuernavaca, Morelos, Mexico
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Da Silva A, Dalmasso G, Larabi A, Hoang MHT, Billard E, Barnich N, Nguyen HTT. Identification of autophagy receptors for the Crohn's disease-associated adherent-invasive Escherichia coli. Front Cell Infect Microbiol 2024; 14:1268243. [PMID: 38606299 PMCID: PMC11007067 DOI: 10.3389/fcimb.2024.1268243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 03/04/2024] [Indexed: 04/13/2024] Open
Abstract
Introduction Crohn's disease (CD) is a chronic inflammatory bowel disease, of which the etiology involves genetic, environmental and microbial factors. Adherent-invasive Escherichia coli (AIEC) and polymorphisms in autophagy-related genes have been implicated in CD etiology. Autophagy is a key process for the maintenance of cellular homeostasis, which allows the degradation of damaged cytoplasmic components and pathogens via lysosome. We have shown that a functional autophagy is necessary for AIEC clearance. Here, we aimed at identifying the autophagy receptor(s) responsible to target AIEC to autophagy for degradation. Methods The levels of autophagy receptors p62, NDP52, NBR1, TAX1BP1 and Optineurin were knocked down in human intestinal epithelial cells T84 using siRNAs. The NDP52 knock-out (KO) and p62 KO HeLa cells, as well as NDP52 KO HeLa cells expressing the wild-type NDP52 or the mutated NDP52Val248Ala protein were used. Results and discussion We showed that, among the tested autophagy receptors (p62, NDP52, NBR1, TAX1BP1 and Optineurin), diminished expression of p62 or NDP52 increased the number of the clinical AIEC LF82 strain inside epithelial cells. This was associated with increased pro-inflammatory cytokine production. Moreover, p62 or NDP52 directly colocalized with AIEC LF82 and LC3, an autophagy marker. As the NDP52Val248Ala polymorphism has been associated with increased CD susceptibility, we investigated its impact on AIEC control. However, in HeLa cell and under our experimental condition, no effect of this polymorphism neither on AIEC LF82 intracellular number nor on pro-inflammatory cytokine production was observed. Together, our results suggest that p62 and NDP52 act as autophagy receptors for AIEC recognition, controlling AIEC intracellular replication and inflammation.
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Affiliation(s)
- Alison Da Silva
- M2iSH (Microbes, Intestine, Inflammation and Susceptibility of the Host), UMR 1071 Inserm, Université Clermont Auvergne, INRAE USC 1382, CNRH, Clermont-Ferrand, France
| | - Guillaume Dalmasso
- M2iSH (Microbes, Intestine, Inflammation and Susceptibility of the Host), UMR 1071 Inserm, Université Clermont Auvergne, INRAE USC 1382, CNRH, Clermont-Ferrand, France
| | - Anaïs Larabi
- M2iSH (Microbes, Intestine, Inflammation and Susceptibility of the Host), UMR 1071 Inserm, Université Clermont Auvergne, INRAE USC 1382, CNRH, Clermont-Ferrand, France
| | - My Hanh Thi Hoang
- M2iSH (Microbes, Intestine, Inflammation and Susceptibility of the Host), UMR 1071 Inserm, Université Clermont Auvergne, INRAE USC 1382, CNRH, Clermont-Ferrand, France
- Department of Cell Biology, Faculty of Biology, University of Science, Vietnam National University, Hanoi, Vietnam
| | - Elisabeth Billard
- M2iSH (Microbes, Intestine, Inflammation and Susceptibility of the Host), UMR 1071 Inserm, Université Clermont Auvergne, INRAE USC 1382, CNRH, Clermont-Ferrand, France
| | - Nicolas Barnich
- M2iSH (Microbes, Intestine, Inflammation and Susceptibility of the Host), UMR 1071 Inserm, Université Clermont Auvergne, INRAE USC 1382, CNRH, Clermont-Ferrand, France
| | - Hang Thi Thu Nguyen
- M2iSH (Microbes, Intestine, Inflammation and Susceptibility of the Host), UMR 1071 Inserm, Université Clermont Auvergne, INRAE USC 1382, CNRH, Clermont-Ferrand, France
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9
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Zhang M, Wang Y, Gong X, Wang Y, Zhang Y, Tang Y, Zhou X, Liu H, Huang Y, Zhang J, Pan L. Mechanistic insights into the interactions of TAX1BP1 with RB1CC1 and mammalian ATG8 family proteins. Proc Natl Acad Sci U S A 2024; 121:e2315550121. [PMID: 38437556 PMCID: PMC10945755 DOI: 10.1073/pnas.2315550121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/02/2024] [Indexed: 03/06/2024] Open
Abstract
TAX1BP1, a multifunctional autophagy adaptor, plays critical roles in different autophagy processes. As an autophagy receptor, TAX1BP1 can interact with RB1CC1, NAP1, and mammalian ATG8 family proteins to drive selective autophagy for relevant substrates. However, the mechanistic bases underpinning the specific interactions of TAX1BP1 with RB1CC1 and mammalian ATG8 family proteins remain elusive. Here, we find that there are two distinct binding sites between TAX1BP1 and RB1CC1. In addition to the previously reported TAX1BP1 SKICH (skeletal muscle and kidney enriched inositol phosphatase (SKIP) carboxyl homology)/RB1CC1 coiled-coil interaction, the first coiled-coil domain of TAX1BP1 can directly bind to the extreme C-terminal coiled-coil and Claw region of RB1CC1. We determine the crystal structure of the TAX1BP1 SKICH/RB1CC1 coiled-coil complex and unravel the detailed binding mechanism of TAX1BP1 SKICH with RB1CC1. Moreover, we demonstrate that RB1CC1 and NAP1 are competitive in binding to the TAX1BP1 SKICH domain, but the presence of NAP1's FIP200-interacting region (FIR) motif can stabilize the ternary TAX1BP1/NAP1/RB1CC1 complex formation. Finally, we elucidate the molecular mechanism governing the selective interactions of TAX1BP1 with ATG8 family members by solving the structure of GABARAP in complex with the non-canonical LIR (LC3-interacting region) motif of TAX1BP1, which unveils a unique binding mode between LIR and ATG8 family protein. Collectively, our findings provide mechanistic insights into the interactions of TAX1BP1 with RB1CC1 and mammalian ATG8 family proteins and are valuable for further understanding the working mode and function of TAX1BP1 in autophagy.
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Affiliation(s)
- Mingfang Zhang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200032, China
| | - Yingli Wang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200032, China
| | - Xinyu Gong
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200032, China
| | - Yaru Wang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200032, China
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou310024, China
| | - Yuchao Zhang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200032, China
| | - Yubin Tang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200032, China
| | - Xindi Zhou
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200032, China
| | - Haobo Liu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200032, China
| | - Yichao Huang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200032, China
| | - Jing Zhang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200032, China
- College of Chemistry and Materials Science, Sichuan Normal University, Chengdu, Sichuan610068, China
| | - Lifeng Pan
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200032, China
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou310024, China
- College of Chemistry and Materials Science, Sichuan Normal University, Chengdu, Sichuan610068, China
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10
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Nambiar A, Manjithaya R. Driving autophagy - the role of molecular motors. J Cell Sci 2024; 137:jcs260481. [PMID: 38329417 DOI: 10.1242/jcs.260481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024] Open
Abstract
Most of the vesicular transport pathways inside the cell are facilitated by molecular motors that move along cytoskeletal networks. Autophagy is a well-explored catabolic pathway that is initiated by the formation of an isolation membrane known as the phagophore, which expands to form a double-membraned structure that captures its cargo and eventually moves towards the lysosomes for fusion. Molecular motors and cytoskeletal elements have been suggested to participate at different stages of the process as the autophagic vesicles move along cytoskeletal tracks. Dynein and kinesins govern autophagosome trafficking on microtubules through the sequential recruitment of their effector proteins, post-translational modifications and interactions with LC3-interacting regions (LIRs). In contrast, myosins are actin-based motors that participate in various stages of the autophagic flux, as well as in selective autophagy pathways. However, several outstanding questions remain with regard to how the dominance of a particular motor protein over another is controlled, and to the molecular mechanisms that underlie specific disease variants in motor proteins. In this Review, we aim to provide an overview of the role of molecular motors in autophagic flux, as well as highlight their dysregulation in diseases, such as neurodegenerative disorders and pathogenic infections, and ageing.
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Affiliation(s)
- Akshaya Nambiar
- Autophagy Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Ravi Manjithaya
- Autophagy Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
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11
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Qian H, Ding WX. SQSTM1/p62 and Hepatic Mallory-Denk Body Formation in Alcohol-Associated Liver Disease. THE AMERICAN JOURNAL OF PATHOLOGY 2023; 193:1415-1426. [PMID: 36906265 PMCID: PMC10642158 DOI: 10.1016/j.ajpath.2023.02.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/14/2023] [Accepted: 02/24/2023] [Indexed: 03/12/2023]
Abstract
Sequestosome 1 (SQSTM1/p62; hereafter p62) is an autophagy receptor protein for selective autophagy primarily due to its direct interaction with the microtubule light chain 3 protein that specifically localizes on autophagosome membranes. As a result, impaired autophagy leads to the accumulation of p62. p62 is also a common component of many human liver disease-related cellular inclusion bodies, such as Mallory-Denk bodies, intracytoplasmic hyaline bodies, α1-antitrypsin aggregates, as well as p62 bodies and condensates. p62 also acts as an intracellular signaling hub, and it involves multiple signaling pathways, including nuclear factor erythroid 2-related factor 2, NF-κB, and the mechanistic target of rapamycin, which are critical for oxidative stress, inflammation, cell survival, metabolism, and liver tumorigenesis. This review discusses the recent insights of p62 in protein quality control, including the role of p62 in the formation and degradation of p62 stress granules and protein aggregates as well as regulation of multiple signaling pathways in the pathogenesis of alcohol-associated liver disease.
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Affiliation(s)
- Hui Qian
- Department of Pharmacology, Toxicology, and Therapeutics, The University of Kansas Medical Center, Kansas City, Kansas
| | - Wen-Xing Ding
- Department of Pharmacology, Toxicology, and Therapeutics, The University of Kansas Medical Center, Kansas City, Kansas; Department of Internal Medicine, The University of Kansas Medical Center, Kansas City, Kansas.
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12
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Tan LX, Germer CJ, Thamban T, La Cunza N, Lakkaraju A. Optineurin tunes outside-in signaling to regulate lysosome biogenesis and phagocytic clearance in the retina. Curr Biol 2023; 33:3805-3820.e7. [PMID: 37586372 PMCID: PMC10529777 DOI: 10.1016/j.cub.2023.07.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/16/2023] [Accepted: 07/19/2023] [Indexed: 08/18/2023]
Abstract
Balancing the competing demands of phagolysosomal degradation and autophagy is a significant challenge for phagocytic tissues. Yet how this plasticity is accomplished in health and disease is poorly understood. In the retina, circadian phagocytosis and degradation of photoreceptor outer segments by the postmitotic retinal pigment epithelium (RPE) are essential for healthy vision. Disrupted autophagy due to mechanistic target of rapamycin (mTOR) overactivation in the RPE is associated with blinding macular degenerations; however, outer segment degradation is unaffected in these diseases, indicating that distinct mechanisms regulate these clearance mechanisms. Here, using advanced imaging and mouse models, we identify optineurin as a key regulator that tunes phagocytosis and lysosomal capacity to meet circadian demands and helps prioritize outer segment clearance by the RPE in macular degenerations. High-resolution live-cell imaging implicates optineurin in scissioning outer segment tips prior to engulfment, analogous to microglial trogocytosis of neuronal processes. Optineurin is essential for recruiting light chain 3 (LC3), which anchors outer segment phagosomes to microtubules and facilitates phagosome maturation and fusion with lysosomes. This dynamically activates transcription factor EB (TFEB) to induce lysosome biogenesis in an mTOR-independent, transient receptor potential-mucolipin 1 (TRPML1)-dependent manner. RNA-seq analyses show that expression of TFEB target genes temporally tracks with optineurin recruitment and that lysosomal and autophagy genes are controlled by distinct transcriptional programs in the RPE. The unconventional plasma membrane-to-nucleus signaling mediated by optineurin ensures outer segment degradation under conditions of impaired autophagy in macular degeneration models. Independent regulation of these critical clearance mechanisms would help safeguard the metabolic fitness of the RPE throughout the organismal lifespan.
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Affiliation(s)
- Li Xuan Tan
- Department of Ophthalmology, School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Colin J Germer
- Department of Ophthalmology, School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Thushara Thamban
- Department of Ophthalmology, School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nilsa La Cunza
- Department of Ophthalmology, School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Aparna Lakkaraju
- Department of Ophthalmology, School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Anatomy, School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
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13
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Watanabe Y, Taguchi K, Tanaka M. Roles of Stress Response in Autophagy Processes and Aging-Related Diseases. Int J Mol Sci 2023; 24:13804. [PMID: 37762105 PMCID: PMC10531041 DOI: 10.3390/ijms241813804] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/02/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
The heat shock factor 1 (HSF1)-mediated stress response pathway and autophagy processes play important roles in the maintenance of proteostasis. Autophagy processes are subdivided into three subtypes: macroautophagy, chaperone-mediated autophagy (CMA), and microautophagy. Recently, molecular chaperones and co-factors were shown to be involved in the selective degradation of substrates by these three autophagy processes. This evidence suggests that autophagy processes are regulated in a coordinated manner by the HSF1-mediated stress response pathway. Recently, various studies have demonstrated that proteostasis pathways including HSF1 and autophagy are implicated in longevity. Furthermore, they serve as therapeutic targets for aging-related diseases such as cancer and neurodegenerative diseases. In the future, these studies will underpin the development of therapies against various diseases.
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Affiliation(s)
- Yoshihisa Watanabe
- Department of Basic Geriatrics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamikyo-ku, Kyoto 602-8566, Japan
| | - Katsutoshi Taguchi
- Department of Anatomy and Neurobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 601-0841, Japan; (K.T.); (M.T.)
| | - Masaki Tanaka
- Department of Anatomy and Neurobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 601-0841, Japan; (K.T.); (M.T.)
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14
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Morrison HM, Craft J, Rivera-Lugo R, Johnson JR, Golovkine GR, Bell SL, Dodd CE, Van Dis E, Beatty WL, Margolis SR, Repasy T, Shaker I, Lee AY, Vance RE, Stanley SA, Watson RO, Krogan NJ, Portnoy DA, Penn BH, Cox JS. Deficiency in Galectin-3, -8, and -9 impairs immunity to chronic Mycobacterium tuberculosis infection but not acute infection with multiple intracellular pathogens. PLoS Pathog 2023; 19:e1011088. [PMID: 37352334 PMCID: PMC10325092 DOI: 10.1371/journal.ppat.1011088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 07/06/2023] [Accepted: 05/01/2023] [Indexed: 06/25/2023] Open
Abstract
Macrophages employ an array of pattern recognition receptors to detect and eliminate intracellular pathogens that access the cytosol. The cytosolic carbohydrate sensors Galectin-3, -8, and -9 (Gal-3, Gal-8, and Gal-9) recognize damaged pathogen-containing phagosomes, and Gal-3 and Gal-8 are reported to restrict bacterial growth via autophagy in cultured cells. However, the contribution of these galectins to host resistance during bacterial infection in vivo remains unclear. We found that Gal-9 binds directly to Mycobacterium tuberculosis (Mtb) and Salmonella enterica serovar Typhimurium (Stm) and localizes to Mtb in macrophages. To determine the combined contribution of membrane damage-sensing galectins to immunity, we generated Gal-3, -8, and -9 triple knockout (TKO) mice. Mtb infection of primary macrophages from TKO mice resulted in defective autophagic flux but normal bacterial replication. Surprisingly, these mice had no discernable defect in resistance to acute infection with Mtb, Stm or Listeria monocytogenes, and had only modest impairments in bacterial growth restriction and CD4 T cell activation during chronic Mtb infection. Collectively, these findings indicate that while Gal-3, -8, and -9 respond to an array of intracellular pathogens, together these membrane damage-sensing galectins play a limited role in host resistance to bacterial infection.
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Affiliation(s)
- Huntly M. Morrison
- Department of Molecular and Cell Biology, Division of Immunology and Molecular Medicine, University of California, Berkeley, Berkeley, California, United States of America
| | - Julia Craft
- Department of Internal Medicine, Division of Infectious Diseases, University of California, Davis, Davis, California, United States of America
| | - Rafael Rivera-Lugo
- Department of Molecular and Cell Biology, Division of Immunology and Molecular Medicine, University of California, Berkeley, Berkeley, California, United States of America
| | - Jeffery R. Johnson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco; Quantitative Biosciences Institute (QBI), University of California, San Francisco; Gladstone Institutes, San Francisco, California, United States of America
| | - Guillaume R. Golovkine
- Department of Molecular and Cell Biology, Division of Immunology and Molecular Medicine, University of California, Berkeley, Berkeley, California, United States of America
| | - Samantha L. Bell
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, School of Medicine, Bryan, Texas, United States of America
| | - Claire E. Dodd
- Department of Molecular and Cell Biology, Division of Immunology and Molecular Medicine, University of California, Berkeley, Berkeley, California, United States of America
| | - Erik Van Dis
- Department of Molecular and Cell Biology, Division of Immunology and Molecular Medicine, University of California, Berkeley, Berkeley, California, United States of America
| | - Wandy L. Beatty
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Shally R. Margolis
- Department of Molecular and Cell Biology, Division of Immunology and Molecular Medicine, University of California, Berkeley, Berkeley, California, United States of America
| | - Teresa Repasy
- Department of Molecular and Cell Biology, Division of Immunology and Molecular Medicine, University of California, Berkeley, Berkeley, California, United States of America
| | - Isaac Shaker
- Department of Internal Medicine, Division of Infectious Diseases, University of California, Davis, Davis, California, United States of America
| | - Angus Y. Lee
- Cancer Research Laboratory, University of California, Berkeley, Berkeley, California, United States of America
| | - Russell E. Vance
- Department of Molecular and Cell Biology, Division of Immunology and Molecular Medicine, University of California, Berkeley, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, California, United States of America
| | - Sarah A. Stanley
- Department of Molecular and Cell Biology, Division of Immunology and Molecular Medicine, University of California, Berkeley, Berkeley, California, United States of America
- School of Public Health, Division of Infectious Diseases and Vaccinology, University of California, Berkeley, Berkeley, California, United States of America
| | - Robert O. Watson
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health, School of Medicine, Bryan, Texas, United States of America
| | - Nevan J. Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco; Quantitative Biosciences Institute (QBI), University of California, San Francisco; Gladstone Institutes, San Francisco, California, United States of America
| | - Daniel A. Portnoy
- Department of Molecular and Cell Biology, Division of Immunology and Molecular Medicine, University of California, Berkeley, Berkeley, California, United States of America
| | - Bennett H. Penn
- Department of Internal Medicine, Division of Infectious Diseases, University of California, Davis, Davis, California, United States of America
| | - Jeffery S. Cox
- Department of Molecular and Cell Biology, Division of Immunology and Molecular Medicine, University of California, Berkeley, Berkeley, California, United States of America
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15
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Farnung J, Muhar M, Liang JR, Tolmachova KA, Benoit RM, Corn JE, Bode JW. Semisynthetic LC3 Probes for Autophagy Pathways Reveal a Noncanonical LC3 Interacting Region Motif Crucial for the Enzymatic Activity of Human ATG3. ACS CENTRAL SCIENCE 2023; 9:1025-1034. [PMID: 37252361 PMCID: PMC10214526 DOI: 10.1021/acscentsci.3c00009] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Indexed: 05/31/2023]
Abstract
Macroautophagy is one of two major degradation systems in eukaryotic cells. Regulation and control of autophagy are often achieved through the presence of short peptide sequences called LC3 interacting regions (LIR) in autophagy-involved proteins. Using a combination of new protein-derived activity-based probes prepared from recombinant LC3 proteins, along with protein modeling and X-ray crystallography of the ATG3-LIR peptide complex, we identified a noncanonical LIR motif in the human E2 enzyme responsible for LC3 lipidation, ATG3. The LIR motif is present in the flexible region of ATG3 and adopts an uncommon β-sheet structure binding to the backside of LC3. We show that the β-sheet conformation is crucial for its interaction with LC3 and used this insight to design synthetic macrocyclic peptide-binders to ATG3. CRISPR-enabled in cellulo studies provide evidence that LIRATG3 is required for LC3 lipidation and ATG3∼LC3 thioester formation. Removal of LIRATG3 negatively impacts the rate of thioester transfer from ATG7 to ATG3.
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Affiliation(s)
- Jakob Farnung
- Laboratory
for Organic Chemistry, Department of Chemistry and Applied Biosciences ETH Zürich, CH-8093 Zürich, Switzerland
| | - Matthias Muhar
- Institute
of Molecular Health Sciences, Department of Biology ETH Zürich, CH-8093 Zürich, Switzerland
| | - Jin Rui Liang
- Institute
of Molecular Health Sciences, Department of Biology ETH Zürich, CH-8093 Zürich, Switzerland
| | - Kateryna A. Tolmachova
- Laboratory
for Organic Chemistry, Department of Chemistry and Applied Biosciences ETH Zürich, CH-8093 Zürich, Switzerland
| | - Roger M. Benoit
- Laboratory
of Nanoscale Biology, Division of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Jacob E. Corn
- Institute
of Molecular Health Sciences, Department of Biology ETH Zürich, CH-8093 Zürich, Switzerland
| | - Jeffrey W. Bode
- Laboratory
for Organic Chemistry, Department of Chemistry and Applied Biosciences ETH Zürich, CH-8093 Zürich, Switzerland
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16
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Dos Santos Á, Rollins DE, Hari-Gupta Y, McArthur H, Du M, Ru SYZ, Pidlisna K, Stranger A, Lorgat F, Lambert D, Brown I, Howland K, Aaron J, Wang L, Ellis PJI, Chew TL, Martin-Fernandez M, Pyne ALB, Toseland CP. Autophagy receptor NDP52 alters DNA conformation to modulate RNA polymerase II transcription. Nat Commun 2023; 14:2855. [PMID: 37202403 PMCID: PMC10195817 DOI: 10.1038/s41467-023-38572-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/09/2023] [Indexed: 05/20/2023] Open
Abstract
NDP52 is an autophagy receptor involved in the recognition and degradation of invading pathogens and damaged organelles. Although NDP52 was first identified in the nucleus and is expressed throughout the cell, to date, there is no clear nuclear functions for NDP52. Here, we use a multidisciplinary approach to characterise the biochemical properties and nuclear roles of NDP52. We find that NDP52 clusters with RNA Polymerase II (RNAPII) at transcription initiation sites and that its overexpression promotes the formation of additional transcriptional clusters. We also show that depletion of NDP52 impacts overall gene expression levels in two model mammalian cells, and that transcription inhibition affects the spatial organisation and molecular dynamics of NDP52 in the nucleus. This directly links NDP52 to a role in RNAPII-dependent transcription. Furthermore, we also show that NDP52 binds specifically and with high affinity to double-stranded DNA (dsDNA) and that this interaction leads to changes in DNA structure in vitro. This, together with our proteomics data indicating enrichment for interactions with nucleosome remodelling proteins and DNA structure regulators, suggests a possible function for NDP52 in chromatin regulation. Overall, here we uncover nuclear roles for NDP52 in gene expression and DNA structure regulation.
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Affiliation(s)
- Ália Dos Santos
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, S10 2RX, UK
- MRC LMB, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Daniel E Rollins
- Department of Materials Science and Engineering, University of Sheffield, Sheffield, S1 3JD, UK
| | - Yukti Hari-Gupta
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
- MRC LMCB, University College London, Gower Street, London, WC1E 6BT, UK
| | - Hannah McArthur
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Mingxue Du
- Department of Materials Science and Engineering, University of Sheffield, Sheffield, S1 3JD, UK
| | | | - Kseniia Pidlisna
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Ane Stranger
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Faeeza Lorgat
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, S10 2RX, UK
| | - Danielle Lambert
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, S10 2RX, UK
| | - Ian Brown
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Kevin Howland
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Jesse Aaron
- Advanced Imaging Center, HHMI Janelia Research Campus, Ashburn, VA, 20147, USA
| | - Lin Wang
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell, Didcot, Oxford, OX11 0QX, UK
| | - Peter J I Ellis
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Teng-Leong Chew
- Advanced Imaging Center, HHMI Janelia Research Campus, Ashburn, VA, 20147, USA
| | - Marisa Martin-Fernandez
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell, Didcot, Oxford, OX11 0QX, UK
| | - Alice L B Pyne
- Department of Materials Science and Engineering, University of Sheffield, Sheffield, S1 3JD, UK
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17
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Themistokleous C, Bagnoli E, Parulekar R, M K Muqit M. Role of autophagy pathway in Parkinson's disease and related Genetic Neurological disorders. J Mol Biol 2023:168144. [PMID: 37182812 DOI: 10.1016/j.jmb.2023.168144] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 05/16/2023]
Abstract
The elucidation of the function of the PINK1 protein kinase and Parkin ubiquitin E3 ligase in the elimination of damaged mitochondria by autophagy (mitophagy) has provided unprecedented understanding of the mechanistic pathways underlying Parkinson's disease (PD). We provide a comprehensive overview of the general importance of autophagy in Parkinson's disease and related disorders of the central nervous system. This reveals a critical link between autophagy and neurodegenerative and neurodevelopmental disorders and suggests that strategies to modulate mitophagy may have greater relevance in the CNS beyond PD.
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Affiliation(s)
- Christos Themistokleous
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK of Dundee, Dundee, DD1 5EH, UK; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Enrico Bagnoli
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK of Dundee, Dundee, DD1 5EH, UK; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Ramaa Parulekar
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK of Dundee, Dundee, DD1 5EH, UK
| | - Miratul M K Muqit
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK of Dundee, Dundee, DD1 5EH, UK; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
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18
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Rubio-Tomás T, Sotiriou A, Tavernarakis N. The interplay between selective types of (macro)autophagy: Mitophagy and xenophagy. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023; 374:129-157. [PMID: 36858654 DOI: 10.1016/bs.ircmb.2022.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Autophagy is a physiological response, activated by a myriad of endogenous and exogenous cues, including DNA damage, perturbation of proteostasis, depletion of nutrients or oxygen and pathogen infection. Upon sensing those stimuli, cells employ multiple non-selective and selective autophagy pathways to promote fitness and survival. Importantly, there are a variety of selective types of autophagy. In this review we will focus on autophagy of bacteria (xenophagy) and autophagy of mitochondria (mitophagy). We provide a brief introduction to bulk autophagy, as well as xenophagy and mitophagy, highlighting their common molecular factors. We also describe the role of xenophagy and mitophagy in the detection and elimination of pathogens by the immune system and the adaptive mechanisms that some pathogens have developed through evolution to escape the host autophagic response. Finally, we summarize the recent articles (from the last five years) linking bulk autophagy with xenophagy and/or mitophagy in the context on developmental biology, cancer and metabolism.
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Affiliation(s)
- Teresa Rubio-Tomás
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Aggeliki Sotiriou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece; Division of Basic Sciences, School of Medicine, University of Crete, Heraklion, Crete, Greece
| | - Nektarios Tavernarakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece; Division of Basic Sciences, School of Medicine, University of Crete, Heraklion, Crete, Greece.
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19
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Claviere M, Lavedrine A, Lamiral G, Bonnet M, Verlhac P, Petkova DS, Espert L, Duclaux-Loras R, Lucifora J, Rivoire M, Boschetti G, Nancey S, Rozières A, Viret C, Faure M. Measles virus-imposed remodeling of the autophagy machinery determines the outcome of bacterial coinfection. Autophagy 2023; 19:858-872. [PMID: 35900944 PMCID: PMC9980578 DOI: 10.1080/15548627.2022.2107309] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 07/24/2022] [Accepted: 07/25/2022] [Indexed: 01/18/2023] Open
Abstract
Although it is admitted that secondary infection can complicate viral diseases, the consequences of viral infection on cell susceptibility to other infections remain underexplored at the cellular level. We though to examine whether the sustained macroautophagy/autophagy associated with measles virus (MeV) infection could help cells oppose invasion by Salmonella Typhimurium, a bacterium sensitive to autophagic restriction. We report here the unexpected finding that Salmonella markedly replicated in MeV-infected cultures due to selective growth within multinucleated cells. Hyper-replicating Salmonella localized outside of LAMP1-positive compartments to an extent that equaled that of the predominantly cytosolic sifA mutant Salmonella. Bacteria were subjected to effective ubiquitination but failed to be targeted by LC3 despite an ongoing productive autophagy. Such a phenotype could not be further aggravated upon silencing of the selective autophagy regulator TBK1 or core autophagy factors ATG5 or ATG7. MeV infection also conditioned primary human epithelial cells for augmented Salmonella replication. The analysis of selective autophagy receptors able to target Salmonella revealed that a lowered expression level of SQSTM1/p62 and TAX1BP1/T6BP autophagy receptors prevented effective anti-Salmonella autophagy in MeV-induced syncytia. Conversely, as SQSTM1/p62 is promoting the cytosolic growth of Shigella flexneri, MeV infection led to reduced Shigella replication. The results indicate that the rarefaction of dedicated autophagy receptors associated with MeV infection differentially affects the outcome of bacterial coinfection depending on the nature of the functional relationship between bacteria and such receptors. Thus, virus-imposed reconfiguration of the autophagy machinery can be instrumental in determining the fate of bacterial coinfection.Abbreviations: ACTB/β-ACTIN: actin beta; ATG: autophagy related; BAFA1: bafilomycin A1; CFU: colony-forming units; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; FIP: fusion inhibitory peptide; GFP: green fluorescent protein; LAMP1: lysosomal associated membrane protein 1; LIR: MAP1LC3/LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MeV: measles virus; MOI: multiplicity of infection; OPTN: optineurin; PHH: primary human hepatocyte; SCV: Salmonella-containing vacuoles; SQSTM1/p62: sequestosome 1; S. flexneri: Shigella flexneri; S. Typhimurium: Salmonella enterica serovar Typhimurium; TAX1BP1/T6BP: Tax1 binding protein 1; TBK1: TANK binding kinase 1.
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Affiliation(s)
- Mathieu Claviere
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Aude Lavedrine
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Guénaëlle Lamiral
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Mariette Bonnet
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Pauline Verlhac
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Denitsa S. Petkova
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Lucile Espert
- IRIM, University of Montpellier, UMR 9004 CNRS, Montpellier, France
| | - Rémi Duclaux-Loras
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
- Department of Pediatric Hepatology, Gastroenterology and Nutrition, Femme-Mère-Enfant Hospital, Hospices Civils de Lyon, Bron, France
| | - Julie Lucifora
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | | | - Gilles Boschetti
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
- Department of Gastroenterology, Lyon-Sud university hospital, Hospices Civils de Lyon, Lyon, France
| | - Stéphane Nancey
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
- Department of Gastroenterology, Lyon-Sud university hospital, Hospices Civils de Lyon, Lyon, France
| | - Aurore Rozières
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Christophe Viret
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Mathias Faure
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
- Equipe Labellisée par la Fondation pour la Recherche Médicale, FRM, France
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20
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Shen ZF, Li L, Zhu XM, Liu XH, Klionsky DJ, Lin FC. Current opinions on mitophagy in fungi. Autophagy 2023; 19:747-757. [PMID: 35793406 PMCID: PMC9980689 DOI: 10.1080/15548627.2022.2098452] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 11/02/2022] Open
Abstract
Mitophagy, as one of the most important cellular processes to ensure quality control of mitochondria, aims at transporting damaged, aging, dysfunctional or excess mitochondria to vacuoles (plants and fungi) or lysosomes (mammals) for degradation and recycling. The normal functioning of mitophagy is critical for cellular homeostasis from yeasts to humans. Although the role of mitophagy has been well studied in mammalian cells and in certain model organisms, especially the budding yeast Saccharomyces cerevisiae, our understanding of its significance in other fungi, particularly in pathogenic filamentous fungi, is still at the preliminary stage. Recent studies have shown that mitophagy plays a vital role in spore production, vegetative growth and virulence of pathogenic fungi, which are very different from its roles in mammal and yeast. In this review, we summarize the functions of mitophagy for mitochondrial quality and quantity control, fungal growth and pathogenesis that have been reported in the field of molecular biology over the past two decades. These findings may help researchers and readers to better understand the multiple functions of mitophagy and provide new perspectives for the study of mitophagy in fungal pathogenesis.Abbreviations: AIM/LIR: Atg8-family interacting motif/LC3-interacting region; BAR: Bin-Amphiphysin-Rvs; BNIP3: BCL2 interacting protein 3; CK2: casein kinase 2; Cvt: cytoplasm-to-vacuole targeting; ER: endoplasmic reticulum; IMM: inner mitochondrial membrane; mETC: mitochondrial electron transport chain; OMM: outer mitochondrial membrane; OPTN: optineurin; PAS: phagophore assembly site; PD: Parkinson disease; PE: phosphatidylethanolamine; PHB2: prohibitin 2; PX: Phox homology; ROS, reactive oxygen species; TM: transmembrane.
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Affiliation(s)
- Zi-Fang Shen
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lin Li
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Xue-Ming Zhu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Xiao-Hong Liu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Daniel J. Klionsky
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Fu-Cheng Lin
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
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21
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Vargas JNS, Hamasaki M, Kawabata T, Youle RJ, Yoshimori T. The mechanisms and roles of selective autophagy in mammals. Nat Rev Mol Cell Biol 2023; 24:167-185. [PMID: 36302887 DOI: 10.1038/s41580-022-00542-2] [Citation(s) in RCA: 249] [Impact Index Per Article: 249.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2022] [Indexed: 11/09/2022]
Abstract
Autophagy is a process that targets various intracellular elements for degradation. Autophagy can be non-selective - associated with the indiscriminate engulfment of cytosolic components - occurring in response to nutrient starvation and is commonly referred to as bulk autophagy. By contrast, selective autophagy degrades specific targets, such as damaged organelles (mitophagy, lysophagy, ER-phagy, ribophagy), aggregated proteins (aggrephagy) or invading bacteria (xenophagy), thereby being importantly involved in cellular quality control. Hence, not surprisingly, aberrant selective autophagy has been associated with various human pathologies, prominently including neurodegeneration and infection. In recent years, considerable progress has been made in understanding mechanisms governing selective cargo engulfment in mammals, including the identification of ubiquitin-dependent selective autophagy receptors such as p62, NBR1, OPTN and NDP52, which can bind cargo and ubiquitin simultaneously to initiate pathways leading to autophagy initiation and membrane recruitment. This progress opens the prospects for enhancing selective autophagy pathways to boost cellular quality control capabilities and alleviate pathology.
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Affiliation(s)
- Jose Norberto S Vargas
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, UK
- UK Dementia Research Institute, University College London, London, UK
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Maho Hamasaki
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan.
- Department of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.
| | - Tsuyoshi Kawabata
- Department of Stem Cell Biology, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Richard J Youle
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
| | - Tamotsu Yoshimori
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan.
- Department of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.
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22
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Gehrer CM, Mitterstiller AM, Grubwieser P, Meyron-Holtz EG, Weiss G, Nairz M. Advances in Ferritin Physiology and Possible Implications in Bacterial Infection. Int J Mol Sci 2023; 24:4659. [PMID: 36902088 PMCID: PMC10003477 DOI: 10.3390/ijms24054659] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/17/2023] [Accepted: 02/25/2023] [Indexed: 03/04/2023] Open
Abstract
Due to its advantageous redox properties, iron plays an important role in the metabolism of nearly all life. However, these properties are not only a boon but also the bane of such life forms. Since labile iron results in the generation of reactive oxygen species by Fenton chemistry, iron is stored in a relatively safe form inside of ferritin. Despite the fact that the iron storage protein ferritin has been extensively researched, many of its physiological functions are hitherto unresolved. However, research regarding ferritin's functions is gaining momentum. For example, recent major discoveries on its secretion and distribution mechanisms have been made as well as the paradigm-changing finding of intracellular compartmentalization of ferritin via interaction with nuclear receptor coactivator 4 (NCOA4). In this review, we discuss established knowledge as well as these new findings and the implications they may have for host-pathogen interaction during bacterial infection.
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Affiliation(s)
- Clemens M. Gehrer
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Anna-Maria Mitterstiller
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Philipp Grubwieser
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Esther G. Meyron-Holtz
- Laboratory of Molecular Nutrition, Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Günter Weiss
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Medical University of Innsbruck, 6020 Innsbruck, Austria
- Christian Doppler Laboratory for Iron Metabolism and Anemia Research, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Manfred Nairz
- Department of Internal Medicine II, Infectious Diseases, Immunology, Rheumatology, Medical University of Innsbruck, 6020 Innsbruck, Austria
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23
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Collier JJ, Oláhová M, McWilliams TG, Taylor RW. Mitochondrial signalling and homeostasis: from cell biology to neurological disease. Trends Neurosci 2023; 46:137-152. [PMID: 36635110 DOI: 10.1016/j.tins.2022.12.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/18/2022] [Accepted: 12/05/2022] [Indexed: 01/11/2023]
Abstract
Efforts to understand how mitochondrial dysfunction contributes to neurodegeneration have primarily focussed on the role of mitochondria in neuronal energy metabolism. However, progress in understanding the etiological nature of emerging mitochondrial functions has yielded new ideas about the mitochondrial basis of neurological disease. Studies aimed at deciphering how mitochondria signal through interorganellar contacts, vesicular trafficking, and metabolic transmission have revealed that mitochondrial regulation of immunometabolism, cell death, organelle dynamics, and neuroimmune interplay are critical determinants of neural health. Moreover, the homeostatic mechanisms that exist to protect mitochondrial health through turnover via nanoscale proteostasis and lysosomal degradation have become integrated within mitochondrial signalling pathways to support metabolic plasticity and stress responses in the nervous system. This review highlights how these distinct mitochondrial pathways converge to influence neurological health and contribute to disease pathology.
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Affiliation(s)
- Jack J Collier
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, Canada.
| | - Monika Oláhová
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Thomas G McWilliams
- Translational Stem Cell Biology & Metabolism Program, Research Programs Unit, University of Helsinki, Helsinki, Finland; Department of Anatomy, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK; NHS Highly Specialised Service for Rare Mitochondrial Disorders of Adults and Children, Newcastle University, Newcastle upon Tyne, UK.
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24
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Kaposi's sarcoma-associated herpesvirus (KSHV) utilizes the NDP52/CALCOCO2 selective autophagy receptor to disassemble processing bodies. PLoS Pathog 2023; 19:e1011080. [PMID: 36634147 PMCID: PMC9876383 DOI: 10.1371/journal.ppat.1011080] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 01/25/2023] [Accepted: 12/22/2022] [Indexed: 01/13/2023] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) causes the inflammatory and angiogenic endothelial cell neoplasm, Kaposi's sarcoma (KS). We previously demonstrated that the KSHV Kaposin B (KapB) protein promotes inflammation via the disassembly of cytoplasmic ribonucleoprotein granules called processing bodies (PBs). PBs modify gene expression by silencing or degrading labile messenger RNAs (mRNAs), including many transcripts that encode inflammatory or angiogenic proteins associated with KS disease. Although our work implicated PB disassembly as one of the causes of inflammation during KSHV infection, the precise mechanism used by KapB to elicit PB disassembly was unclear. Here we reveal a new connection between the degradative process of autophagy and PB disassembly. We show that both latent KSHV infection and KapB expression enhanced autophagic flux via phosphorylation of the autophagy regulatory protein, Beclin. KapB was necessary for this effect, as infection with a recombinant virus that does not express the KapB protein did not induce Beclin phosphorylation or autophagic flux. Moreover, we showed that PB disassembly mediated by KSHV or KapB, depended on autophagy genes and the selective autophagy receptor NDP52/CALCOCO2 and that the PB scaffolding protein, Pat1b, co-immunoprecipitated with NDP52. These studies reveal a new role for autophagy and the selective autophagy receptor NDP52 in promoting PB turnover and the concomitant synthesis of inflammatory molecules during KSHV infection.
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25
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Shariq M, Quadir N, Alam A, Zarin S, Sheikh JA, Sharma N, Samal J, Ahmad U, Kumari I, Hasnain SE, Ehtesham NZ. The exploitation of host autophagy and ubiquitin machinery by Mycobacterium tuberculosis in shaping immune responses and host defense during infection. Autophagy 2023; 19:3-23. [PMID: 35000542 PMCID: PMC9809970 DOI: 10.1080/15548627.2021.2021495] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Intracellular pathogens have evolved various efficient molecular armaments to subvert innate defenses. Cellular ubiquitination, a normal physiological process to maintain homeostasis, is emerging one such exploited mechanism. Ubiquitin (Ub), a small protein modifier, is conjugated to diverse protein substrates to regulate many functions. Structurally diverse linkages of poly-Ub to target proteins allow enormous functional diversity with specificity being governed by evolutionarily conserved enzymes (E3-Ub ligases). The Ub-binding domain (UBD) and LC3-interacting region (LIR) are critical features of macroautophagy/autophagy receptors that recognize Ub-conjugated on protein substrates. Emerging evidence suggests that E3-Ub ligases unexpectedly protect against intracellular pathogens by tagging poly-Ub on their surfaces and targeting them to phagophores. Two E3-Ub ligases, PRKN and SMURF1, provide immunity against Mycobacterium tuberculosis (M. tb). Both enzymes conjugate K63 and K48-linked poly-Ub to M. tb for successful delivery to phagophores. Intriguingly, M. tb exploits virulence factors to effectively dampen host-directed autophagy utilizing diverse mechanisms. Autophagy receptors contain LIR-motifs that interact with conserved Atg8-family proteins to modulate phagophore biogenesis and fusion to the lysosome. Intracellular pathogens have evolved a vast repertoire of virulence effectors to subdue host-immunity via hijacking the host ubiquitination process. This review highlights the xenophagy-mediated clearance of M. tb involving host E3-Ub ligases and counter-strategy of autophagy inhibition by M. tb using virulence factors. The role of Ub-binding receptors and their mode of autophagy regulation is also explained. We also discuss the co-opting and utilization of the host Ub system by M. tb for its survival and virulence.Abbreviations: APC: anaphase promoting complex/cyclosome; ATG5: autophagy related 5; BCG: bacille Calmette-Guerin; C2: Ca2+-binding motif; CALCOCO2: calcium binding and coiled-coil domain 2; CUE: coupling of ubiquitin conjugation to ER degradation domains; DUB: deubiquitinating enzyme; GABARAP: GABA type A receptor-associated protein; HECT: homologous to the E6-AP carboxyl terminus; IBR: in-between-ring fingers; IFN: interferon; IL1B: interleukin 1 beta; KEAP1: kelch like ECH associated protein 1; LAMP1: lysosomal associated membrane protein 1; LGALS: galectin; LIR: LC3-interacting region; MAPK11/p38: mitogen-activated protein kinase 11; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MAP3K7/TAK1: mitogen-activated protein kinase kinase kinase 7; MAPK8/JNK: mitogen-activated protein kinase 8; MHC-II: major histocompatibility complex-II; MTOR: mechanistic target of rapamycin kinase; NBR1: NBR1 autophagy cargo receptor; NFKB1/p50: nuclear factor kappa B subunit 1; OPTN: optineurin; PB1: phox and bem 1; PE/PPE: proline-glutamic acid/proline-proline-glutamic acid; PknG: serine/threonine-protein kinase PknG; PRKN: parkin RBR E3 ubiquitin protein ligase; RBR: RING-in between RING; RING: really interesting new gene; RNF166: RING finger protein 166; ROS: reactive oxygen species; SMURF1: SMAD specific E3 ubiquitin protein ligase 1; SQSTM1: sequestosome 1; STING1: stimulator of interferon response cGAMP interactor 1; TAX1BP1: Tax1 binding protein 1; TBK1: TANK binding kinase 1; TNF: tumor necrosis factor; TRAF6: TNF receptor associated factor 6; Ub: ubiquitin; UBA: ubiquitin-associated; UBAN: ubiquitin-binding domain in ABIN proteins and NEMO; UBD: ubiquitin-binding domain; UBL: ubiquitin-like; ULK1: unc-51 like autophagy activating kinase 1.
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Affiliation(s)
- Mohd Shariq
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India
| | - Neha Quadir
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India,Department of Molecular Medicine, Jamia Hamdard-Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Anwar Alam
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India
| | - Sheeba Zarin
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India,Department of Molecular Medicine, Jamia Hamdard-Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Javaid A. Sheikh
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Neha Sharma
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India,Department of Molecular Medicine, Jamia Hamdard-Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Jasmine Samal
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India
| | - Uzair Ahmad
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India
| | - Indu Kumari
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India
| | - Seyed E. Hasnain
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi (IIT-D), New Delhi, India,Department of Life Science, School of Basic Sciences and Research, Sharda University, Greater Noida, India,Seyed E. Hasnain ; ; Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi (IIT-D), Hauz Khas, New Delhi 110 016, India
| | - Nasreen Z. Ehtesham
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India,CONTACT Nasreen Z. Ehtesham ; ICMR-National Institute of Pathology, Ansari Nagar West, New Delhi110029, India
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26
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White J, Suklabaidya S, Vo MT, Choi YB, Harhaj EW. Multifaceted roles of TAX1BP1 in autophagy. Autophagy 2023; 19:44-53. [PMID: 35470757 PMCID: PMC9809930 DOI: 10.1080/15548627.2022.2070331] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 04/21/2022] [Accepted: 04/21/2022] [Indexed: 01/09/2023] Open
Abstract
TAX1BP1 is a selective macroautophagy/autophagy receptor that plays a central role in host defense to pathogens and in regulating the innate immune system. TAX1BP1 facilitates the xenophagic clearance of pathogenic bacteria such as Salmonella typhimurium and Mycobacterium tuberculosis and regulates TLR3 (toll-like receptor 3)-TLR4 and DDX58/RIG-I-like receptor (RLR) signaling by targeting TICAM1 and MAVS for autophagic degradation respectively. In addition to these canonical autophagy receptor functions, TAX1BP1 can also exert multiple accessory functions that influence the biogenesis and maturation of autophagosomes. In this review, we will discuss and integrate recent findings related to the autophagy function of TAX1BP1 and highlight outstanding questions regarding its functions in autophagy and regulation of innate immunity and host defense.Abbreviations: ATG: autophagy related; CALCOCO: calcium binding and coiled-coil domain; CC: coiled-coil; CHUK/IKKα: conserved helix-loop-helix ubiquitous kinase; CLIR: noncanonical LC3-interacting region; GABARAP: gamma-aminobutyric acid receptor associated protein; HTLV-1: human T-lymphotropic virus 1; IFN: interferon; IL1B/IL1β: interleukin 1 beta; LIR: LC3-interacting region; LPS: lipopolysaccharide; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MAPK/JNK: mitogen-activated protein kinase; mATG8: mammalian Atg8 homolog; MAVS: mitochondrial antiviral signaling protein; MEF: mouse embryonic fibroblast; MTB: Mycobacterium tuberculosis; MYD88: myeloid differentiation primary response gene 88; NBR1: NBR1, autophagy cargo receptor; NFKB/NF-κB: nuclear factor of kappa light polypeptide gene enhancer in B cells; OPTN: optineurin; Poly(I:C): polyinosinic:polycytidylic acid; PTM: post-translational modification; RB1CC1: RB1-inducible coiled-coil 1; RIPK: receptor (TNFRSF)-interacting serine-threonine kinase; RLR: DDX58/RIG-I-like receptor; RSV: respiratory syncytia virus; SKICH: SKIP carboxyl homology; SLR: SQSTM1 like receptor; SQSTM1: sequestosome 1; TAX1BP1: Tax1 (human T cell leukemia virus type I) binding protein 1; TBK1: TANK-binding kinase 1; TICAM1: toll-like receptor adaptor molecule 1; TLR: toll-like receptor; TNF: tumor necrosis factor; TNFAIP3: TNF alpha induced protein 3; TNFR: tumor necrosis factor receptor; TOM1: target of myb1 trafficking protein; TRAF: TNF receptor-associated factor; TRIM32: tripartite motif-containing 32; UBD: ubiquitin binding domain; ZF: zinc finger.
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Affiliation(s)
- Jesse White
- Department of Microbiology and Immunology, Penn State College School of Medicine, Hershey, Pennsylvania, USA
| | - Sujit Suklabaidya
- Department of Microbiology and Immunology, Penn State College School of Medicine, Hershey, Pennsylvania, USA
| | - Mai Tram Vo
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Young Bong Choi
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Edward W. Harhaj
- Department of Microbiology and Immunology, Penn State College School of Medicine, Hershey, Pennsylvania, USA
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27
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Huyghe J, Priem D, Van Hove L, Gilbert B, Fritsch J, Uchiyama Y, Hoste E, van Loo G, Bertrand MJM. ATG9A prevents TNF cytotoxicity by an unconventional lysosomal targeting pathway. Science 2022; 378:1201-1207. [PMID: 36520901 DOI: 10.1126/science.add6967] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cell death induced by tumor necrosis factor (TNF) can be beneficial during infection by helping to mount proper immune responses. However, TNF-induced death can also drive a variety of inflammatory pathologies. Protectives brakes, or cell-death checkpoints, normally repress TNF cytotoxicity to protect the organism from its potential detrimental consequences. Thus, although TNF can kill, this only occurs when one of the checkpoints is inactivated. Here, we describe a checkpoint that prevents apoptosis through the detoxification of the cytotoxic complex IIa that forms upon TNF sensing. We found that autophagy-related 9A (ATG9A) and 200kD FAK family kinase-interacting protein (FIP200) promote the degradation of this complex through a light chain 3 (LC3)-independent lysosomal targeting pathway. This detoxification mechanism was found to counteract TNF receptor 1 (TNFR1)-mediated embryonic lethality and inflammatory skin disease in mouse models.
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Affiliation(s)
- Jon Huyghe
- VIB Center for Inflammation Research, 9052 Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium
| | - Dario Priem
- VIB Center for Inflammation Research, 9052 Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium
| | - Lisette Van Hove
- VIB Center for Inflammation Research, 9052 Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium
| | - Barbara Gilbert
- VIB Center for Inflammation Research, 9052 Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium
| | - Jürgen Fritsch
- Department of Infection Prevention and Infectious Diseases, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Yasuo Uchiyama
- Department of Cell Biology and Neuroscience, Juntendo University Graduate School of Medicine, 113-8654 Tokyo, Japan
| | - Esther Hoste
- VIB Center for Inflammation Research, 9052 Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium
| | - Geert van Loo
- VIB Center for Inflammation Research, 9052 Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium
| | - Mathieu J M Bertrand
- VIB Center for Inflammation Research, 9052 Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium
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28
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Walsh SC, Reitano JR, Dickinson MS, Kutsch M, Hernandez D, Barnes AB, Schott BH, Wang L, Ko DC, Kim SY, Valdivia RH, Bastidas RJ, Coers J. The bacterial effector GarD shields Chlamydia trachomatis inclusions from RNF213-mediated ubiquitylation and destruction. Cell Host Microbe 2022; 30:1671-1684.e9. [PMID: 36084633 PMCID: PMC9772000 DOI: 10.1016/j.chom.2022.08.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 05/13/2022] [Accepted: 08/12/2022] [Indexed: 01/26/2023]
Abstract
Chlamydia trachomatis is the leading cause of sexually transmitted bacterial infections and a major threat to women's reproductive health in particular. This obligate intracellular pathogen resides and replicates within a cellular compartment termed an inclusion, where it is sheltered by unknown mechanisms from gamma-interferon (IFNγ)-induced cell-autonomous host immunity. Through a genetic screen, we uncovered the Chlamydia inclusion membrane protein gamma resistance determinant (GarD) as a bacterial factor protecting inclusions from cell-autonomous immunity. In IFNγ-primed human cells, inclusions formed by garD loss-of-function mutants become decorated with linear ubiquitin and are eliminated. Leveraging cellular genome-wide association data, we identified the ubiquitin E3 ligase RNF213 as a candidate anti-Chlamydia protein. We demonstrate that IFNγ-inducible RNF213 facilitates the ubiquitylation and destruction of GarD-deficient inclusions. Furthermore, we show that GarD operates as a cis-acting stealth factor barring RNF213 from targeting inclusions, thus functionally defining GarD as an RNF213 antagonist essential for chlamydial growth during IFNγ-stimulated immunity.
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Affiliation(s)
- Stephen C Walsh
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Jeffrey R Reitano
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA; Department of Immunology, Duke University Medical Center, Durham, NC, USA
| | - Mary S Dickinson
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Miriam Kutsch
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Dulcemaria Hernandez
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Alyson B Barnes
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Benjamin H Schott
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - So Young Kim
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Raphael H Valdivia
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Robert J Bastidas
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Jörn Coers
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA; Department of Immunology, Duke University Medical Center, Durham, NC, USA.
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29
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Park SW, Jeon P, Yamasaki A, Lee HE, Choi H, Mun JY, Jun YW, Park JH, Lee SH, Lee SK, Lee YK, Song HK, Lazarou M, Cho DH, Komatsu M, Noda NN, Jang DJ, Lee JA. Development of new tools to study membrane-anchored mammalian Atg8 proteins. Autophagy 2022:1-20. [PMID: 36250672 DOI: 10.1080/15548627.2022.2132040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
ABBREVIATIONS A:C autophagic membrane:cytosol; ALS amyotrophic lateral sclerosis; ATG4 autophagy related 4; Atg8 autophagy related 8; BafA1 bafilomycin A1; BNIP3L/Nix BCL2 interacting protein 3 like; CALCOCO2/NDP52 calcium binding and coiled-coil domain 2; EBSS Earle's balanced salt solution; GABARAP GABA type A receptor-associated protein; GST glutathione S transferase; HKO hexa knockout; Kd dissociation constant; LIR LC3-interacting region; MAP1LC3/LC3 microtubule associated protein 1 light chain 3; NLS nuclear localization signal/sequence; PE phosphatidylethanolamine; SpHfl1 Schizosaccharomyces pombeorganic solute transmembrane transporter; SQSTM1/p62 SQSTM1/p62; TARDBP/TDP-43 TAR DNA binding protein; TKO triple knockout.
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Affiliation(s)
- Sang-Won Park
- Department of Vector Entomology, College of Ecology and Environment, Kyungpook National University, Sangju, Korea
| | - Pureum Jeon
- Department of Biological Sciences and Biotechnology, College of Life Sciences and Nanotechnology, Hannam University, Daejeon, Korea
| | | | - Hye Eun Lee
- Neural circuit research group, Korea Brain Research Institute, Daegu, Korea
| | - Haneul Choi
- Department of Biological Sciences and Biotechnology, College of Life Sciences and Nanotechnology, Hannam University, Daejeon, Korea
| | - Ji Young Mun
- Neural circuit research group, Korea Brain Research Institute, Daegu, Korea
| | - Yong-Woo Jun
- Department of Ecological Science, College of Ecology and Environment, Kyungpook National University, Sangju, Korea
| | - Ju-Hui Park
- Department of Ecological Science, College of Ecology and Environment, Kyungpook National University, Sangju, Korea
| | - Seung-Hwan Lee
- Department of Ecological Science, College of Ecology and Environment, Kyungpook National University, Sangju, Korea
| | - Soo-Kyeong Lee
- Department of Biological Sciences and Biotechnology, College of Life Sciences and Nanotechnology, Hannam University, Daejeon, Korea
| | - You-Kyung Lee
- Department of Biological Sciences and Biotechnology, College of Life Sciences and Nanotechnology, Hannam University, Daejeon, Korea
| | - Hyun Kyu Song
- Department of Life Sciences, Korea University, Seoul, Korea
| | - Michael Lazarou
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Victoria, Australia
| | - Dong-Hyong Cho
- School of Life Sciences, Kyungpook National University, Daegu, Korea
| | - Masaaki Komatsu
- Department of Physiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Nobuo N Noda
- Institute of Microbial Chemistry, Tokyo, Japan.,Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Deok-Jin Jang
- Department of Vector Entomology, College of Ecology and Environment, Kyungpook National University, Sangju, Korea.,Department of Ecological Science, College of Ecology and Environment, Kyungpook National University, Sangju, Korea
| | - Jin-A Lee
- Department of Biological Sciences and Biotechnology, College of Life Sciences and Nanotechnology, Hannam University, Daejeon, Korea
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30
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Sarango G, Richetta C, Pereira M, Kumari A, Ghosh M, Bertrand L, Pionneau C, Le Gall M, Grégoire S, Jeger‐Madiot R, Rosoy E, Subra F, Delelis O, Faure M, Esclatine A, Graff‐Dubois S, Stevanović S, Manoury B, Ramirez BC, Moris A. The Autophagy Receptor TAX1BP1 (T6BP) improves antigen presentation by MHC-II molecules. EMBO Rep 2022; 23:e55470. [PMID: 36215666 PMCID: PMC9724678 DOI: 10.15252/embr.202255470] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 09/16/2022] [Accepted: 09/23/2022] [Indexed: 12/12/2022] Open
Abstract
CD4+ T lymphocytes play a major role in the establishment and maintenance of immunity. They are activated by antigenic peptides derived from extracellular or newly synthesized (endogenous) proteins presented by the MHC-II molecules. The pathways leading to endogenous MHC-II presentation remain poorly characterized. We demonstrate here that the autophagy receptor, T6BP, influences both autophagy-dependent and -independent endogenous presentation of HIV- and HCMV-derived peptides. By studying the immunopeptidome of MHC-II molecules, we show that T6BP affects both the quantity and quality of peptides presented. T6BP silencing induces the mislocalization of the MHC-II-loading compartments and rapid degradation of the invariant chain (CD74) without altering the expression and internalization kinetics of MHC-II molecules. Defining the interactome of T6BP, we identify calnexin as a T6BP partner. We show that the calnexin cytosolic tail is required for this interaction. Remarkably, calnexin silencing replicates the functional consequences of T6BP silencing: decreased CD4+ T cell activation and exacerbated CD74 degradation. Altogether, we unravel T6BP as a key player of the MHC-II-restricted endogenous presentation pathway, and we propose one potential mechanism of action.
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Affiliation(s)
- Gabriela Sarango
- Université Paris‐Saclay, CEA, CNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance,Sorbonne UniversitéINSERM, CNRS, Center for Immunology and Microbial Infections (CIMI‐Paris)ParisFrance
| | - Clémence Richetta
- Sorbonne UniversitéINSERM, CNRS, Center for Immunology and Microbial Infections (CIMI‐Paris)ParisFrance,LBPA, ENS‐Paris Saclay, CNRS UMR8113Université Paris SaclayGif‐sur‐YvetteFrance
| | - Mathias Pereira
- Université Paris‐Saclay, CEA, CNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance,Sorbonne UniversitéINSERM, CNRS, Center for Immunology and Microbial Infections (CIMI‐Paris)ParisFrance
| | - Anita Kumari
- Université Paris‐Saclay, CEA, CNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance,Sorbonne UniversitéINSERM, CNRS, Center for Immunology and Microbial Infections (CIMI‐Paris)ParisFrance
| | - Michael Ghosh
- Department of Immunology, Institute for Cell BiologyUniversity of TübingenTübingenGermany
| | - Lisa Bertrand
- Université Paris‐Saclay, CEA, CNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance,Sorbonne UniversitéINSERM, CNRS, Center for Immunology and Microbial Infections (CIMI‐Paris)ParisFrance
| | - Cédric Pionneau
- Sorbonne UniversitéINSERM, UMS Production et Analyse de Données en Sciences de la vie et en Santé, PASS, Plateforme Post‐génomique de la Pitié SalpêtrièreParisFrance
| | - Morgane Le Gall
- 3P5 proteom'IC facilityUniversité de Paris, Institut Cochin, INSERM U1016, CNRS‐UMR 8104ParisFrance
| | - Sylvie Grégoire
- Université Paris‐Saclay, CEA, CNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance,Sorbonne UniversitéINSERM, CNRS, Center for Immunology and Microbial Infections (CIMI‐Paris)ParisFrance
| | - Raphaël Jeger‐Madiot
- Sorbonne UniversitéINSERM, CNRS, Center for Immunology and Microbial Infections (CIMI‐Paris)ParisFrance,Present address:
Sorbonne Université, INSERM U959, Immunology‐Immunopathology‐Immunotherapy (i3)ParisFrance
| | - Elina Rosoy
- Sorbonne UniversitéINSERM, CNRS, Center for Immunology and Microbial Infections (CIMI‐Paris)ParisFrance
| | - Frédéric Subra
- LBPA, ENS‐Paris Saclay, CNRS UMR8113Université Paris SaclayGif‐sur‐YvetteFrance
| | - Olivier Delelis
- LBPA, ENS‐Paris Saclay, CNRS UMR8113Université Paris SaclayGif‐sur‐YvetteFrance
| | - Mathias Faure
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de LyonLyonFrance,Equipe Labellisée par la Fondation pour la Recherche Médicale, FRM
| | - Audrey Esclatine
- Université Paris‐Saclay, CEA, CNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
| | - Stéphanie Graff‐Dubois
- Sorbonne UniversitéINSERM, CNRS, Center for Immunology and Microbial Infections (CIMI‐Paris)ParisFrance,Present address:
Sorbonne Université, INSERM U959, Immunology‐Immunopathology‐Immunotherapy (i3)ParisFrance
| | - Stefan Stevanović
- Department of Immunology, Institute for Cell BiologyUniversity of TübingenTübingenGermany
| | - Bénédicte Manoury
- Institut Necker Enfants Malades, INSERM U1151‐CNRS UMR 8253, Faculté de médecine NeckerUniversité de ParisParisFrance
| | - Bertha Cecilia Ramirez
- Université Paris‐Saclay, CEA, CNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance,Sorbonne UniversitéINSERM, CNRS, Center for Immunology and Microbial Infections (CIMI‐Paris)ParisFrance
| | - Arnaud Moris
- Université Paris‐Saclay, CEA, CNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance,Sorbonne UniversitéINSERM, CNRS, Center for Immunology and Microbial Infections (CIMI‐Paris)ParisFrance
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31
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Ohshima T, Yamamoto H, Sakamaki Y, Saito C, Mizushima N. NCOA4 drives ferritin phase separation to facilitate macroferritinophagy and microferritinophagy. J Cell Biol 2022; 221:213442. [PMID: 36066504 PMCID: PMC9452830 DOI: 10.1083/jcb.202203102] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/15/2022] [Accepted: 08/03/2022] [Indexed: 12/11/2022] Open
Abstract
A ferritin particle consists of 24 ferritin proteins (FTH1 and FTL) and stores iron ions within it. During iron deficiency, ferritin particles are transported to lysosomes to release iron ions. Two transport pathways have been reported: macroautophagy and ESCRT-dependent endosomal microautophagy. Although the membrane dynamics of these pathways differ, both require NCOA4, which is thought to be an autophagy receptor for ferritin. However, it is unclear whether NCOA4 only acts as an autophagy receptor in ferritin degradation. Here, we found that ferritin particles form liquid-like condensates in a NCOA4-dependent manner. Homodimerization of NCOA4 and interaction between FTH1 and NCOA4 (i.e., multivalent interactions between ferritin particles and NCOA4) were required for the formation of ferritin condensates. Disruption of these interactions impaired ferritin degradation. Time-lapse imaging and three-dimensional correlative light and electron microscopy revealed that these ferritin-NCOA4 condensates were directly engulfed by autophagosomes and endosomes. In contrast, TAX1BP1 was not required for the formation of ferritin-NCOA4 condensates but was required for their incorporation into autophagosomes and endosomes. These results suggest that NCOA4 acts not only as a canonical autophagy receptor but also as a driver to form ferritin condensates to facilitate the degradation of these condensates by macroautophagy (i.e., macroferritinophagy) and endosomal microautophagy (i.e., microferritinophagy).
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Affiliation(s)
- Tomoko Ohshima
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hayashi Yamamoto
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Molecular Oncology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Yuriko Sakamaki
- Microscopy Research Support Unit, Research Core, Tokyo Medical and Dental University, Tokyo, Japan
| | - Chieko Saito
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
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32
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Wu QQ, Yao Q, Hu TT, Wan Y, Xie QW, Zhao JH, Yuan Y, Tang QZ. Tax1 banding protein 1 exacerbates heart failure in mice by activating ITCH-P73-BNIP3-mediated cardiomyocyte apoptosis. Acta Pharmacol Sin 2022; 43:2562-2572. [PMID: 35948751 PMCID: PMC9525615 DOI: 10.1038/s41401-022-00950-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/26/2022] [Indexed: 11/09/2022] Open
Abstract
Tax1 banding protein 1 (Tax1bp1) was originally identified as an NF-κB regulatory protein that participated in inflammatory, antiviral and innate immune processes. Tax1bp1 also functions as an autophagy receptor that plays a role in autophagy. Our previous study shows that Tax1bp1 protects against cardiomyopathy in STZ-induced diabetic mice. In this study we investigated the role of Tax1bp1 in heart failure. Pressure overload-induced heart failure model was established in mice by aortic banding (AB) surgery, and angiotensin II (Ang II)-induced heart failure model was established by infusion of Ang II through osmotic minipump for 4 weeks. We showed that the expression levels of Tax1bp1 in the heart were markedly increased 2 and 4 weeks after AB surgery. Knockdown of Tax1bp1 in mouse hearts significantly ameliorated both AB- and Ang II infusion-induced heart failure parameters. On the contrary, AB-induced heart failure was aggravated in cardiac-specific Tax1bp1 transgenic mice. Similar results were observed in neonatal rat cardiomyocytes (NRCMs) under Ang II insult. We demonstrated that the pro-heart failure effect of Tax1bp1 resulted from its interaction with the E3 ligase ITCH to promote the transcription factor P73 ubiquitination and degradation, causing enhanced BCL2 interacting protein 3 (BNIP3)-mediated cardiomyocyte apoptosis. Knockdown ITCH or BNIP3 in NRCMs significantly reduced Ang II-induced apoptosis in vitro. Similarly, BNIP3 knockdown attenuated heart failure in cardiac-specific Tax1bp1 transgenic mice. In the left ventricles of heart failure patients, Tax1bp1 expression level was significantly increased; Tax1bp1 gene expression was negatively correlated with left ventricular ejection fraction in heart failure patients. Collectively, the Tax1bp1 increase in heart failure enhances ITCH-P73-BNIP3-mediated cardiomyocyte apoptosis and induced cardiac injury. Tax1bp1 may serve as a potent therapeutic target for the treatment of heart failure.• Cardiac Tax1bp1 transgene mice were more vulnerable to cardiac dysfunction under stress.• Cardiac Tax1bp1 transgene mice were more vulnerable to cardiac dysfunction under stress.• Knockout of Tax1bp1 in mouse hearts ameliorated heart failure induced by pressure overload.• Tax1bp1 interacts with the E3 ligase Itch to promote P73 ubiquitination and degradation, causing enhanced BNIP3-mediated apoptosis.• Tax1bp1 may become a target of new therapeutic methods for treating heart failure.
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Affiliation(s)
- Qing-Qing Wu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
- Cardiovascular Research Institute, Wuhan University, Wuhan, 430060, China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, 430060, China
| | - Qi Yao
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
- Cardiovascular Research Institute, Wuhan University, Wuhan, 430060, China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, 430060, China
| | - Tong-Tong Hu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
- Cardiovascular Research Institute, Wuhan University, Wuhan, 430060, China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, 430060, China
| | - Ying Wan
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
- Cardiovascular Research Institute, Wuhan University, Wuhan, 430060, China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, 430060, China
| | - Qing-Wen Xie
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
- Cardiovascular Research Institute, Wuhan University, Wuhan, 430060, China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, 430060, China
| | - Jin-Hua Zhao
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
- Cardiovascular Research Institute, Wuhan University, Wuhan, 430060, China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, 430060, China
| | - Yuan Yuan
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
- Cardiovascular Research Institute, Wuhan University, Wuhan, 430060, China
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, 430060, China
| | - Qi-Zhu Tang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
- Cardiovascular Research Institute, Wuhan University, Wuhan, 430060, China.
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, 430060, China.
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33
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Gennari L, Rendina D, Merlotti D, Cavati G, Mingiano C, Cosso R, Materozzi M, Pirrotta F, Abate V, Calabrese M, Falchetti A. Update on the pathogenesis and genetics of Paget’s disease of bone. Front Cell Dev Biol 2022; 10:932065. [PMID: 36035996 PMCID: PMC9412102 DOI: 10.3389/fcell.2022.932065] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/25/2022] [Indexed: 11/24/2022] Open
Abstract
Studies over the past two decades have led to major advances in the pathogenesis of Paget’s disease of bone (PDB) and particularly on the role of genetic factors. Germline mutations of different genes have been identified, as a possible cause of this disorder, and most of the underlying pathways are implicated in the regulation of osteoclast differentiation and function, whereas other are involved in cell autophagy mechanisms. In particular, about 30 different germline mutations of the Sequestosome 1 gene (SQSTM1) have been described in a significant proportion of familial and sporadic PDB cases. The majority of SQSTM1 mutations affect the ubiquitin-binding domain of the protein and are associated to a more severe clinical expression of the disease. Also, germline mutations in the ZNF687 and PFN1 genes have been associated to severe, early onset, polyostotic PDB with increased susceptibly to neoplastic degeneration, particularly giant cell tumor. Mutations in the VCP (Valosin Containing Protein) gene cause the autosomal dominant syndrome “Inclusion Body Myopathy, PDB, Fronto-temporal Dementia,” characterized by pagetic manifestations, associated with myopathy, amyotrophic lateral sclerosis and fronto-temporal dementia. Moreover, germline mutations in the TNFRSF11A gene, which encodes for RANK, were associated with rare syndromes showing some histopathological, radiological, and clinical overlap with PDB and in two cases of early onset PDB-like disease. Likewise, genome wide association studies performed in unrelated PDB cases identified other potential predisposition genes and/or susceptibility loci. Thus, it is likely that polygenic factors are involved in the PDB pathogenesis in many individuals and that modifying genes may contribute in refining the clinical phenotype. Moreover, the contribution of somatic mutations of SQSTM1 gene and/or epigenetic mechanisms in the pathogenesis of skeletal pagetic abnormalities and eventually neoplastic degeneration, cannot be excluded. Indeed, clinical and experimental observations indicate that genetic susceptibility might not be a sufficient condition for the clinical development of PDB without the concomitant intervention of viral infection, in primis paramixoviruses, and/or other environmental factors (e.g., pesticides, heavy metals or tobacco exposure), at least in a subset of cases. This review summarizes the most important advances that have been made in the field of cellular and molecular biology PDB over the past decades.
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Affiliation(s)
- Luigi Gennari
- Department of Medicine Surgery and Neurosciences, University of Siena Italy, Siena, Italy
- *Correspondence: Luigi Gennari, ; Alberto Falchetti,
| | - Domenico Rendina
- Department of Clinical Medicine and Surgery, Federico II University, Naples, Italy
| | - Daniela Merlotti
- Department of Medical Sciences, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Guido Cavati
- Department of Medicine Surgery and Neurosciences, University of Siena Italy, Siena, Italy
| | - Christian Mingiano
- Department of Medicine Surgery and Neurosciences, University of Siena Italy, Siena, Italy
| | - Roberta Cosso
- Unit of Rehabilitation Medicine, San Giuseppe Hospital, Istituto Auxologico Italiano, Piancavallo, Italy
| | - Maria Materozzi
- Department of Medicine Surgery and Neurosciences, University of Siena Italy, Siena, Italy
- Age Related Diseases Unit, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milano, Italy
| | - Filippo Pirrotta
- Department of Medicine Surgery and Neurosciences, University of Siena Italy, Siena, Italy
| | - Veronica Abate
- Department of Clinical Medicine and Surgery, Federico II University, Naples, Italy
| | - Marco Calabrese
- Department of Medicine Surgery and Neurosciences, University of Siena Italy, Siena, Italy
| | - Alberto Falchetti
- Experimental Research Laboratory on Bone Metabolism, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Istituto Auxologico Italiano, Milano, Italy
- *Correspondence: Luigi Gennari, ; Alberto Falchetti,
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34
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Chen W, Ouyang X, Chen L, Li L. Multiple functions of CALCOCO family proteins in selective autophagy. J Cell Physiol 2022; 237:3505-3516. [DOI: 10.1002/jcp.30836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 06/21/2022] [Accepted: 07/07/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Wei Chen
- Hunan Provincial Key Laboratory of tumor microenvironment responsive drug research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Institute of Pharmacy and Pharmacology University of South China Hengyang Hunan China
| | - Xueqian Ouyang
- Hunan Provincial Key Laboratory of tumor microenvironment responsive drug research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Institute of Pharmacy and Pharmacology University of South China Hengyang Hunan China
| | - Linxi Chen
- Hunan Provincial Key Laboratory of tumor microenvironment responsive drug research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Institute of Pharmacy and Pharmacology University of South China Hengyang Hunan China
| | - Lanfang Li
- Hunan Provincial Key Laboratory of tumor microenvironment responsive drug research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Institute of Pharmacy and Pharmacology University of South China Hengyang Hunan China
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Deretic V, Lazarou M. A guide to membrane atg8ylation and autophagy with reflections on immunity. J Cell Biol 2022; 221:e202203083. [PMID: 35699692 PMCID: PMC9202678 DOI: 10.1083/jcb.202203083] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/16/2022] [Accepted: 05/26/2022] [Indexed: 12/11/2022] Open
Abstract
The process of membrane atg8ylation, defined herein as the conjugation of the ATG8 family of ubiquitin-like proteins to membrane lipids, is beginning to be appreciated in its broader manifestations, mechanisms, and functions. Classically, membrane atg8ylation with LC3B, one of six mammalian ATG8 family proteins, has been viewed as the hallmark of canonical autophagy, entailing the formation of characteristic double membranes in the cytoplasm. However, ATG8s are now well described as being conjugated to single membranes and, most recently, proteins. Here we propose that the atg8ylation is coopted by multiple downstream processes, one of which is canonical autophagy. We elaborate on these biological outputs, which impact metabolism, quality control, and immunity, emphasizing the context of inflammation and immunological effects. In conclusion, we propose that atg8ylation is a modification akin to ubiquitylation, and that it is utilized by different systems participating in membrane stress responses and membrane remodeling activities encompassing autophagy and beyond.
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Affiliation(s)
- Vojo Deretic
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM
| | - Michael Lazarou
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
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36
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Kang S, Dai A, Wang H, Ding PH. Interaction Between Autophagy and Porphyromonas gingivalis-Induced Inflammation. Front Cell Infect Microbiol 2022; 12:892610. [PMID: 35846745 PMCID: PMC9283780 DOI: 10.3389/fcimb.2022.892610] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Autophagy is an immune homeostasis process induced by multiple intracellular and extracellular signals. Inflammation is a protective response to harmful stimuli such as pathogen microbial infection and body tissue damage. Porphyromonas gingivalis infection elicits both autophagy and inflammation, and dysregulation of autophagy and inflammation promotes pathology. This review focuses on the interaction between autophagy and inflammation caused by Porphyromonas gingivalis infection, aiming to elaborate on the possible mechanism involved in the interaction.
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37
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Luong AM, Koestel J, Bhati KK, Batoko H. Cargo receptors and adaptors for selective autophagy in plant cells. FEBS Lett 2022; 596:2104-2132. [PMID: 35638898 DOI: 10.1002/1873-3468.14412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 05/08/2022] [Accepted: 05/23/2022] [Indexed: 11/06/2022]
Abstract
Plant selective (macro)autophagy is a highly regulated process whereby eukaryotic cells spatiotemporally degrade some of their constituents that have become superfluous or harmful. The identification and characterization of the factors determining this selectivity make it possible to integrate selective (macro)autophagy into plant cell physiology and homeostasis. The specific cargo receptors and/or scaffold proteins involved in this pathway are generally not structurally conserved, as are the biochemical mechanisms underlying recognition and integration of a given cargo into the autophagosome in different cell types. This review discusses the few specific cargo receptors described in plant cells to highlight key features of selective autophagy in the plant kingdom and its integration with plant physiology, so as to identify evolutionary convergence and knowledge gaps to be filled by future research.
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Affiliation(s)
- Ai My Luong
- Louvain Institute of Biomolecular Science and Technology, University of Louvain Croix du Sud 4, L7.07.14, 1348, Louvain-la-Neuve, Belgium
| | - Jérôme Koestel
- Louvain Institute of Biomolecular Science and Technology, University of Louvain Croix du Sud 4, L7.07.14, 1348, Louvain-la-Neuve, Belgium
| | - Kaushal Kumar Bhati
- Louvain Institute of Biomolecular Science and Technology, University of Louvain Croix du Sud 4, L7.07.14, 1348, Louvain-la-Neuve, Belgium
| | - Henri Batoko
- Louvain Institute of Biomolecular Science and Technology, University of Louvain Croix du Sud 4, L7.07.14, 1348, Louvain-la-Neuve, Belgium
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Liu Y, Zhou T, Hu J, Jin S, Wu J, Guan X, Wu Y, Cui J. Targeting Selective Autophagy as a Therapeutic Strategy for Viral Infectious Diseases. Front Microbiol 2022; 13:889835. [PMID: 35572624 PMCID: PMC9096610 DOI: 10.3389/fmicb.2022.889835] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 03/29/2022] [Indexed: 12/13/2022] Open
Abstract
Autophagy is an evolutionarily conserved lysosomal degradation system which can recycle multiple cytoplasmic components under both physiological and stressful conditions. Autophagy could be highly selective to deliver different cargoes or substrates, including protein aggregates, pathogenic proteins or superfluous organelles to lysosome using a series of cargo receptor proteins. During viral invasion, cargo receptors selectively target pathogenic components to autolysosome to defense against infection. However, viruses not only evolve different strategies to counteract and escape selective autophagy, but also utilize selective autophagy to restrict antiviral responses to expedite viral replication. Furthermore, several viruses could activate certain forms of selective autophagy, including mitophagy, lipophagy, aggrephagy, and ferritinophagy, for more effective infection and replication. The complicated relationship between selective autophagy and viral infection indicates that selective autophagy may provide potential therapeutic targets for human infectious diseases. In this review, we will summarize the recent progress on the interplay between selective autophagy and host antiviral defense, aiming to arouse the importance of modulating selective autophagy as future therapies toward viral infectious diseases.
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Affiliation(s)
- Yishan Liu
- Department of Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Tao Zhou
- Ministry of Education (MOE) Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jiajia Hu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Shouheng Jin
- Ministry of Education (MOE) Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jianfeng Wu
- Department of Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiangdong Guan
- Department of Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yaoxing Wu
- Department of Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jun Cui
- Ministry of Education (MOE) Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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Kuno S, Fujita H, Tanaka Y, Ogra Y, Iwai K. Iron-induced NCOA4 condensation regulates ferritin fate and iron homeostasis. EMBO Rep 2022; 23:e54278. [PMID: 35318808 PMCID: PMC9066066 DOI: 10.15252/embr.202154278] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 03/08/2022] [Accepted: 03/08/2022] [Indexed: 12/26/2022] Open
Abstract
Iron is not only essential but also a toxic trace element. Under iron repletion, ferritin maintains cellular iron homeostasis by storing iron to avoid iron toxicity. Under iron depletion, the ferritin-specific autophagy adaptor NCOA4 delivers ferritin to lysosomes via macroautophagy to enable cells to use stored iron. Here, we show that NCOA4 also plays crucial roles in the regulation of ferritin fate under iron repletion. NCOA4 forms insoluble condensates via multivalent interactions generated by the binding of iron to its intrinsically disordered region. This sequesters NCOA4 away from ferritin and allows ferritin accumulation in the early phase of iron repletion. Under prolonged iron repletion, NCOA4 condensates can deliver ferritin to lysosomes via a TAX1BP1-dependent non-canonical autophagy pathway, thereby preventing relative iron deficiency due to excessive iron storage and reduced iron uptake. Together, these observations suggest that the NCOA4-ferritin axis modulates intracellular iron homeostasis in accordance with cellular iron availability.
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Affiliation(s)
- Sota Kuno
- Department of Molecular and Cellular PhysiologyGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Hiroaki Fujita
- Department of Molecular and Cellular PhysiologyGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Yu‐ki Tanaka
- Laboratory of Toxicology and Environmental HealthGraduate School of Pharmaceutical SciencesChiba UniversityChibaJapan
| | - Yasumitsu Ogra
- Laboratory of Toxicology and Environmental HealthGraduate School of Pharmaceutical SciencesChiba UniversityChibaJapan
| | - Kazuhiro Iwai
- Department of Molecular and Cellular PhysiologyGraduate School of MedicineKyoto UniversityKyotoJapan
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40
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Reggiori F, Molinari M. ER-phagy: mechanisms, regulation and diseases connected to the lysosomal clearance of the endoplasmic reticulum. Physiol Rev 2022; 102:1393-1448. [PMID: 35188422 PMCID: PMC9126229 DOI: 10.1152/physrev.00038.2021] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
ER-phagy (reticulo-phagy) defines the degradation of portions of the endoplasmic reticulum (ER) within lysosomes or vacuoles. It is part of the self-digestion (i.e., auto-phagic) programs recycling cytoplasmic material and organelles, which rapidly mobilize metabolites in cells confronted with nutrient shortage. Moreover, selective clearance of ER subdomains participates to the control of ER size and activity during ER stress, the re-establishment of ER homeostasis after ER stress resolution and the removal of ER parts, in which aberrant and potentially cytotoxic material has been segregated. ER-phagy relies on the individual and/or concerted activation of the ER-phagy receptors, ER peripheral or integral membrane proteins that share the presence of LC3/Atg8-binding motifs in their cytosolic domains. ER-phagy involves the physical separation of portions of the ER from the bulk ER network, and their delivery to the endolysosomal/vacuolar catabolic district. This last step is accomplished by a variety of mechanisms including macro-ER-phagy (in which ER fragments are sequestered by double-membrane autophagosomes that eventually fuse with lysosomes/vacuoles), micro-ER-phagy (in which ER fragments are directly engulfed by endosomes/lysosomes/vacuoles), or direct fusion of ER-derived vesicles with lysosomes/vacuoles. ER-phagy is dysfunctional in specific human diseases and its regulators are subverted by pathogens, highlighting its crucial role for cell and organism life.
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Affiliation(s)
- Fulvio Reggiori
- Department of Biomedical Sciences of Cells & Systems, grid.4830.fUniversity of Groningen, Netherlands
| | - Maurizio Molinari
- Protein Folding and Quality Control, grid.7722.0Institute for Research in Biomedicine, Bellinzona, Switzerland
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41
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Descamps D, Peres de Oliveira A, Gonnin L, Madrières S, Fix J, Drajac C, Marquant Q, Bouguyon E, Pietralunga V, Iha H, Morais Ventura A, Tangy F, Vidalain PO, Eléouët JF, Galloux M. Depletion of TAX1BP1 Amplifies Innate Immune Responses during Respiratory Syncytial Virus Infection. J Virol 2021; 95:e0091221. [PMID: 34431698 PMCID: PMC8549506 DOI: 10.1128/jvi.00912-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/20/2021] [Indexed: 12/15/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the main cause of acute respiratory infections in young children and also has a major impact on the elderly and immunocompromised people. In the absence of a vaccine or efficient treatment, a better understanding of RSV interactions with the host antiviral response during infection is needed. Previous studies revealed that cytoplasmic inclusion bodies (IBs), where viral replication and transcription occur, could play a major role in the control of innate immunity during infection by recruiting cellular proteins involved in the host antiviral response. We recently showed that the morphogenesis of IBs relies on a liquid-liquid-phase separation mechanism depending on the interaction between viral nucleoprotein (N) and phosphoprotein (P). These scaffold proteins are expected to play a central role in the recruitment of cellular proteins to IBs. Here, we performed a yeast two-hybrid screen using RSV N protein as bait and identified the cellular protein TAX1BP1 as a potential partner of this viral protein. This interaction was validated by pulldown and immunoprecipitation assays. We showed that TAX1BP1 suppression has only a limited impact on RSV infection in cell cultures. However, RSV replication is decreased in TAX1BP1-deficient (TAX1BP1 knockout [TAX1BP1KO]) mice, whereas the production of inflammatory and antiviral cytokines is enhanced. In vitro infection of wild-type or TAX1BP1KO alveolar macrophages confirmed that the innate immune response to RSV infection is enhanced in the absence of TAX1BP1. Altogether, our results suggest that RSV could hijack TAX1BP1 to restrain the host immune response during infection. IMPORTANCE Respiratory syncytial virus (RSV), which is the leading cause of lower respiratory tract illness in infants, remains a medical problem in the absence of a vaccine or efficient treatment. This virus is also recognized as a main pathogen in the elderly and immunocompromised people, and the occurrence of coinfections (with other respiratory viruses and bacteria) amplifies the risks of developing respiratory distress. In this context, a better understanding of the pathogenesis associated with viral respiratory infections, which depends on both viral replication and the host immune response, is needed. The present study reveals that the cellular protein TAX1BP1, which interacts with the RSV nucleoprotein N, participates in the control of the innate immune response during RSV infection, suggesting that the N-TAX1BP1 interaction represents a new target for the development of antivirals.
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Affiliation(s)
| | - Andressa Peres de Oliveira
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Lorène Gonnin
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | - Sarah Madrières
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | - Jenna Fix
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | - Carole Drajac
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | - Quentin Marquant
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | - Edwige Bouguyon
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | | | - Hidekatsu Iha
- Department of Infectious Diseases, Faculty of Medicine, Oita University Idaiga-oka, Hasama Yufu, Japan
| | - Armando Morais Ventura
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Frédéric Tangy
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France
| | - Pierre-Olivier Vidalain
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France
- CIRI, Centre International de Recherche en Infectiologie, Université Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | | | - Marie Galloux
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
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42
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Shang M, Weng L, Xu G, Wu S, Liu B, Yin X, Mao A, Zou X, Wang Z. TRIM11 suppresses ferritinophagy and gemcitabine sensitivity through UBE2N/TAX1BP1 signaling in pancreatic ductal adenocarcinoma. J Cell Physiol 2021; 236:6868-6883. [PMID: 33629745 DOI: 10.1002/jcp.30346] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 02/01/2021] [Accepted: 02/15/2021] [Indexed: 12/12/2022]
Abstract
Gemcitabine is first-line chemotherapy for pancreatic cancer, however, the development of resistance limits its effectiveness. The tripartite motif-containing 11 (TRIM11) protein plays crucial roles in tumor development and undergoes auto-polyubiquitination to promote interactions in selective autophagy. Therefore, Understanding whether TRIM11 is involved in ferritinophagy and gemcitabine resistance in pancreatic cancer is critical in developing pancreatic cancer therapeutics. TRIM11 expression was validated by Western blot analysis, real-time polymease chain reaction, and immunohistochemical staining. 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide and Colony formation assays were performed to investigate pancreatic ductal adenocarcinomas (PDAC) cell viability. Mouse xenograft model of PDAC cells was established to verify the role of TRIM11 in vivo. Coimmunoprecipitation was used to identify the reciprocal regulation between TRIM11 and UBE2N. In this study, we found that TRIM11 expression were higher in PDAC cells and tissues. TRIM11 overexpression promotes PDAC cell proliferation in vitro and tumor growth in vivo. Decreased expression of TRIM11 in PDAC patients is associated with decreased UBE2N and increased TAX1BP1 expression. Coimmunoprecipitation established that TRIM11 interacts and colocalizes with UBE2N. Mechanistically, TRIM11 promoted gemcitabine resistance and suppressed ferritinophagy through UBE2N-TAX1BP1 signaling. Our findings identify TRIM11 as a key regulator of TAX1BP1 signaling with a crucial role in ferritinophagy and gemcitabine resistance in PDAC.
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MESH Headings
- Animals
- Antimetabolites, Antineoplastic/pharmacology
- Autophagy/drug effects
- Carcinoma, Pancreatic Ductal/drug therapy
- Carcinoma, Pancreatic Ductal/genetics
- Carcinoma, Pancreatic Ductal/metabolism
- Carcinoma, Pancreatic Ductal/pathology
- Cell Line, Tumor
- Deoxycytidine/analogs & derivatives
- Deoxycytidine/pharmacology
- Drug Resistance, Neoplasm
- Female
- Ferroptosis/drug effects
- Gene Expression Regulation, Neoplastic
- Humans
- Intracellular Signaling Peptides and Proteins/genetics
- Intracellular Signaling Peptides and Proteins/metabolism
- Mice, Inbred BALB C
- Mice, Nude
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- Pancreatic Neoplasms/drug therapy
- Pancreatic Neoplasms/genetics
- Pancreatic Neoplasms/metabolism
- Pancreatic Neoplasms/pathology
- Signal Transduction
- Tripartite Motif Proteins/genetics
- Tripartite Motif Proteins/metabolism
- Tumor Burden/drug effects
- Ubiquitin-Conjugating Enzymes/genetics
- Ubiquitin-Conjugating Enzymes/metabolism
- Ubiquitin-Protein Ligases/genetics
- Ubiquitin-Protein Ligases/metabolism
- Xenograft Model Antitumor Assays
- Gemcitabine
- Mice
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Affiliation(s)
- Mingyi Shang
- Department of Interventional Radiology, Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Li Weng
- Department of Interventional Radiology, Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Guifang Xu
- Department of gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Shaoqiu Wu
- Department of Interventional Radiology, Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Bingyan Liu
- Department of Interventional Radiology, Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiang Yin
- Department of Interventional Radiology, Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Aiwu Mao
- Department of Interventional Radiology, Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiaoping Zou
- Department of interventional radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhongmin Wang
- Department of gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
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43
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Eapen VV, Swarup S, Hoyer MJ, Paulo JA, Harper JW. Quantitative proteomics reveals the selectivity of ubiquitin-binding autophagy receptors in the turnover of damaged lysosomes by lysophagy. eLife 2021; 10:e72328. [PMID: 34585663 PMCID: PMC8523161 DOI: 10.7554/elife.72328] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/25/2021] [Indexed: 12/14/2022] Open
Abstract
Removal of damaged organelles via the process of selective autophagy constitutes a major form of cellular quality control. Damaged organelles are recognized by a dedicated surveillance machinery, leading to the assembly of an autophagosome around the damaged organelle, prior to fusion with the degradative lysosomal compartment. Lysosomes themselves are also prone to damage and are degraded through the process of lysophagy. While early steps involve recognition of ruptured lysosomal membranes by glycan-binding galectins and ubiquitylation of transmembrane lysosomal proteins, many steps in the process, and their interrelationships, remain poorly understood, including the role and identity of cargo receptors required for completion of lysophagy. Here, we employ quantitative organelle capture and proximity biotinylation proteomics of autophagy adaptors, cargo receptors, and galectins in response to acute lysosomal damage, thereby revealing the landscape of lysosome-associated proteome remodeling during lysophagy. Among the proteins dynamically recruited to damaged lysosomes were ubiquitin-binding autophagic cargo receptors. Using newly developed lysophagic flux reporters including Lyso-Keima, we demonstrate that TAX1BP1, together with its associated kinase TBK1, are both necessary and sufficient to promote lysophagic flux in both HeLa cells and induced neurons (iNeurons). While the related receptor Optineurin (OPTN) can drive damage-dependent lysophagy when overexpressed, cells lacking either OPTN or CALCOCO2 still maintain significant lysophagic flux in HeLa cells. Mechanistically, TAX1BP1-driven lysophagy requires its N-terminal SKICH domain, which binds both TBK1 and the autophagy regulatory factor RB1CC1, and requires upstream ubiquitylation events for efficient recruitment and lysophagic flux. These results identify TAX1BP1 as a central component in the lysophagy pathway and provide a proteomic resource for future studies of the lysophagy process.
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Affiliation(s)
- Vinay V Eapen
- Department of Cell Biology, Harvard Medical School, BostonBostonUnited States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkChevy ChaseUnited States
| | - Sharan Swarup
- Department of Cell Biology, Harvard Medical School, BostonBostonUnited States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkChevy ChaseUnited States
| | - Melissa J Hoyer
- Department of Cell Biology, Harvard Medical School, BostonBostonUnited States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkChevy ChaseUnited States
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, BostonBostonUnited States
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, BostonBostonUnited States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkChevy ChaseUnited States
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Bell SL, Lopez KL, Cox JS, Patrick KL, Watson RO. Galectin-8 Senses Phagosomal Damage and Recruits Selective Autophagy Adapter TAX1BP1 To Control Mycobacterium tuberculosis Infection in Macrophages. mBio 2021; 12:e0187120. [PMID: 34225486 PMCID: PMC8406326 DOI: 10.1128/mbio.01871-20] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 06/03/2021] [Indexed: 12/26/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) causes one of the deadliest infectious diseases worldwide. Upon infection, Mtb is phagocytosed by macrophages and uses its virulence-associated ESX-1 secretion system to modulate the host cell. We showed previously that the ESX-1 secretion system perturbs the Mtb-containing phagosome, and a population (∼30%) of intracellular Mtb is tagged with ubiquitin and targeted to selective autophagy. However, our understanding of how macrophages sense and respond to damaged Mtb-containing phagosomes remains incomplete. Here, we demonstrate that several cytosolic glycan-binding proteins called galectins recognize Mtb-containing phagosomes; in macrophage cell lines and in primary macrophages, galectin-3, -8, and -9 are all recruited to the same Mtb population that colocalizes with selective autophagy markers (ubiquitin, p62, and LC3). To test whether galectins are required for controlling Mtb replication in macrophages, we generated CRISPR/Cas9 knockouts and found that galectin-8-/- and galectin-3/8/9-/- macrophages were similarly defective in targeting Mtb to selective autophagy and controlling replication. This suggests galectin-8 plays a unique role in anti-Mtb autophagy. In investigating galectin-8's role, we identified a novel and specific interaction between galectin-8 and the selective autophagy adapter TAX1BP1 and found that this galectin-8/TAX1BP1 interaction was necessary for macrophages to efficiently target Mtb to selective autophagy. Remarkably, overexpressing galectin-8 increased targeting of Mtb to autophagy and limited Mtb replication. Taken together, these data demonstrate that while several galectins are capable of recognizing damaged Mtb-containing phagosomes, galectin-8 plays a privileged role in recruiting downstream autophagy machinery and may represent a promising target for host-directed tuberculosis therapies. IMPORTANCE Mycobacterium tuberculosis (Mtb) infects one-quarter of the global population and causes one of the deadliest infectious diseases worldwide. Macrophages are the first line of defense against Mtb infection and are typically incredibly efficient at destroying intracellular pathogens, but Mtb has evolved to survive and replicate in this harsh environment. Previous work has found that a portion of intracellular Mtb bacilli damage their phagosomes, leaving them vulnerable to detection by the host and delivery to an antibacterial pathway called selective autophagy. Here, we show that in macrophages, galectin-8 recognizes damaged Mtb-containing phagosomes and targets Mtb to selective autophagy; we found that galectin-8, unlike other highly similar and closely related galectins, is required for targeting and controlling Mtb in macrophages. The specific role for galectin-8 appears to stem from its interaction with TAX1BP1, a selective autophagy adapter protein. Interestingly, overexpressing galectin-8 helps macrophages target and control Mtb, highlighting the importance of galectin-8 in the innate immune response to Mtb.
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Affiliation(s)
- Samantha L. Bell
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Bryan, Texas, USA
| | - Kayla L. Lopez
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Bryan, Texas, USA
| | - Jeffery S. Cox
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - Kristin L. Patrick
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Bryan, Texas, USA
| | - Robert O. Watson
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Bryan, Texas, USA
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Chen W, Shen T, Wang L, Lu K. Oligomerization of Selective Autophagy Receptors for the Targeting and Degradation of Protein Aggregates. Cells 2021; 10:cells10081989. [PMID: 34440758 PMCID: PMC8394947 DOI: 10.3390/cells10081989] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 07/31/2021] [Accepted: 08/02/2021] [Indexed: 02/05/2023] Open
Abstract
The selective targeting and disposal of solid protein aggregates are essential for cells to maintain protein homoeostasis. Autophagy receptors including p62, NBR1, Cue5/TOLLIP (CUET), and Tax1-binding protein 1 (TAX1BP1) proteins function in selective autophagy by targeting ubiquitinated aggregates through ubiquitin-binding domains. Here, we summarize previous beliefs and recent findings on selective receptors in aggregate autophagy. Since there are many reviews on selective autophagy receptors, we focus on their oligomerization, which enables receptors to function as pathway determinants and promotes phase separation.
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Affiliation(s)
- Wenjun Chen
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; (W.C.); (T.S.); (L.W.)
- Department of Neurology, Shanxi Provincial People’s Hospital, Taiyuan 030012, China
| | - Tianyun Shen
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; (W.C.); (T.S.); (L.W.)
| | - Lijun Wang
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; (W.C.); (T.S.); (L.W.)
| | - Kefeng Lu
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; (W.C.); (T.S.); (L.W.)
- Correspondence:
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Yamano K, Kojima W. Molecular functions of autophagy adaptors upon ubiquitin-driven mitophagy. Biochim Biophys Acta Gen Subj 2021; 1865:129972. [PMID: 34332032 DOI: 10.1016/j.bbagen.2021.129972] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/16/2021] [Accepted: 07/21/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Perturbations in organellar health can lead to an accumulation of unwanted and/or damaged organelles that are toxic to the cell and which can contribute to the onset of neurodegenerative diseases such as Parkinson's disease. Mitochondrial health is particularly critical given the indispensable role the organelle has not only in adenosine triphosphate production but also other metabolic processes. Byproducts of oxidative respiration, such as reactive oxygen species, however, can negatively impact mitochondrial fitness. Consequently, selective degradation of damaged mitochondria, which occurs via a specific autophagic process termed mitophagy, is essential for normal cell maintenance. SCOPE OF REVIEW Recent accumulating evidence has shown that autophagy adaptors (also referred to as autophagy receptors) play critical roles in connecting ubiquitinated mitochondria with the autophagic machinery of the autophagy-lysosome pathway that is required for degradation. In this review, we focus on our current understanding of the autophagy adaptor mechanisms underlying PINK1/Parkin-driven mitophagy. MAJOR CONCLUSIONS Although autophagy adaptors are canonically defined as proteins that possess ubiquitin-binding domains and ATG8s-binding motifs, the recent identification of novel binding partners has contributed to the development of a more sophisticated model for how autophagy adaptors contribute to the molecular hub that organizes autophagic cargo-degradation. GENERAL SIGNIFICANCE Although mitophagy is recognized as one of the selective autophagy pathways that removes dysfunctional mitochondria, a more nuanced understanding of the interactions connecting autophagy adaptors and their associated proteins is needed to gain deeper insights into the fundamental biological processes underlying human diseases, including neurodegenerative disorders. This review is part of a Special Issue entitled Mitophagy.
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Affiliation(s)
- Koji Yamano
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan.
| | - Waka Kojima
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
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Abstract
Selective autophagy is the lysosomal degradation of specific intracellular components sequestered into autophagosomes, late endosomes, or lysosomes through the activity of selective autophagy receptors (SARs). SARs interact with autophagy-related (ATG)8 family proteins via sequence motifs called LC3-interacting region (LIR) motifs in vertebrates and Atg8-interacting motifs (AIMs) in yeast and plants. SARs can be divided into two broad groups: soluble or membrane bound. Cargo or substrate selection may be independent or dependent of ubiquitin labeling of the cargo. In this review, we discuss mechanisms of mammalian selective autophagy with a focus on the unifying principles employed in substrate recognition, interaction with the forming autophagosome via LIR-ATG8 interactions, and the recruitment of core autophagy components for efficient autophagosome formation on the substrate. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Trond Lamark
- Molecular Cancer Research Group, Department of Medical Biology, University of Tromsø - The Arctic University of Norway, 9037 Tromsø, Norway; ,
| | - Terje Johansen
- Molecular Cancer Research Group, Department of Medical Biology, University of Tromsø - The Arctic University of Norway, 9037 Tromsø, Norway; ,
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Kara E, Crimi A, Wiedmer A, Emmenegger M, Manzoni C, Bandres-Ciga S, D'Sa K, Reynolds RH, Botía JA, Losa M, Lysenko V, Carta M, Heinzer D, Avar M, Chincisan A, Blauwendraat C, García-Ruiz S, Pease D, Mottier L, Carrella A, Beck-Schneider D, Magalhães AD, Aemisegger C, Theocharides APA, Fan Z, Marks JD, Hopp SC, Abramov AY, Lewis PA, Ryten M, Hardy J, Hyman BT, Aguzzi A. An integrated genomic approach to dissect the genetic landscape regulating the cell-to-cell transfer of α-synuclein. Cell Rep 2021; 35:109189. [PMID: 34107263 PMCID: PMC8207177 DOI: 10.1016/j.celrep.2021.109189] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 02/08/2021] [Accepted: 05/07/2021] [Indexed: 12/13/2022] Open
Abstract
Neuropathological and experimental evidence suggests that the cell-to-cell transfer of α-synuclein has an important role in the pathogenesis of Parkinson's disease (PD). However, the mechanism underlying this phenomenon is not fully understood. We undertook a small interfering RNA (siRNA), genome-wide screen to identify genes regulating the cell-to-cell transfer of α-synuclein. A genetically encoded reporter, GFP-2A-αSynuclein-RFP, suitable for separating donor and recipient cells, was transiently transfected into HEK cells stably overexpressing α-synuclein. We find that 38 genes regulate the transfer of α-synuclein-RFP, one of which is ITGA8, a candidate gene identified through a recent PD genome-wide association study (GWAS). Weighted gene co-expression network analysis (WGCNA) and weighted protein-protein network interaction analysis (WPPNIA) show that those hits cluster in networks that include known PD genes more frequently than expected by random chance. The findings expand our understanding of the mechanism of α-synuclein spread.
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Affiliation(s)
- Eleanna Kara
- Institute of Neuropathology, University of Zurich and University Hospital Zurich, Zurich 8091, Switzerland; Department of Neurodegenerative disease, University College London, London WC1N 3BG, UK
| | - Alessandro Crimi
- Institute of Neuropathology, University of Zurich and University Hospital Zurich, Zurich 8091, Switzerland
| | - Anne Wiedmer
- Institute of Neuropathology, University of Zurich and University Hospital Zurich, Zurich 8091, Switzerland
| | - Marc Emmenegger
- Institute of Neuropathology, University of Zurich and University Hospital Zurich, Zurich 8091, Switzerland
| | - Claudia Manzoni
- Department of Pharmacology, University College London School of Pharmacy, London WC1N 1AX, UK; School of Pharmacy, University of Reading, Reading RG6 6AP, UK
| | - Sara Bandres-Ciga
- Laboratory of Neurogenetics, National Institutes of Health, Bethesda, MD 20814, USA
| | - Karishma D'Sa
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK; Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Regina H Reynolds
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK; NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
| | - Juan A Botía
- Department of Neurodegenerative disease, University College London, London WC1N 3BG, UK; Departamento de Ingeniería de la Información y las Comunicaciones, Universidad de Murcia, Murcia 30100, Spain
| | - Marco Losa
- Institute of Neuropathology, University of Zurich and University Hospital Zurich, Zurich 8091, Switzerland
| | - Veronika Lysenko
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Zurich 8091, Switzerland
| | - Manfredi Carta
- Institute of Neuropathology, University of Zurich and University Hospital Zurich, Zurich 8091, Switzerland
| | - Daniel Heinzer
- Institute of Neuropathology, University of Zurich and University Hospital Zurich, Zurich 8091, Switzerland
| | - Merve Avar
- Institute of Neuropathology, University of Zurich and University Hospital Zurich, Zurich 8091, Switzerland
| | - Andra Chincisan
- Institute of Neuropathology, University of Zurich and University Hospital Zurich, Zurich 8091, Switzerland
| | | | - Sonia García-Ruiz
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK; NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
| | - Daniel Pease
- Institute of Neuropathology, University of Zurich and University Hospital Zurich, Zurich 8091, Switzerland
| | - Lorene Mottier
- Institute of Neuropathology, University of Zurich and University Hospital Zurich, Zurich 8091, Switzerland
| | - Alessandra Carrella
- Institute of Neuropathology, University of Zurich and University Hospital Zurich, Zurich 8091, Switzerland
| | - Dezirae Beck-Schneider
- Institute of Neuropathology, University of Zurich and University Hospital Zurich, Zurich 8091, Switzerland
| | - Andreia D Magalhães
- Institute of Neuropathology, University of Zurich and University Hospital Zurich, Zurich 8091, Switzerland
| | - Caroline Aemisegger
- Center for Microscopy and Image Analysis, University of Zurich, Zurich 8057, Switzerland
| | - Alexandre P A Theocharides
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Zurich 8091, Switzerland
| | - Zhanyun Fan
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
| | - Jordan D Marks
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA; Mayo Clinic Alix School of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Sarah C Hopp
- Department of Pharmacology, UT Health San Antonio, San Antonio, TX 78229, USA; Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX 78229, USA
| | - Andrey Y Abramov
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Patrick A Lewis
- Department of Neurodegenerative disease, University College London, London WC1N 3BG, UK; School of Pharmacy, University of Reading, Reading RG6 6AP, UK; Department of Comparative Biomedical Sciences, Royal Veterinary College, London NW1 0TU, UK
| | - Mina Ryten
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK; NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
| | - John Hardy
- Department of Neurodegenerative disease, University College London, London WC1N 3BG, UK; UK Dementia Research Institute, University College London, London WC1N 3BG, UK; Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, 1 Wakefield Street, London WC1N 1PJ, UK; Institute for Advanced Study, the Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Bradley T Hyman
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
| | - Adriano Aguzzi
- Institute of Neuropathology, University of Zurich and University Hospital Zurich, Zurich 8091, Switzerland.
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Chang C, Shi X, Jensen LE, Yokom AL, Fracchiolla D, Martens S, Hurley JH. Reconstitution of cargo-induced LC3 lipidation in mammalian selective autophagy. SCIENCE ADVANCES 2021; 7:7/17/eabg4922. [PMID: 33893090 PMCID: PMC8064641 DOI: 10.1126/sciadv.abg4922] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/05/2021] [Indexed: 05/14/2023]
Abstract
Selective autophagy of damaged mitochondria, protein aggregates, and other cargoes is essential for health. Cargo initiates phagophore biogenesis, which entails the conjugation of LC3 to phosphatidylethanolamine. Current models suggest that clustered ubiquitin chains on a cargo trigger a cascade from autophagic cargo receptors through the core complexes ULK1 and class III phosphatidylinositol 3-kinase complex I, WIPI2, and the ATG7, ATG3, and ATG12ATG5-ATG16L1 machinery of LC3 lipidation. This was tested using giant unilamellar vesicles (GUVs), GST-Ub4 as a model cargo, the cargo receptors NDP52, TAX1BP1, and OPTN, and the autophagy core complexes. All three cargo receptors potently stimulated LC3 lipidation on GUVs. NDP52- and TAX1BP1-induced LC3 lipidation required all components, but not ULK1 kinase activity. However, OPTN bypassed the ULK1 requirement. Thus, cargo-dependent stimulation of LC3 lipidation is common to multiple autophagic cargo receptors, yet the details of core complex engagement vary between the different receptors.
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Affiliation(s)
- Chunmei Chang
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD 20185, USA
| | - Xiaoshan Shi
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD 20185, USA
| | - Liv E Jensen
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD 20185, USA
| | - Adam L Yokom
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD 20185, USA
| | - Dorotea Fracchiolla
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD 20185, USA
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Sascha Martens
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD 20185, USA
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - James H Hurley
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD 20185, USA
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50
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Molinari M. ER-phagy responses in yeast, plants, and mammalian cells and their crosstalk with UPR and ERAD. Dev Cell 2021; 56:949-966. [PMID: 33765438 DOI: 10.1016/j.devcel.2021.03.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 02/23/2021] [Accepted: 02/27/2021] [Indexed: 12/24/2022]
Abstract
ER-phagy, literally endoplasmic reticulum (ER)-eating, defines the constitutive or regulated clearance of ER portions within metazoan endolysosomes or yeast and plant vacuoles. The advent of electron microscopy led to the first observations of ER-phagy over 60 years ago, but only recently, with the discovery of a set of regulatory proteins named ER-phagy receptors, has it been dissected mechanistically. ER-phagy receptors are activated by a variety of pleiotropic and ER-centric stimuli. They promote ER fragmentation and engage luminal, membrane-bound, and cytosolic factors, eventually driving lysosomal clearance of select ER domains along with their content. After short historical notes, this review introduces the concept of ER-phagy responses (ERPRs). ERPRs ensure lysosomal clearance of ER portions expendable during nutrient shortage, nonfunctional, present in excess, or containing misfolded proteins. They cooperate with unfolded protein responses (UPRs) and with ER-associated degradation (ERAD) in determining ER size, function, and homeostasis.
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Affiliation(s)
- Maurizio Molinari
- Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Institute for Research in Biomedicine, CH-6500 Bellinzona, Switzerland; School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
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