1
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Tian R, Zhao P, Ding X, Wang X, Jiang X, Chen S, Cai Z, Li L, Chen S, Liu W, Sun Q. TBC1D4 antagonizes RAB2A-mediated autophagic and endocytic pathways. Autophagy 2024:1-19. [PMID: 38964379 DOI: 10.1080/15548627.2024.2367907] [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: 09/25/2023] [Revised: 05/30/2024] [Accepted: 06/10/2024] [Indexed: 07/06/2024] Open
Abstract
Macroautophagic/autophagic and endocytic pathways play essential roles in maintaining homeostasis at different levels. It remains poorly understood how both pathways are coordinated and fine-tuned for proper lysosomal degradation of diverse cargoes. We and others recently identified a Golgi-resident RAB GTPase, RAB2A, as a positive regulator that controls both autophagic and endocytic pathways. In the current study, we report that TBC1D4 (TBC1 domain family member 4), a TBC domain-containing protein that plays essential roles in glucose homeostasis, suppresses RAB2A-mediated autophagic and endocytic pathways. TBC1D4 bound to RAB2A through its N-terminal PTB2 domain, which impaired RAB2A-mediated autophagy at the early stage by preventing ULK1 complex activation. During the late stage of autophagy, TBC1D4 impeded the association of RUBCNL/PACER and RAB2A with STX17 on autophagosomes by direct interaction with RUBCNL via its N-terminal PTB1 domain. Disruption of the autophagosomal trimeric complex containing RAB2A, RUBCNL and STX17 resulted in defective HOPS recruitment and eventually abortive autophagosome-lysosome fusion. Furthermore, TBC1D4 inhibited RAB2A-mediated endocytic degradation independent of RUBCNL. Therefore, TBC1D4 and RAB2A form a dual molecular switch to modulate autophagic and endocytic pathways. Importantly, hepatocyte- or adipocyte-specific tbc1d4 knockout in mice led to elevated autophagic flux and endocytic degradation and tissue damage. Together, this work establishes TBC1D4 as a critical molecular brake in autophagic and endocytic pathways, providing further mechanistic insights into how these pathways are intertwined both in vitro and in vivo.Abbreviations: ACTB: actin beta; ATG9: autophagy related 9; ATG14: autophagy related 14; ATG16L1: autophagy related 16 like 1; CLEM: correlative light electron microscopy; Ctrl: control; DMSO: dimethyl sulfoxide; EGF: epidermal growth factor; EGFR: epidermal growth factor receptor; FL: full length; GAP: GTPase-activating protein; GFP: green fluorescent protein; HOPS: homotypic fusion and protein sorting; IP: immunoprecipitation; KD: knockdown; KO: knockout; LAMP1: lysosomal associated membrane protein 1; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; OE: overexpression; PG: phagophore; PtdIns3K: class III phosphatidylinositol 3-kinase; SLC2A4/GLUT4: solute carrier family 2 member 4; SQSTM1/p62: sequestosome 1; RUBCNL/PACER: rubicon like autophagy enhancer; STX17: syntaxin 17; TAP: tandem affinity purification; TBA: total bile acid; TBC1D4: TBC1 domain family member 4; TUBA1B: tubulin alpha 1b; ULK1: unc-51 like autophagy activating kinase 1; VPS39: VPS39 subunit of HOPS complex; WB: western blot; WT: wild type.
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Affiliation(s)
- Rui Tian
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, China
- Department of Biochemistry, and Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Pengwei Zhao
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, China
- Department of Biochemistry, and Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xianming Ding
- Department of Biochemistry, and Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xinyi Wang
- Department of Biochemistry, and Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiao Jiang
- Department of Biochemistry, and Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shuai Chen
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, Nanjing, China
| | - Zhijian Cai
- Institute of Immunology, and Department of Orthopaedics of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lin Li
- Proteomics Center, National Institute of Biological Sciences, Beijing, China
| | - She Chen
- Proteomics Center, National Institute of Biological Sciences, Beijing, China
| | - Wei Liu
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, China
- Department of Biochemistry, and Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qiming Sun
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, China
- Department of Biochemistry, and Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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2
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Sun Y, Tao X, Han Y, Lin X, Tian R, Wang H, Chang P, Sun Q, Ge L, Zhang M. A dual role of ERGIC-localized Rabs in TMED10-mediated unconventional protein secretion. Nat Cell Biol 2024; 26:1077-1092. [PMID: 38926505 DOI: 10.1038/s41556-024-01445-4] [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: 11/22/2023] [Accepted: 05/23/2024] [Indexed: 06/28/2024]
Abstract
Cargo translocation across membranes is a crucial aspect of secretion. In conventional secretion signal peptide-equipped proteins enter the endoplasmic reticulum (ER), whereas a subset of cargo lacking signal peptides translocate into the ER-Golgi intermediate compartment (ERGIC) in a process called unconventional protein secretion (UcPS). The regulatory events at the ERGIC in UcPS are unclear. Here we reveal the involvement of ERGIC-localized small GTPases, Rab1 (Rab1A and Rab1B) and Rab2A, in regulating UcPS cargo transport via TMED10 on the ERGIC. Rab1 enhances TMED10 translocator activity, promoting cargo translocation into the ERGIC, whereas Rab2A, in collaboration with KIF5B, regulates ERGIC compartmentalization, establishing a UcPS-specific compartment. This study highlights the pivotal role of ERGIC-localized Rabs in governing cargo translocation and specifying the ERGIC's function in UcPS.
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Affiliation(s)
- Yuxin Sun
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xuan Tao
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Yaping Han
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xubo Lin
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
| | - Rui Tian
- Department of Biochemistry and Department of Cardiology of Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Haodong Wang
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Pei Chang
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Qiming Sun
- Department of Biochemistry and Department of Cardiology of Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Liang Ge
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Min Zhang
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China.
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3
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Yarychkivska O, Sharmin R, Elkhalil A, Ghose P. Apoptosis and beyond: A new era for programmed cell death in Caenorhabditis elegans. Semin Cell Dev Biol 2024; 154:14-22. [PMID: 36792437 DOI: 10.1016/j.semcdb.2023.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 01/27/2023] [Accepted: 02/02/2023] [Indexed: 02/16/2023]
Abstract
Programmed cell death (PCD) is crucial for normal development and homeostasis. Our first insights into the genetic regulation of apoptotic cell death came from in vivo studies in the powerful genetic model system of C. elegans. More recently, novel developmental cell death programs occurring both embryonically and post-embryonically, and sex-specifically, have been elucidated. Recent studies in the apoptotic setting have also shed new light on the intricacies of phagocytosis in particular. This review provides a brief historical perspective of the origins of PCD studies in C. elegans, followed by a more detailed description of non-canonical apoptotic and non-apoptotic death programs. We conclude by posing open questions and commenting on our outlook on the future of PCD studies in C. elegans, highlighting the importance of advanced imaging tools and the continued leveraging of C. elegans genetics both with classical and modern cutting-edge approaches.
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Affiliation(s)
| | | | | | - Piya Ghose
- The University of Texas at Arlington, USA.
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4
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Yoshida K, Suehiro Y, Dejima K, Yoshina S, Mitani S. Distinct pathways for export of silencing RNA in Caenorhabditis elegans systemic RNAi. iScience 2023; 26:108067. [PMID: 37854694 PMCID: PMC10579535 DOI: 10.1016/j.isci.2023.108067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/08/2023] [Accepted: 09/25/2023] [Indexed: 10/20/2023] Open
Abstract
Dietary supplied double-stranded RNA (dsRNA) can trigger RNA interference (RNAi) systemically in some animals, including the nematode Caenorhabditis elegans. Although this phenomenon has been utilized as a major tool for gene silencing in C. elegans, how cells spread the silencing RNA throughout the organism is largely unknown. Here, we identify two novel systemic RNAi-related factors, REXD-1 and TBC-3, and show that these two factors together with SID-5 act redundantly to promote systemic spreading of dsRNA. Animals that are defective in all REXD-1, TBC-3, and SID-5 functions show strong deficiency in export of dsRNA from intestinal cells, whereas cellular uptake and processing of dsRNA and general secretion events other than dsRNA secretion are still functional in the triple mutant animals. Our findings reveal pathways that specifically regulate the export of dsRNA in parallel, implying the importance of spreading RNA molecules for intercellular communication in organisms.
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Affiliation(s)
- Keita Yoshida
- Department of Physiology, Tokyo Women’s Medical University School of Medicine, 8-1, Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Yuji Suehiro
- Department of Physiology, Tokyo Women’s Medical University School of Medicine, 8-1, Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Katsufumi Dejima
- Department of Physiology, Tokyo Women’s Medical University School of Medicine, 8-1, Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Sawako Yoshina
- Department of Physiology, Tokyo Women’s Medical University School of Medicine, 8-1, Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Shohei Mitani
- Department of Physiology, Tokyo Women’s Medical University School of Medicine, 8-1, Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
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5
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Gingerich MA, Liu X, Chai B, Pearson GL, Vincent MP, Stromer T, Zhu J, Sidarala V, Renberg A, Sahu D, Klionsky DJ, Schnell S, Soleimanpour SA. An intrinsically disordered protein region encoded by the human disease gene CLEC16A regulates mitophagy. Autophagy 2023; 19:525-543. [PMID: 35604110 PMCID: PMC9851259 DOI: 10.1080/15548627.2022.2080383] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
CLEC16A regulates mitochondrial health through mitophagy and is associated with over 20 human diseases. However, the key structural and functional regions of CLEC16A, and their relevance for human disease, remain unknown. Here, we report that a disease-associated CLEC16A variant lacks a C-terminal intrinsically disordered protein region (IDPR) that is critical for mitochondrial quality control. IDPRs comprise nearly half of the human proteome, yet their mechanistic roles in human disease are poorly understood. Using carbon detect NMR, we find that the CLEC16A C terminus lacks secondary structure, validating the presence of an IDPR. Loss of the CLEC16A C-terminal IDPR in vivo impairs mitophagy, mitochondrial function, and glucose-stimulated insulin secretion, ultimately causing glucose intolerance. Deletion of the CLEC16A C-terminal IDPR increases CLEC16A ubiquitination and degradation, thus impairing assembly of the mitophagy regulatory machinery. Importantly, CLEC16A stability is dependent on proline bias within the C-terminal IDPR, but not amino acid sequence order or charge. Together, we elucidate how an IDPR in CLEC16A regulates mitophagy and implicate pathogenic human gene variants that disrupt IDPRs as novel contributors to diabetes and other CLEC16A-associated diseases.Abbreviations : CAS: carbon-detect amino-acid specific; IDPR: intrinsically disordered protein region; MEFs: mouse embryonic fibroblasts; NMR: nuclear magnetic resonance.
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Affiliation(s)
- Morgan A. Gingerich
- Department of Internal Medicine and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA,Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, USA
| | - Xueying Liu
- Department of Internal Medicine and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA,Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Biaoxin Chai
- Department of Internal Medicine and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Gemma L. Pearson
- Department of Internal Medicine and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Michael P. Vincent
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Tracy Stromer
- Department of Internal Medicine and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Jie Zhu
- Department of Internal Medicine and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Vaibhav Sidarala
- Department of Internal Medicine and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Aaron Renberg
- Department of Internal Medicine and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Debashish Sahu
- BioNMR Core Facility, Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Daniel J. Klionsky
- Life Sciences Institute and Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Santiago Schnell
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Scott A. Soleimanpour
- Department of Internal Medicine and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Ann Arbor, MI, USA,Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA,Medicine Service, Endocrinology and Metabolism Section, VA Ann Arbor Health Care System, Ann Arbor, MI, USA,CONTACT Scott A. Soleimanpour Department of Internal Medicine and Division of Metabolism, Endocrinology & Diabetes, University of Michigan, Wall Street, Brehm Tower Room, Ann Arbor, MI, USA
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6
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Shang J, Yang Q, Fan W, Chen Y, Tang D, Guo H, Xiong B, Huang S, Zhang XB. Probing Dynamic Features of Phagosome Maturation in Macrophage using Au@MnO x @SiO 2 Nanoparticles as pH-Sensitive Plasmonic Nanoprobes. Chem Asian J 2021; 16:1150-1156. [PMID: 33724702 DOI: 10.1002/asia.202100031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/13/2021] [Indexed: 11/05/2022]
Abstract
Phagosome maturation in macrophage is essential to the clearance of pathogenic materials in host defence but the dynamic features remain difficult to be measured in real time. Herein, we reported the multilayered Au@MnOx @SiO2 nanoparticle as a robust pH-sensitive plasmonic nanosensor for monitoring the dynamic acidification features over the phagosome maturation process in macrophage under darkfield microscopy. For this multilayered nanosensor, the gold nanoparticle core plays a role of signal reporter, the MnOx shell and the outmost SiO2 act as the sensing layer and the protecting layer, respectively. After subject to the acidic buffer solution, the MnOx layer in the multilayered nanoprobe could be decomposed rapidly, resulting in a remarkable spectral shift and color change under darkfield microscopy. We demonstrated this nanosensor for the investigation of single phagosome acidification dynamics by monitoring the color changes of nanoprobes after phagocytosis over time. The nanoprobes after phagocytosized in macrophage displayed a slight color change within the first hour and then cost several minutes to change from red to green in the next stage, indicating the phagosome undergoes a slow first and then fast acidification feature as well as a slow-to-fast acidification translation over the phagosome maturation process. Moreover, we validated that the slow-to-fast acidification translation was dependent on the activation of V-ATPase from the ATP depletion assay. We believed that this nanosensor is promising for studying the dynamic acidification features as well as disorders in phagosome maturation in phagocytic cells, which might provide valuable information for understanding the disease pathogenesis related to phagosome dysfunctions.
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Affiliation(s)
- Jinhui Shang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Qian Yang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Wenjun Fan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Yancao Chen
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Decui Tang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Haowei Guo
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Bin Xiong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Shuangyan Huang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Xiao-Bing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
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7
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Yin C, Heit B. Cellular Responses to the Efferocytosis of Apoptotic Cells. Front Immunol 2021; 12:631714. [PMID: 33959122 PMCID: PMC8093429 DOI: 10.3389/fimmu.2021.631714] [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: 11/20/2020] [Accepted: 03/29/2021] [Indexed: 12/17/2022] Open
Abstract
The rapid and efficient phagocytic clearance of apoptotic cells, termed efferocytosis, is a critical mechanism in the maintenance of tissue homeostasis. Removal of apoptotic cells through efferocytosis prevents secondary necrosis and the resultant inflammation caused by the release of intracellular contents. The importance of efferocytosis in homeostasis is underscored by the large number of inflammatory and autoimmune disorders, including atherosclerosis and systemic lupus erythematosus, that are characterized by defective apoptotic cell clearance. Although mechanistically similar to the phagocytic clearance of pathogens, efferocytosis differs from phagocytosis in that it is immunologically silent and induces a tissue repair response. Efferocytes face unique challenges resulting from the internalization of apoptotic cells, including degradation of the apoptotic cell, dealing with the extra metabolic load imposed by the processing of apoptotic cell contents, and the coordination of an anti-inflammatory, pro-tissue repair response. This review will discuss recent advances in our understanding of the cellular response to apoptotic cell uptake, including trafficking of apoptotic cell cargo and antigen presentation, signaling and transcriptional events initiated by efferocytosis, the coordination of an anti-inflammatory response and tissue repair, unique cellular metabolic responses and the role of efferocytosis in host defense. A better understanding of how efferocytic cells respond to apoptotic cell uptake will be critical in unraveling the complex connections between apoptotic cell removal and inflammation resolution and maintenance of tissue homeostasis.
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Affiliation(s)
- Charles Yin
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Center for Human Immunology, Western University, London, ON, Canada
| | - Bryan Heit
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Center for Human Immunology, Western University, London, ON, Canada
- Robarts Research Institute, London, ON, Canada
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8
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Lund VK, Lycas MD, Schack A, Andersen RC, Gether U, Kjaerulff O. Rab2 drives axonal transport of dense core vesicles and lysosomal organelles. Cell Rep 2021; 35:108973. [PMID: 33852866 DOI: 10.1016/j.celrep.2021.108973] [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: 06/05/2020] [Revised: 02/10/2021] [Accepted: 03/19/2021] [Indexed: 12/18/2022] Open
Abstract
Fast axonal transport of neuropeptide-containing dense core vesicles (DCVs), endolysosomal organelles, and presynaptic components is critical for maintaining neuronal functionality. How the transport of DCVs is orchestrated remains an important unresolved question. The small GTPase Rab2 mediates DCV biogenesis and endosome-lysosome fusion. Here, we use Drosophila to demonstrate that Rab2 also plays a critical role in bidirectional axonal transport of DCVs, endosomes, and lysosomal organelles, most likely by controlling molecular motors. We further show that the lysosomal motility factor Arl8 is required as well for axonal transport of DCVs, but unlike Rab2, it is also critical for DCV exit from cell bodies into axons. We also provide evidence that the upstream regulators of Rab2 and Arl8, Ema and BORC, activate these GTPases during DCV transport. Our results uncover the mechanisms underlying axonal transport of DCVs and reveal surprising parallels between the regulation of DCV and lysosomal motility.
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Affiliation(s)
- Viktor Karlovich Lund
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Matthew Domenic Lycas
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Anders Schack
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Rita Chan Andersen
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Ulrik Gether
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Ole Kjaerulff
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark.
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9
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Ghose P, Wehman AM. The developmental and physiological roles of phagocytosis in Caenorhabditis elegans. Curr Top Dev Biol 2020; 144:409-432. [PMID: 33992160 DOI: 10.1016/bs.ctdb.2020.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Phagocytosis is an essential process by which cellular debris and pathogens are cleared from the environment. Cells extend their plasma membrane to engulf objects and contain them within a limiting membrane for isolation from the cytosol or for intracellular degradation in phagolysosomes. The basic mechanisms of phagocytosis and intracellular clearance are well conserved between animals. Indeed, much of our understanding is derived from studies on the nematode worm, Caenorhabditis elegans. Here, we review the latest progress in understanding the mechanisms and functions of phagocytic clearance from C. elegans studies. In particular, we highlight new insights into phagocytic signaling pathways, phagosome formation and phagolysosome resolution, as well as the challenges in studying these cyclic processes.
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Affiliation(s)
- Piya Ghose
- Department of Biology, University of Texas, Arlington, TX, United States.
| | - Ann M Wehman
- Department of Biological Sciences, University of Denver, Denver, CO, United States.
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10
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Serrano-Saiz E, Vogt MC, Levy S, Wang Y, Kaczmarczyk KK, Mei X, Bai G, Singson A, Grant BD, Hobert O. SLC17A6/7/8 Vesicular Glutamate Transporter Homologs in Nematodes. Genetics 2020; 214:163-178. [PMID: 31776169 PMCID: PMC6944403 DOI: 10.1534/genetics.119.302855] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 11/24/2019] [Indexed: 01/04/2023] Open
Abstract
Members of the superfamily of solute carrier (SLC) transmembrane proteins transport diverse substrates across distinct cellular membranes. Three SLC protein families transport distinct neurotransmitters into synaptic vesicles to enable synaptic transmission in the nervous system. Among them is the SLC17A6/7/8 family of vesicular glutamate transporters, which endows specific neuronal cell types with the ability to use glutamate as a neurotransmitter. The genome of the nematode Caenorhabditis elegans encodes three SLC17A6/7/8 family members, one of which, eat-4/VGLUT, has been shown to be involved in glutamatergic neurotransmission. Here, we describe our analysis of the two remaining, previously uncharacterized SLC17A6/7/8 family members, vglu-2 and vglu-3 These two genes directly neighbor one another and are the result of a recent gene duplication event in C. elegans, but not in other Caenorhabditis species. Compared to EAT-4, the VGLU-2 and VGLU-3 protein sequences display a more distant similarity to canonical, vertebrate VGLUT proteins. We tagged both genomic loci with gfp and detected no expression of vglu-3 at any stage of development in any cell type of both C. elegans sexes. In contrast, vglu-2::gfp is dynamically expressed in a restricted set of distinct cell types. Within the nervous system, vglu-2::gfp is exclusively expressed in a single interneuron class, AIA, where it localizes to vesicular structures in the soma, but not along the axon, suggesting that VGLU-2 may not be involved in synaptic transport of glutamate. Nevertheless, vglu-2 mutants are partly defective in the function of the AIA neuron in olfactory behavior. Outside the nervous system, VGLU-2 is expressed in collagen secreting skin cells where VGLU-2 most prominently localizes to early endosomes, and to a lesser degree to apical clathrin-coated pits, the trans-Golgi network, and late endosomes. On early endosomes, VGLU-2 colocalizes most strongly with the recycling promoting factor SNX-1, a retromer component. Loss of vglu-2 affects the permeability of the collagen-containing cuticle of the worm, and based on the function of a vertebrate VGLUT1 protein in osteoclasts, we speculate that vglu-2 may have a role in collagen trafficking in the skin. We conclude that C. elegans SLC17A6/7/8 family members have diverse functions within and outside the nervous system.
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Affiliation(s)
- Esther Serrano-Saiz
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, New York 10027
- Centro de Biologia Molecular Severo Ochoa/Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Merly C Vogt
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, New York 10027
| | - Sagi Levy
- Rockefeller University, New York, New York 10065
| | - Yu Wang
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854
| | - Karolina K Kaczmarczyk
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, New York 10027
| | - Xue Mei
- Waksman Institute, Rutgers University, Piscataway, New Jersey 08854
| | - Ge Bai
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854
| | - Andrew Singson
- Waksman Institute, Rutgers University, Piscataway, New Jersey 08854
- Department of Genetics, Rutgers University, Piscataway, New Jersey 08854
| | - Barth D Grant
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854
| | - Oliver Hobert
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, New York 10027
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11
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Clarifying the function of genes at the chromosome 16p13 locus in type 1 diabetes: CLEC16A and DEXI. Genes Immun 2019; 21:79-82. [PMID: 31570815 DOI: 10.1038/s41435-019-0087-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 09/09/2019] [Accepted: 09/18/2019] [Indexed: 01/07/2023]
Abstract
More than a decade after the discovery of a novel type 1 diabetes risk locus on chromosome 16p13, there remains complexity and controversy over the specific gene(s) that regulate diabetes pathogenesis. A new study by Nieves-Bonilla et al. shows that one of these genes, DEXI, is unlikely to contribute to type 1 diabetes pathogenesis and positions the endolysosomal E3 ubiquitin ligase CLEC16A as the primary culprit by which this gene locus influences diabetes risk.
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12
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Gillingham AK, Bertram J, Begum F, Munro S. In vivo identification of GTPase interactors by mitochondrial relocalization and proximity biotinylation. eLife 2019; 8:45916. [PMID: 31294692 PMCID: PMC6639074 DOI: 10.7554/elife.45916] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 07/10/2019] [Indexed: 12/11/2022] Open
Abstract
The GTPases of the Ras superfamily regulate cell growth, membrane traffic and the cytoskeleton, and a wide range of diseases are caused by mutations in particular members. They function as switchable landmarks with the active GTP-bound form recruiting to the membrane a specific set of effector proteins. The GTPases are precisely controlled by regulators that promote acquisition of GTP (GEFs) or its hydrolysis to GDP (GAPs). We report here MitoID, a method for identifying effectors and regulators by performing in vivo proximity biotinylation with mitochondrially-localized forms of the GTPases. Applying this to 11 human Rab GTPases identified many known effectors and GAPs, as well as putative novel effectors, with examples of the latter validated for Rab2, Rab5, Rab9 and Rab11. MitoID can also efficiently identify effectors and GAPs of Rho and Ras family GTPases such as Cdc42, RhoA, Rheb, and N-Ras, and can identify GEFs by use of GDP-bound forms.
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Affiliation(s)
| | - Jessie Bertram
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Farida Begum
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Sean Munro
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
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13
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Ding X, Jiang X, Tian R, Zhao P, Li L, Wang X, Chen S, Zhu Y, Mei M, Bao S, Liu W, Tang Z, Sun Q. RAB2 regulates the formation of autophagosome and autolysosome in mammalian cells. Autophagy 2019; 15:1774-1786. [PMID: 30957628 PMCID: PMC6735470 DOI: 10.1080/15548627.2019.1596478] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Multiple sources contribute membrane and protein machineries to construct functional macroautophagic/autophagic structures. However, the underlying molecular mechanisms remain elusive. Here, we show that RAB2 connects the Golgi network to autophagy pathway by delivering membrane and by sequentially engaging distinct autophagy machineries. In unstressed cells, RAB2 resides primarily in the Golgi apparatus, as evidenced by its interaction and colocalization with GOLGA2/GM130. Importantly, autophagy stimuli dissociate RAB2 from GOLGA2 to interact with ULK1 complex, which facilitates the recruitment of ULK1 complex to form phagophores. Intriguingly, RAB2 appears to modulate ULK1 kinase activity to propagate signals for autophagosome formation. Subsequently, RAB2 switches to interact with autophagosomal RUBCNL/PACER and STX17 to further specify the recruitment of HOPS complex for autolysosome formation. Together, our study reveals a multivalent pathway in bulk autophagy regulation, and provides mechanistic insights into how the Golgi apparatus contributes to the formation of different autophagic structures. Abbreviations: ACTB: actin beta; ATG9: autophagy related 9A; ATG14: autophagy related 14; ATG16L1: autophagy related 16 like 1; BCAP31: B cell receptor associated protein 31; BECN1: beclin 1; Ctrl: control; CQ: chloroquine; CTSD: cathepsin D; DMSO: dimethyl sulfoxide; EBSS: Earle’s balanced salt solution; EEA1: early endosome antigen 1; GDI: guanine nucleotide dissociation inhibitor; GFP: green fluorescent protein; GOLGA2: golgin A2; HOPS: homotypic fusion and protein sorting complex; IP: immunoprecipitation; KD: knockdown; KO: knockout; LAMP1: lysosomal associated membrane protein 1; LC3: microtubule-associated protein 1 light chain 3; OE: overexpression; PtdIns3K: class III phosphatidylinositol 3-kinase; SQSTM1/p62: sequestosome 1; RAB2: RAB2A, member RAS oncogene family; RAB7: RAB7A, member RAS oncogene family; RAB11: RAB11A, member RAS oncogene family; RUBCNL/PACER: rubicon like autophagy enhancer; STX17: syntaxin 17; TBC1D14: TBC1 domain family member 14; TFRC: transferrin receptor; TGOLN2: trans-golgi network protein 2; TUBB: tubulin beta class I; ULK1: unc-51 like autophagy activating kinase 1; VPS41: VPS41, HOPS complex subunit; WB: western blot; WT: wild type; YPT1: GTP-binding protein YPT1.
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Affiliation(s)
- Xianming Ding
- Department of Biochemistry, and Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine , Hangzhou , China
| | - Xiao Jiang
- Department of Biochemistry, and Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine , Hangzhou , China
| | - Rui Tian
- Department of Biochemistry, and Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine , Hangzhou , China
| | - Pengwei Zhao
- Department of Biochemistry, and Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine , Hangzhou , China
| | - Lin Li
- Proteomics Center, National Institute of Biological Sciences , Beijing , China
| | - Xinyi Wang
- Department of Biochemistry, and Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine , Hangzhou , China
| | - She Chen
- Proteomics Center, National Institute of Biological Sciences , Beijing , China
| | - Yushan Zhu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, College of Life Sciences, Nankai University , Tianjin , China
| | - Mei Mei
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences , Beijing , China
| | - Shilai Bao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences , Beijing , China
| | - Wei Liu
- Department of Biochemistry, and Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine , Hangzhou , China
| | - Zaiming Tang
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University , Shanghai , China
| | - Qiming Sun
- Department of Biochemistry, and Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine , Hangzhou , China
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14
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Morris C, Foster OK, Handa S, Peloza K, Voss L, Somhegyi H, Jian Y, Vo MV, Harp M, Rambo FM, Yang C, Hermann GJ. Function and regulation of the Caenorhabditis elegans Rab32 family member GLO-1 in lysosome-related organelle biogenesis. PLoS Genet 2018; 14:e1007772. [PMID: 30419011 PMCID: PMC6268011 DOI: 10.1371/journal.pgen.1007772] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 11/30/2018] [Accepted: 10/17/2018] [Indexed: 02/07/2023] Open
Abstract
Cell type-specific modifications of conventional endosomal trafficking pathways lead to the formation of lysosome-related organelles (LROs). C. elegans gut granules are intestinally restricted LROs that coexist with conventional degradative lysosomes. The formation of gut granules requires the Rab32 family member GLO-1. We show that the loss of glo-1 leads to the mistrafficking of gut granule proteins but does not significantly alter conventional endolysosome biogenesis. GLO-3 directly binds to CCZ-1 and they both function to promote the gut granule association of GLO-1, strongly suggesting that together, GLO-3 and CCZ-1 activate GLO-1. We found that a point mutation in GLO-1 predicted to spontaneously activate, and function independently of it guanine nucleotide exchange factor (GEF), localizes to gut granules and partially restores gut granule protein localization in ccz-1(-) and glo-3(-) mutants. CCZ-1 forms a heterodimeric complex with SAND-1(MON1), which does not function in gut granule formation, to activate RAB-7 in trafficking pathways to conventional lysosomes. Therefore, our data suggest a model whereby the function of a Rab GEF can be altered by subunit exchange. glo-3(-) mutants, which retain low levels of GLO-3 activity, generate gut granules that lack GLO-1 and improperly accumulate RAB-7 in a SAND-1 dependent process. We show that GLO-1 and GLO-3 restrict the distribution of RAB-7 to conventional endolysosomes, providing insights into the segregation of pathways leading to conventional lysosomes and LROs.
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Affiliation(s)
- Caitlin Morris
- Department of Biology, Lewis & Clark College, Portland, Oregon, United States of America
| | - Olivia K. Foster
- Department of Biology, Lewis & Clark College, Portland, Oregon, United States of America
| | - Simran Handa
- Department of Biology, Lewis & Clark College, Portland, Oregon, United States of America
| | - Kimberly Peloza
- Department of Biology, Lewis & Clark College, Portland, Oregon, United States of America
| | - Laura Voss
- Department of Biology, Lewis & Clark College, Portland, Oregon, United States of America
| | - Hannah Somhegyi
- Department of Biology, Lewis & Clark College, Portland, Oregon, United States of America
| | - Youli Jian
- State Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - My Van Vo
- Department of Biology, Lewis & Clark College, Portland, Oregon, United States of America
| | - Marie Harp
- Department of Biology, Lewis & Clark College, Portland, Oregon, United States of America
| | - Fiona M. Rambo
- Department of Biology, Lewis & Clark College, Portland, Oregon, United States of America
| | - Chonglin Yang
- State Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Greg J. Hermann
- Department of Biology, Lewis & Clark College, Portland, Oregon, United States of America
- * E-mail:
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15
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Abstract
Phagosomes form during engulfment of large particles and become increasingly acidic and proteolytic, ultimately fusing with lysosomes, in a process termed "phagosome maturation." In this issue, Yin et al. (2017. J. Cell Biol. https://doi.org/10.1083/jcb.201610001) identify GOP-1 as essential for the maturation of phagosomes containing apoptotic cells, through recruitment of the Rab GTPase UNC108.
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Affiliation(s)
- Lynda M Stuart
- Immunology Program, Benaroya Research Institute, Bill and Melinda Gates Foundation, Seattle, WA .,Discovery and Translational Sciences, Bill and Melinda Gates Foundation, Seattle, WA
| | - Adam Lacy-Hulbert
- Immunology Program, Benaroya Research Institute, Bill and Melinda Gates Foundation, Seattle, WA
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