1
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Lu Q, Zhu Z, Zhang J, Xu C. Structure of GDP-bound Rab7 Q67L in complex with ORP1L. Biochem Biophys Res Commun 2024; 725:150232. [PMID: 38897042 DOI: 10.1016/j.bbrc.2024.150232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 06/21/2024]
Abstract
Molecular processes are orchestrated by various proteins that promote early endosomes to become late endosomes and eventually fuse with lysosomes, guaranteeing the degradation of the content. Rab7, which is localized to late endosomes, is one of the most well-known GTPases. ORP1L is recruited by Rab7 to facilitate the fusion of late endosomes and lysosomes. Here, we present the structure of GDP-bound Rab7 Q67L with ORP1L. Structural analysis, supported by biochemical and ITC binding experiments, not only provides structural insight into the interactions between the ORP1L ANK domain and Rab7 but also suggests that the GTPase activity of Rab7 does not interfere with its ORP1L-binding capacity.
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Affiliation(s)
- Qian Lu
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, PR China
| | - Zhongliang Zhu
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, PR China
| | - Jiahai Zhang
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, PR China.
| | - Chao Xu
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, PR China.
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2
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Han Y, Liu X, Xu L, Wei Z, Gu Y, Ren Y, Hua W, Zhang Y, Liu X, Jiang C, Zhuang R, Hong W, Wang T. RILP Induces Cholesterol Accumulation in Lysosomes by Inhibiting Endoplasmic Reticulum-Endolysosome Interactions. Cells 2024; 13:1313. [PMID: 39195203 DOI: 10.3390/cells13161313] [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: 06/03/2024] [Revised: 07/26/2024] [Accepted: 07/28/2024] [Indexed: 08/29/2024] Open
Abstract
Endoplasmic reticulum (ER)-endolysosome interactions regulate cholesterol exchange between the ER and the endolysosome. ER-endolysosome membrane contact sites mediate the ER-endolysosome interaction. VAP-ORP1L (vesicle-associated membrane protein-associated protein- OSBP-related protein 1L) interaction forms the major contact site between the ER and the lysosome, which is regulated by Rab7. RILP (Rab7-interacting lysosomal protein) is the downstream effector of Rab7, but its role in the organelle interaction between the ER and the lysosome is not clear. In this study, we found RILP interacts with ORP1L to competitively inhibit the formation of the VAP-ORP1L contact site. Immunofluorescence microscopy revealed that RILP induces late endosome/lysosome clustering, which reduces the contact of endolysosomes with the ER, interfering with the ER-endolysosome interaction. Further examination demonstrated that over-expression of RILP results in the accumulation of cholesterol in the clustered endolysosomes, which triggers cellular autophagy depending on RILP. Our results suggest that RILP interferes with the ER-endolysosome interaction to inhibit cholesterol flow from the endolysosome to the ER, which feedbacks to trigger autophagy.
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Affiliation(s)
- Yang Han
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen 361102, China
| | - Xiaoqing Liu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen 361102, China
| | - Liju Xu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen 361102, China
| | - Ziheng Wei
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen 361102, China
| | - Yueting Gu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen 361102, China
| | - Yandan Ren
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen 361102, China
| | - Wenyi Hua
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen 361102, China
| | - Yongtao Zhang
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen 361102, China
| | - Xiaoxi Liu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen 361102, China
| | - Cong Jiang
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen 361102, China
| | - Ruijuan Zhuang
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen 361102, China
| | - Wanjin Hong
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen 361102, China
- Institute of Molecular and Cell Biology, A*STAR (Agency of Science, Technology and Research), Singapore 138673, Singapore
| | - Tuanlao Wang
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen 361102, China
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3
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Chen L, Zhang J, Xu W, Chen J, Tang Y, Xiong S, Li Y, Zhang H, Li M, Liu Z. Cholesterol-rich lysosomes induced by respiratory syncytial virus promote viral replication by blocking autophagy flux. Nat Commun 2024; 15:6311. [PMID: 39060258 PMCID: PMC11282085 DOI: 10.1038/s41467-024-50711-4] [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: 10/19/2023] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
Respiratory syncytial virus (RSV) hijacks cholesterol or autophagy pathways to facilitate optimal replication. However, our understanding of the associated molecular mechanisms remains limited. Here, we show that RSV infection blocks cholesterol transport from lysosomes to the endoplasmic reticulum by downregulating the activity of lysosomal acid lipase, activates the SREBP2-LDLR axis, and promotes uptake and accumulation of exogenous cholesterol in lysosomes. High cholesterol levels impair the VAP-A-binding activity of ORP1L and promote the recruitment of dynein-dynactin, PLEKHM1, or HOPS VPS39 to Rab7-RILP, thereby facilitating minus-end transport of autophagosomes and autolysosome formation. Acidification inhibition and dysfunction of cholesterol-rich lysosomes impair autophagy flux by inhibiting autolysosome degradation, which promotes the accumulation of RSV fusion protein. RSV-F storage is nearly abolished after cholesterol depletion or knockdown of LDLR. Most importantly, the knockout of LDLR effectively inhibits RSV infection in vivo. These findings elucidate the molecular mechanism of how RSV co-regulates lysosomal cholesterol reprogramming and autophagy and reveal LDLR as a novel target for anti-RSV drug development.
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Affiliation(s)
- Lifeng Chen
- State Key Laboratory of Bioactive Molecules and Druggability Assessment & College of Pharmacy, Jinan University, Guangzhou, China
- Department of Dermatology, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Jingjing Zhang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment & College of Pharmacy, Jinan University, Guangzhou, China
| | - Weibin Xu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment & College of Pharmacy, Jinan University, Guangzhou, China
| | - Jiayi Chen
- State Key Laboratory of Bioactive Molecules and Druggability Assessment & College of Pharmacy, Jinan University, Guangzhou, China
| | - Yujun Tang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment & College of Pharmacy, Jinan University, Guangzhou, China
| | - Si Xiong
- State Key Laboratory of Bioactive Molecules and Druggability Assessment & College of Pharmacy, Jinan University, Guangzhou, China
| | - Yaolan Li
- State Key Laboratory of Bioactive Molecules and Druggability Assessment & College of Pharmacy, Jinan University, Guangzhou, China
| | - Hong Zhang
- Department of Dermatology, The First Affiliated Hospital, Jinan University, Guangzhou, China.
| | - Manmei Li
- State Key Laboratory of Bioactive Molecules and Druggability Assessment & College of Pharmacy, Jinan University, Guangzhou, China.
| | - Zhong Liu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment & College of Pharmacy, Jinan University, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Bioengineering Medicine & College of Life Science and Technology, Jinan University, Guangzhou, China.
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4
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Mulligan RJ, Magaj MM, Digilio L, Redemann S, Yap CC, Winckler B. Collapse of late endosomal pH elicits a rapid Rab7 response via the V-ATPase and RILP. J Cell Sci 2024; 137:jcs261765. [PMID: 38578235 PMCID: PMC11166203 DOI: 10.1242/jcs.261765] [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: 11/02/2023] [Accepted: 03/26/2024] [Indexed: 04/06/2024] Open
Abstract
Endosomal-lysosomal trafficking is accompanied by the acidification of endosomal compartments by the H+-V-ATPase to reach low lysosomal pH. Disruption of the correct pH impairs lysosomal function and the balance of protein synthesis and degradation (proteostasis). Here, we treated mammalian cells with the small dipeptide LLOMe, which is known to permeabilize lysosomal membranes, and find that LLOMe also impacts late endosomes (LEs) by neutralizing their pH without causing membrane permeabilization. We show that LLOMe leads to hyperactivation of Rab7 (herein referring to Rab7a), and disruption of tubulation and mannose-6-phosphate receptor (CI-M6PR; also known as IGF2R) recycling on pH-neutralized LEs. pH neutralization (NH4Cl) and expression of Rab7 hyperactive mutants alone can both phenocopy the alterations in tubulation and CI-M6PR trafficking. Mechanistically, pH neutralization increases the assembly of the V1G1 subunit (encoded by ATP6V1G1) of the V-ATPase on endosomal membranes, which stabilizes GTP-bound Rab7 via RILP, a known interactor of Rab7 and V1G1. We propose a novel pathway by which V-ATPase and RILP modulate LE pH and Rab7 activation in concert. This pathway might broadly contribute to pH control during physiologic endosomal maturation or starvation and during pathologic pH neutralization, which occurs via lysosomotropic compounds and in disease states.
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Affiliation(s)
- Ryan J. Mulligan
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908, USA
- Cell and Developmental Biology Graduate Program, University of Virginia, Charlottesville, VA 22908, USA
- Medical Scientist Training Program, University of Virginia, Charlottesville, VA 22908, USA
| | - Magdalena M. Magaj
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
- Cell and Developmental Biology Graduate Program, University of Virginia, Charlottesville, VA 22908, USA
| | - Laura Digilio
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908, USA
| | - Stefanie Redemann
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA
| | - Chan Choo Yap
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908, USA
| | - Bettina Winckler
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908, USA
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5
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Mulligan R, Magaj M, Digilio L, Redemann S, Yap C, Winckler B. Collapse of late endosomal pH elicits a rapid Rab7 response via V-ATPase and RILP. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.24.563658. [PMID: 37961579 PMCID: PMC10634777 DOI: 10.1101/2023.10.24.563658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Endosomal-lysosomal trafficking is accompanied by the acidification of endosomal compartments by the H+-V-ATPase to reach low lysosomal pH. Disruption of proper pH impairs lysosomal function and the balance of protein synthesis and degradation (proteostasis). We used the small dipeptide LLOMe, which is known to permeabilize lysosomal membranes, and find that LLOMe also impacts late endosomes (LEs) by neutralizing their pH without causing membrane permeabilization. We show that LLOMe leads to hyper-activation of Rab7 and disruption of tubulation and mannose-6-phosphate receptor (CI-M6PR) recycling on pH-neutralized LEs. Either pH neutralization (NH4Cl) or Rab7 hyper-active mutants alone can phenocopy the alterations in tubulation and CI-M6PR trafficking. Mechanistically, pH neutralization increases the assembly of the V1G1 subunit of the V-ATPase on endosomal membranes, which stabilizes GTP-bound Rab7 via RILP, a known interactor of Rab7 and V1G1. We propose a novel pathway by which V-ATPase and RILP modulate LE pH and Rab7 activation in concert. This pathway might broadly contribute to pH control during physiologic endosomal maturation or starvation and during pathologic pH neutralization, which occurs via lysosomotropic compounds or in disease states.
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Affiliation(s)
- R.J. Mulligan
- Department of Cell Biology, University of Virginia, Charlottesville, VA
- Cell and Developmental Biology Graduate Program, University of Virginia, Charlottesville, VA
- Medical Scientist Training Program, University of Virginia, Charlottesville, VA
| | - M.M. Magaj
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville VA
- Cell and Developmental Biology Graduate Program, University of Virginia, Charlottesville, VA
| | - L. Digilio
- Department of Cell Biology, University of Virginia, Charlottesville, VA
| | - S. Redemann
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville VA
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA
| | - C.C. Yap
- Department of Cell Biology, University of Virginia, Charlottesville, VA
| | - B Winckler
- Department of Cell Biology, University of Virginia, Charlottesville, VA
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6
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Diao J, Yip CK, Zhong Q. Molecular structures and function of the autophagosome-lysosome fusion machinery. AUTOPHAGY REPORTS 2024; 3:2305594. [PMID: 38344192 PMCID: PMC10852212 DOI: 10.1080/27694127.2024.2305594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/09/2024] [Indexed: 02/15/2024]
Abstract
Macroautophagy (also known as autophagy) plays a pivotal role in maintaining cellular homeostasis. The terminal step of the multi-step autophagy degradation pathway involves fusion between the cargo-laden, double-membraned autophagosome and the lytic organelle lysosome/vacuole. Over the past decade, various core components of the molecular machinery that execute this critical terminal autophagy event have been identified. This review highlights recent advances in understanding the molecular structures, biochemical functions, and regulatory mechanisms of key components of this highly sophisticated machinery including the SNARE fusogens, tethering factors, Rab GTPases and associated guanine nucleotide exchange factors, and other accessory factors.
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Affiliation(s)
- Jiajie Diao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, U.S.A
| | - Calvin K. Yip
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Qing Zhong
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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7
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Steinbach AM, Bhadkamkar VL, Jimenez-Morales D, Stevenson E, Jang GM, Krogan NJ, Swaney DL, Mukherjee S. Cross-family small GTPase ubiquitination by the intracellular pathogen Legionella pneumophila. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551750. [PMID: 37577546 PMCID: PMC10418220 DOI: 10.1101/2023.08.03.551750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
The intracellular bacterial pathogen Legionella pneumophila (L.p.) manipulates eukaryotic host ubiquitination machinery to form its replicative vacuole. While nearly 10% of L.p.'s arsenal of ~330 secreted effector proteins have been biochemically characterized as ubiquitin ligases or deubiquitinases, a comprehensive measure of temporally resolved changes in the endogenous host ubiquitinome during infection has not been undertaken. To elucidate how L.p hijacks ubiquitin signaling within the host cell, we undertook a proteome-wide analysis of changes in protein ubiquitination during infection. We discover that L.p. infection results in increased ubiquitination of host proteins regulating subcellular trafficking and membrane dynamics, most notably 63 of ~160 mammalian Ras superfamily small GTPases. We determine that these small GTPases predominantly undergo non-degradative monoubiquitination, and link ubiquitination to recruitment to the Legionella-containing vacuole membrane. Finally, we find that the bacterial effectors SidC/SdcA play a central, but likely indirect, role in cross-family small GTPase ubiquitination. This work highlights the extensive reconfiguration of host ubiquitin signaling by bacterial effectors during infection and establishes simultaneous ubiquitination of small GTPases across the Ras superfamily as a novel consequence of L.p. infection. This work positions L.p. as a tool to better understand how small GTPases can be regulated by ubiquitination in uninfected contexts.
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Affiliation(s)
- Adriana M. Steinbach
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
- George Williams Hooper Foundation, University of California, San Francisco, San Francisco, California, United States of America
| | - Varun L. Bhadkamkar
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
- George Williams Hooper Foundation, University of California, San Francisco, San Francisco, California, United States of America
| | - David Jimenez-Morales
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, United States of America
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, California, United States of America
| | - Erica Stevenson
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, United States of America
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
- Quantitative Biosciences Institute, University of California, San Francisco, California, United States of America
| | - Gwendolyn M. Jang
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, United States of America
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
- Quantitative Biosciences Institute, University of California, San Francisco, California, United States of America
| | - Nevan J. Krogan
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, United States of America
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
- Quantitative Biosciences Institute, University of California, San Francisco, California, United States of America
| | - Danielle L. Swaney
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, United States of America
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
- Quantitative Biosciences Institute, University of California, San Francisco, California, United States of America
| | - Shaeri Mukherjee
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
- George Williams Hooper Foundation, University of California, San Francisco, San Francisco, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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8
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Cui G, Jiang Z, Chen Y, Li Y, Ai S, Sun R, Yi X, Zhong G. Evolutional insights into the interaction between Rab7 and RILP in lysosome motility. iScience 2023; 26:107040. [PMID: 37534141 PMCID: PMC10391735 DOI: 10.1016/j.isci.2023.107040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 12/12/2022] [Accepted: 06/01/2023] [Indexed: 08/04/2023] Open
Abstract
Lysosome motility is critical for the cellular function. However, Rab7-related transport elements showed genetic differences between vertebrates and invertebrates, making the mechanism of lysosomal motility mysterious. We suggested that Rab7 interacted with RILP as a feature of highly evolved organisms since they could interact with each other in Spodoptera frugiperda but not in Drosophila melanogaster. The N-terminus of Sf-RILP was identified to be necessary for their interaction, and Glu61 was supposed to be the key point for the stability of the interaction. A GC-rich domain on the C-terminal parts of Sf-RILP hampered the expression of Sf-RILP and its interaction with Sf-Rab7. Although the corresponding vital amino acids in the mammalian model at the C-terminus of Sf-RILP turned to be neutral, the C-terminus would also help with the homologous interactions between RILP fragments in insects. The significantly different interactions in invertebrates shed light on the biodiversity and complexity of lysosomal motility.
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Affiliation(s)
- Gaofeng Cui
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, China
| | - Zhiyan Jiang
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Yaoyao Chen
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Yun Li
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Shupei Ai
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Ranran Sun
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Xin Yi
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Guohua Zhong
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
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9
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Vöing K, Michgehl U, Mertens ND, Picciotto C, Maywald ML, Goretzko J, Waimann S, Gilhaus K, Rogg M, Schell C, Klingauf J, Tsytsyura Y, Hansen U, van Marck V, Edinger AL, Vollenbröker B, Rescher U, Braun DA, George B, Weide T, Pavenstädt H. Disruption of the Rab7-Dependent Final Common Pathway of Endosomal and Autophagic Processing Results in a Severe Podocytopathy. J Am Soc Nephrol 2023; 34:1191-1206. [PMID: 37022133 PMCID: PMC10356157 DOI: 10.1681/asn.0000000000000126] [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: 10/26/2022] [Accepted: 03/03/2023] [Indexed: 04/07/2023] Open
Abstract
SIGNIFICANCE STATEMENT Endocytosis, recycling, and degradation of proteins are essential functions of mammalian cells, especially for terminally differentiated cells with limited regeneration rates and complex morphology, such as podocytes. To improve our understanding on how disturbances of these trafficking pathways are linked to podocyte depletion and slit diaphragm (SD) injury, the authors explored the role of the small GTPase Rab7, which is linked to endosomal, lysosomal, and autophagic pathways, using as model systems mice and Drosophila with podocyte-specific or nephrocyte-specific loss of Rab7, and a human podocyte cell line depleted for Rab7. Their findings point to maturation and fusion events during endolysosomal and autophagic maturation as key processes for podocyte homeostasis and function and identify altered lysosomal pH values as a putative novel mechanism for podocytopathies. BACKGROUND Endocytosis, recycling, and degradation of proteins are essential functions of mammalian cells, especially for terminally differentiated cells with limited regeneration rates, such as podocytes. How disturbances within these trafficking pathways may act as factors in proteinuric glomerular diseases is poorly understood. METHODS To explore how disturbances in trafficking pathways may act as factors in proteinuric glomerular diseases, we focused on Rab7, a highly conserved GTPase that controls the homeostasis of late endolysosomal and autophagic processes. We generated mouse and Drosophila in vivo models lacking Rab7 exclusively in podocytes or nephrocytes, and performed histologic and ultrastructural analyses. To further investigate Rab7 function on lysosomal and autophagic structures, we used immortalized human cell lines depleted for Rab7. RESULTS Depletion of Rab7 in mice, Drosophila , and immortalized human cell lines resulted in an accumulation of diverse vesicular structures resembling multivesicular bodies, autophagosomes, and autoendolysosomes. Mice lacking Rab7 developed a severe and lethal renal phenotype with early-onset proteinuria and global or focal segmental glomerulosclerosis, accompanied by an altered distribution of slit diaphragm proteins. Remarkably, structures resembling multivesicular bodies began forming within 2 weeks after birth, prior to the glomerular injuries. In Drosophila nephrocytes, Rab7 knockdown resulted in the accumulation of vesicles and reduced slit diaphragms. In vitro , Rab7 knockout led to similar enlarged vesicles and altered lysosomal pH values, accompanied by an accumulation of lysosomal marker proteins. CONCLUSIONS Disruption within the final common pathway of endocytic and autophagic processes may be a novel and insufficiently understood mechanism regulating podocyte health and disease.
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Affiliation(s)
- Kristin Vöing
- Department of Internal Medicine and Nephrology, University Hospital of Münster, Medical Clinic D, Munster, Germany
| | - Ulf Michgehl
- Department of Internal Medicine and Nephrology, University Hospital of Münster, Medical Clinic D, Munster, Germany
| | - Nils David Mertens
- Department of Internal Medicine and Nephrology, University Hospital of Münster, Medical Clinic D, Munster, Germany
| | - Cara Picciotto
- Department of Internal Medicine and Nephrology, University Hospital of Münster, Medical Clinic D, Munster, Germany
| | - Mee-Ling Maywald
- Department of Internal Medicine and Nephrology, University Hospital of Münster, Medical Clinic D, Munster, Germany
| | - Jonas Goretzko
- Research Group Regulatory Mechanisms of Inflammation, Institute of Medical Biochemistry, Centre for Molecular Biology of Inflammation, University of Muenster, Muenster, Germany
| | - Sofie Waimann
- Department of Internal Medicine and Nephrology, University Hospital of Münster, Medical Clinic D, Munster, Germany
| | - Kevin Gilhaus
- Department of Internal Medicine and Nephrology, University Hospital of Münster, Medical Clinic D, Munster, Germany
| | - Manuel Rogg
- Institute of Surgical Pathology, Faculty of Medicine, Medical Center-University of Freiburg, Freiburg, Germany
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany
| | - Christoph Schell
- Institute of Surgical Pathology, Faculty of Medicine, Medical Center-University of Freiburg, Freiburg, Germany
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany
| | - Jürgen Klingauf
- Institute of Medical Physics and Biophysics, University of Muenster, Muenster, Germany
| | - Yaroslav Tsytsyura
- Institute of Medical Physics and Biophysics, University of Muenster, Muenster, Germany
| | - Uwe Hansen
- Institute for Musculoskeletal Medicine (IMM), University of Muenster, Muenster, Germany
| | - Veerle van Marck
- Department of Pathology, University Hospital Muenster Muenster, Germany
| | - Aimee L. Edinger
- Department of Developmental & Cell Biology, University of California, Irvine, California
| | - Beate Vollenbröker
- Department of Internal Medicine and Nephrology, University Hospital of Münster, Medical Clinic D, Munster, Germany
| | - Ursula Rescher
- Research Group Regulatory Mechanisms of Inflammation, Institute of Medical Biochemistry, Centre for Molecular Biology of Inflammation, University of Muenster, Muenster, Germany
| | - Daniela Anne Braun
- Department of Internal Medicine and Nephrology, University Hospital of Münster, Medical Clinic D, Munster, Germany
| | - Britta George
- Department of Internal Medicine and Nephrology, University Hospital of Münster, Medical Clinic D, Munster, Germany
| | - Thomas Weide
- Department of Internal Medicine and Nephrology, University Hospital of Münster, Medical Clinic D, Munster, Germany
| | - Hermann Pavenstädt
- Department of Internal Medicine and Nephrology, University Hospital of Münster, Medical Clinic D, Munster, Germany
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10
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Yong X, Jia G, Liu Z, Zhou C, Yi J, Tang Y, Chen L, Chen L, Wang Y, Sun Q, Billadeau D, Su Z, Jia D. Cryo-EM structure of the Mon1-Ccz1-RMC1 complex reveals molecular basis of metazoan RAB7A activation. Proc Natl Acad Sci U S A 2023; 120:e2301725120. [PMID: 37216550 PMCID: PMC10235969 DOI: 10.1073/pnas.2301725120] [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: 02/07/2023] [Accepted: 04/18/2023] [Indexed: 05/24/2023] Open
Abstract
Understanding of the evolution of metazoans from their unicellular ancestors is a fundamental question in biology. In contrast to fungi which utilize the Mon1-Ccz1 dimeric complex to activate the small GTPase RAB7A, metazoans rely on the Mon1-Ccz1-RMC1 trimeric complex. Here, we report a near-atomic resolution cryogenic-electron microscopy structure of the Drosophila Mon1-Ccz1-RMC1 complex. RMC1 acts as a scaffolding subunit and binds to both Mon1 and Ccz1 on the surface opposite to the RAB7A-binding site, with many of the RMC1-contacting residues from Mon1 and Ccz1 unique to metazoans, explaining the binding specificity. Significantly, the assembly of RMC1 with Mon1-Ccz1 is required for cellular RAB7A activation, autophagic functions and organismal development in zebrafish. Our studies offer a molecular explanation for the different degree of subunit conservation across species, and provide an excellent example of how metazoan-specific proteins take over existing functions in unicellular organisms.
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Affiliation(s)
- Xin Yong
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu610041, China
| | - Guowen Jia
- Department of Geriatrics and National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University610044Chengdu, China
| | - Zhe Liu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu610041, China
| | - Chunzhuang Zhou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu610041, China
| | - Jiamin Yi
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu610041, China
| | - Yingying Tang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu610041, China
| | - Li Chen
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu610041, China
| | - Lu Chen
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu610041, China
| | - Yuan Wang
- Department of Geriatrics and National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University610044Chengdu, China
| | - Qingxiang Sun
- Department of Geriatrics and National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University610044Chengdu, China
| | - Daniel D. Billadeau
- Division of Oncology Research and Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, MN55905
| | - Zhaoming Su
- Department of Geriatrics and National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University610044Chengdu, China
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu610041, China
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11
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Hertel A, Alves LM, Dutz H, Tascher G, Bonn F, Kaulich M, Dikic I, Eimer S, Steinberg F, Bremm A. USP32-regulated LAMTOR1 ubiquitination impacts mTORC1 activation and autophagy induction. Cell Rep 2022; 41:111653. [PMID: 36476874 DOI: 10.1016/j.celrep.2022.111653] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 08/16/2022] [Accepted: 10/20/2022] [Indexed: 12/12/2022] Open
Abstract
The endosomal-lysosomal system is a series of organelles in the endocytic pathway that executes trafficking and degradation of proteins and lipids and mediates the internalization of nutrients and growth factors to ensure cell survival, growth, and differentiation. Here, we reveal regulatory, non-proteolytic ubiquitin signals in this complex system that are controlled by the enigmatic deubiquitinase USP32. Knockout (KO) of USP32 in primary hTERT-RPE1 cells results among others in hyperubiquitination of the Ragulator complex subunit LAMTOR1. Accumulation of LAMTOR1 ubiquitination impairs its interaction with the vacuolar H+-ATPase, reduces Ragulator function, and ultimately limits mTORC1 recruitment. Consistently, in USP32 KO cells, less mTOR kinase localizes to lysosomes, mTORC1 activity is decreased, and autophagy is induced. Furthermore, we demonstrate that depletion of USP32 homolog CYK-3 in Caenorhabditis elegans results in mTOR inhibition and autophagy induction. In summary, we identify a control mechanism of the mTORC1 activation cascade at lysosomes via USP32-regulated LAMTOR1 ubiquitination.
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Affiliation(s)
- Alexandra Hertel
- Institute of Biochemistry II, Goethe University Frankfurt - Medical Faculty, University Hospital, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Ludovico Martins Alves
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Henrik Dutz
- Center for Biological Systems Analysis, University of Freiburg, Habsburgerstr. 49, 79104 Freiburg, Germany
| | - Georg Tascher
- Institute of Biochemistry II, Goethe University Frankfurt - Medical Faculty, University Hospital, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Florian Bonn
- Institute of Biochemistry II, Goethe University Frankfurt - Medical Faculty, University Hospital, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Manuel Kaulich
- Institute of Biochemistry II, Goethe University Frankfurt - Medical Faculty, University Hospital, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Frankfurt Cancer Institute, 60596 Frankfurt am Main, Germany; Cardio-Pulmonary Institute, 60590 Frankfurt am Main, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Goethe University Frankfurt - Medical Faculty, University Hospital, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany; Frankfurt Cancer Institute, 60596 Frankfurt am Main, Germany; Cardio-Pulmonary Institute, 60590 Frankfurt am Main, Germany
| | - Stefan Eimer
- Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60439 Frankfurt am Main, Germany
| | - Florian Steinberg
- Center for Biological Systems Analysis, University of Freiburg, Habsburgerstr. 49, 79104 Freiburg, Germany
| | - Anja Bremm
- Institute of Biochemistry II, Goethe University Frankfurt - Medical Faculty, University Hospital, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany.
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12
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Rep15 interacts with several Rab GTPases and has a distinct fold for a Rab effector. Nat Commun 2022; 13:4262. [PMID: 35871249 PMCID: PMC9308819 DOI: 10.1038/s41467-022-31831-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 06/30/2022] [Indexed: 11/08/2022] Open
Abstract
AbstractIn their GTP-bound (active) form, Rab proteins interact with effector proteins that control downstream signaling. One such Rab15 effector is Rep15, which is known to have a role in receptor recycling from the endocytic recycling compartment but otherwise remains poorly characterized. Here, we report the characterization of the Rep15:Rab15 interaction and identification of Rab3 paralogs and Rab34 as Rep15 interacting partners from a yeast two-hybrid assay. Biochemical validation of the interactions is presented and crystal structures of the Rep15:Rab3B and Rep15:Rab3C complexes provide additional mechanistic insight. We find that Rep15 adopts a globular structure that is distinct from other reported Rab15, Rab3 and Rab34 effectors. Structure-based mutagenesis experiments explain the Rep15:Rab interaction specificity. Rep15 depletion in U138MG glioblastoma cells impairs cell proliferation, cell migration and receptor recycling, underscoring the need for further clarification of the role of Rep15 in cancer.
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13
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d'Amico EA, Ud Din Ahmad M, Cmentowski V, Girbig M, Müller F, Wohlgemuth S, Brockmeyer A, Maffini S, Janning P, Vetter IR, Carter AP, Perrakis A, Musacchio A. Conformational transitions of the Spindly adaptor underlie its interaction with Dynein and Dynactin. J Cell Biol 2022; 221:213466. [PMID: 36107127 PMCID: PMC9481740 DOI: 10.1083/jcb.202206131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/02/2022] [Accepted: 08/17/2022] [Indexed: 11/22/2022] Open
Abstract
Cytoplasmic Dynein 1, or Dynein, is a microtubule minus end-directed motor. Dynein motility requires Dynactin and a family of activating adaptors that stabilize the Dynein-Dynactin complex and promote regulated interactions with cargo in space and time. How activating adaptors limit Dynein activation to specialized subcellular locales is unclear. Here, we reveal that Spindly, a mitotic Dynein adaptor at the kinetochore corona, exists natively in a closed conformation that occludes binding of Dynein-Dynactin to its CC1 box and Spindly motif. A structure-based analysis identified various mutations promoting an open conformation of Spindly that binds Dynein-Dynactin. A region of Spindly downstream from the Spindly motif and not required for cargo binding faces the CC1 box and stabilizes the intramolecular closed conformation. This region is also required for robust kinetochore localization of Spindly, suggesting that kinetochores promote Spindly activation to recruit Dynein. Thus, our work illustrates how specific Dynein activation at a defined cellular locale may require multiple factors.
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Affiliation(s)
- Ennio A d'Amico
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Misbha Ud Din Ahmad
- Oncode Institute and Department of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Verena Cmentowski
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.,Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | | | - Franziska Müller
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Sabine Wohlgemuth
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Andreas Brockmeyer
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Stefano Maffini
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Petra Janning
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Ingrid R Vetter
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | | | - Anastassis Perrakis
- Oncode Institute and Department of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Andrea Musacchio
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.,Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
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14
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Pozo F, Rodriguez JM, Martínez Gómez L, Vázquez J, Tress ML. APPRIS principal isoforms and MANE Select transcripts define reference splice variants. Bioinformatics 2022; 38:ii89-ii94. [PMID: 36124785 PMCID: PMC9486585 DOI: 10.1093/bioinformatics/btac473] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
MOTIVATION Selecting the splice variant that best represents a coding gene is a crucial first step in many experimental analyses, and vital for mapping clinically relevant variants. This study compares the longest isoforms, MANE Select transcripts, APPRIS principal isoforms, and expression data, and aims to determine which method is best for selecting biological important reference splice variants for large-scale analyses. RESULTS Proteomics analyses and human genetic variation data suggest that most coding genes have a single main protein isoform. We show that APPRIS principal isoforms and MANE Select transcripts best describe these main cellular isoforms, and find that using the longest splice variant as the representative is a poor strategy. Exons unique to the longest splice isoforms are not under selective pressure, and so are unlikely to be functionally relevant. Expression data are also a poor means of selecting the main splice variant. APPRIS principal and MANE Select exons are under purifying selection, while exons specific to alternative transcripts are not. There are MANE and APPRIS representatives for almost 95% of genes, and where they agree they are particularly effective, coinciding with the main proteomics isoform for over 98.2% of genes. AVAILABILITY AND IMPLEMENTATION APPRIS principal isoforms for human, mouse and other model species can be downloaded from the APPRIS database (https://appris.bioinfo.cnio.es), GENCODE genes (https://www.gencodegenes.org/) and the Ensembl website (https://www.ensembl.org). MANE Select transcripts for the human reference set are available from the Ensembl, GENCODE and RefSeq databases (https://www.ncbi.nlm.nih.gov/refseq/). Lists of splice variants where MANE and APPRIS coincide are available from the APPRIS database. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Fernando Pozo
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - José Manuel Rodriguez
- Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Laura Martínez Gómez
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Jesús Vázquez
- Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain,CIBER de Investigaciones Cardiovasculares (CIBERCV), 28029 Madrid, Spain
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15
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Celestino R, Gama JB, Castro-Rodrigues AF, Barbosa DJ, Rocha H, d’Amico EA, Musacchio A, Carvalho AX, Morais-Cabral JH, Gassmann R. JIP3 interacts with dynein and kinesin-1 to regulate bidirectional organelle transport. J Cell Biol 2022; 221:e202110057. [PMID: 35829703 PMCID: PMC9284427 DOI: 10.1083/jcb.202110057] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 06/04/2022] [Accepted: 06/23/2022] [Indexed: 01/16/2023] Open
Abstract
The MAP kinase and motor scaffold JIP3 prevents excess lysosome accumulation in axons of vertebrates and invertebrates. How JIP3's interaction with dynein and kinesin-1 contributes to organelle clearance is unclear. We show that human dynein light intermediate chain (DLIC) binds the N-terminal RH1 domain of JIP3, its paralog JIP4, and the lysosomal adaptor RILP. A point mutation in RH1 abrogates DLIC binding without perturbing the interaction between JIP3's RH1 domain and kinesin heavy chain. Characterization of this separation-of-function mutation in Caenorhabditis elegans shows that JIP3-bound dynein is required for organelle clearance in the anterior process of touch receptor neurons. Unlike JIP3 null mutants, JIP3 that cannot bind DLIC causes prominent accumulation of endo-lysosomal organelles at the neurite tip, which is rescued by a disease-associated point mutation in JIP3's leucine zipper that abrogates kinesin light chain binding. These results highlight that RH1 domains are interaction hubs for cytoskeletal motors and suggest that JIP3-bound dynein and kinesin-1 participate in bidirectional organelle transport.
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Affiliation(s)
- Ricardo Celestino
- Instituto de Investigação e Inovação em Saúde—i3S, Universidade do Porto, Porto, Portugal
| | - José B. Gama
- Instituto de Investigação e Inovação em Saúde—i3S, Universidade do Porto, Porto, Portugal
| | | | - Daniel J. Barbosa
- Instituto de Investigação e Inovação em Saúde—i3S, Universidade do Porto, Porto, Portugal
- TOXRUN—Toxicology Research Unit, University Institute of Health Sciences, Advanced Polytechnic and University Cooperative (CESPU), Cooperative of Limited Liability (CRL), Gandra, Portugal
| | - Helder Rocha
- Instituto de Investigação e Inovação em Saúde—i3S, Universidade do Porto, Porto, Portugal
| | - Ennio A. d’Amico
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Andrea Musacchio
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Ana Xavier Carvalho
- Instituto de Investigação e Inovação em Saúde—i3S, Universidade do Porto, Porto, Portugal
| | - João H. Morais-Cabral
- Instituto de Investigação e Inovação em Saúde—i3S, Universidade do Porto, Porto, Portugal
| | - Reto Gassmann
- Instituto de Investigação e Inovação em Saúde—i3S, Universidade do Porto, Porto, Portugal
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16
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Yap CC, Digilio L, McMahon LP, Wang T, Winckler B. Dynein Is Required for Rab7-Dependent Endosome Maturation, Retrograde Dendritic Transport, and Degradation. J Neurosci 2022; 42:4415-4434. [PMID: 35474277 PMCID: PMC9172292 DOI: 10.1523/jneurosci.2530-21.2022] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/30/2022] [Accepted: 04/15/2022] [Indexed: 11/21/2022] Open
Abstract
In all cell types, endocytosed cargo is transported along a set of endosomal compartments, which are linked maturationally from early endosomes (EEs) via late endosomes (LEs) to lysosomes. Lysosomes are critical for degradation of proteins that enter through endocytic as well as autophagic pathways. Rab7 is the master regulator of early-to-late endosome maturation, motility, and fusion with lysosomes. We previously showed that most degradative lysosomes are localized in the soma and in the first 25 µm of the dendrite and that bulk degradation of dendritic membrane proteins occurs in/near the soma. Dendritic late endosomes therefore move retrogradely in a Rab7-dependent manner for fusion with somatic lysosomes. We now used cultured E18 rat hippocampal neurons of both sexes to determine which microtubule motor is responsible for degradative flux of late endosomes. Based on multiple approaches (inhibiting dynein/dynactin itself or inhibiting dynein recruitment to endosomes by expressing the C-terminus of the Rab7 effector, RILP), we now demonstrate that net retrograde flux of late endosomes in dendrites is supported by dynein. Inhibition of dynein also delays maturation of somatic endosomes, as evidenced by excessive accumulation of Rab7. In addition, degradation of dendritic cargos is inhibited. Our results also suggest that GDP-GTP cycling of Rab7 appears necessary not only for endosomal maturation but also for fusion with lysosomes subsequent to arrival in the soma. In conclusion, Rab7-dependent dynein/dynactin recruitment to dendritic endosomes plays multifaceted roles in dendritic endosome maturation as well as retrograde transport of late endosomes to sustain normal degradative flux.SIGNIFICANCE STATEMENT Lysosomes are critical for degradation of membrane and extracellular proteins that enter through endocytosis. Lysosomes are also the endpoint of autophagy and thus responsible for protein and organelle homeostasis. Endosomal-lysosomal dysfunction is linked to neurodegeneration and aging. We identify roles in dendrites for two proteins with links to human diseases, Rab7 and dynein. Our previous work identified a process that requires directional retrograde transport in dendrites, namely, efficient degradation of short-lived membrane proteins. Based on multiple approaches, we demonstrate that Rab7-dependent recruitment of dynein motors supports net retrograde transport to lysosomes and is needed for endosome maturation. Our data also suggest that GDP-GTP cycling of Rab7 is required for fusion with lysosomes and degradation, subsequent to arrival in the soma.
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Affiliation(s)
- Chan Choo Yap
- Department of Cell Biology, University of Virginia, Charlottesville, Virginia 22908
| | - Laura Digilio
- Department of Cell Biology, University of Virginia, Charlottesville, Virginia 22908
| | - Lloyd P McMahon
- Department of Cell Biology, University of Virginia, Charlottesville, Virginia 22908
| | - Tuanlao Wang
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian Province 361005, China
| | - Bettina Winckler
- Department of Cell Biology, University of Virginia, Charlottesville, Virginia 22908
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17
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Jung J, Baek J, Tae K, Shin D, Han S, Yang W, Yu W, Jung SM, Park SH, Choi CY, Lee S. Structural mechanism for regulation of Rab7 by site-specific monoubiquitination. Int J Biol Macromol 2022; 194:347-357. [PMID: 34801583 DOI: 10.1016/j.ijbiomac.2021.11.074] [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: 09/17/2021] [Revised: 11/08/2021] [Accepted: 11/11/2021] [Indexed: 11/30/2022]
Abstract
Site-specific ubiquitination can regulate the functions of Rab proteins in membrane trafficking. Previously we showed that site-specific monoubiquitination on Rab5 downregulates its function. Rab7 acts in the downstream of Rab5. Although site-specific ubiquitination of Rab7 can affect its function, it remains elusive how the ubiquitination is involved in modulation of the function of Rab7 at molecular level. Here, we report molecular basis for the regulation of Rab7 by site-specific monoubiquitination. Rab7 was predominantly monoubiquitinated at multiple sites in the membrane fraction of cultured cells. Two major ubiquitination sites (K191 and K194), identified by mutational analysis with single K mutants, were responsible for membrane localization of monoubiquitinated Rab7. Using small-angle X-ray scattering, we derived structural models of site-specifically monoubiquitinated Rab7 in solution. Structural analysis combined with molecular dynamics simulation corroborated that the ubiquitin moieties on K191 and K194 are key determinants for exclusion of Rab7 from the endosomal membrane. Ubiquitination on the two major sites apparently mitigated colocalization of Rab7 with ORF3a of SARS-CoV-2, potentially deterring the egression of SARS-CoV-2. Our results establish that the regulatory effects of a Rab protein through site-specific monoubiquitination are commonly observed among Rab GTPases while the ubiquitination sites differ in each Rab protein.
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Affiliation(s)
- Jaeeun Jung
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jiseok Baek
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Kun Tae
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Donghyuk Shin
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Seungsu Han
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Wonjin Yang
- Department of Brain and Cognitive Sciences, DGIST, Daegu 42988, Republic of Korea
| | - Wookyung Yu
- Department of Brain and Cognitive Sciences, DGIST, Daegu 42988, Republic of Korea
| | - Su Myung Jung
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Seok Hee Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Cheol Yong Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Sangho Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea; Biomedical Institute for Convergence at SKKU, Sungkyunkwan University, Suwon 16419, Republic of Korea.
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18
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Structural basis of human PDZD8-Rab7 interaction for the ER-late endosome tethering. Sci Rep 2021; 11:18859. [PMID: 34552186 PMCID: PMC8458453 DOI: 10.1038/s41598-021-98419-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/31/2021] [Indexed: 02/02/2023] Open
Abstract
The membrane contact sites (MCSs) between the ER and late endosomes (LEs) are essential for the regulation of endosomal protein sorting, dynamics, and motility. PDZD8 is an ER transmembrane protein containing a Synaptotagmin-like Mitochondrial lipid-binding Proteins (SMP) domain. PDZD8 tethers the ER to late endosomes and lysosomes by associating its C-terminal coiled-coil (CC) with the LE Rab7. To identify the structural determinants for the PDZD8–Rab7 interaction, we determined the crystal structure of the human PDZD8 CC domain in complex with the GTP-bound form of Rab7. The PDZD8 CC contains one short helix and the two helices forming an antiparallel coiled-coil. Two Rab7 molecules bind to the opposite sides of the PDZD8 CC in a 2:1 ratio. The switch I/II and interswitch regions of the GTP-loaded Rab7 form the binding interfaces, which correlates with the GTP-dependent interaction of PDZD8 and Rab7. Analysis of the protein interaction by isothermal titration calorimetry confirms that two Rab7 molecules bind the PDZD8 CC in a GTP-dependent manner. The structural model of the PDZD8 CC–Rab7 complex correlates with the recruitment of PDZD8 at the LE–ER interface and its role in lipid transport and regulation.
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19
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Omar J, Rosenbaum E, Efergan A, Sneineh BA, Yeheskel A, Maruta Y, Fukuda M, Sagi-Eisenberg R. Biochemical and structural insights into Rab12 interactions with RILP and its family members. Sci Rep 2021; 11:10317. [PMID: 33986343 PMCID: PMC8119438 DOI: 10.1038/s41598-021-89394-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 04/15/2021] [Indexed: 11/09/2022] Open
Abstract
Alongside its biosynthetic functions, the small GTPase Rab12 negatively regulates mast cell (MC) exocytosis by its interaction with RILP to promote retrograde transport of the MC secretory granules. Given the role of Rab effectors in mediating Rab functions, in this study we used biochemical and in silico tools to decipher Rab12 interactions with its RILP family effectors. We show that Rab12 interacts with RILP, RILP-L1 and RILP-L2 independently of each other, whereby lysine-71, in mouse Rab12, is critical for Rab12 interactions with RILP-L1 or RILP-L2, but is dispensable for the binding of RILP. Focusing on RILP, and relying on molecular dynamics simulations, functional mutational analyses and peptide inhibition assays, we propose a model for the Rab12-RILP complex, consisting of a RILP homodimer and a single molecule of active Rab12, that interacts with the RILP homology domain (RHD) of one RILP monomer and a C-terminal threonine in the other monomer via its switch I and switch II regions. Mutational analyses of RILP RHD also demonstrate its involvement in the regulation of MC secretory granule transport. Jointly, our results provide structural and functional insights into the Rab12-RILP complex on the basis of which new tools could be generated for decoding Rab12 functions.
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Affiliation(s)
- Jana Omar
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Efrat Rosenbaum
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Adi Efergan
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Bayan Abu Sneineh
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Adva Yeheskel
- Bioinformatics Unit, Faculty of Life Sciences and Computational assisted drug-design unit, Blavatnik Center for Drug Discovery, Tel-Aviv University, 69978, Tel Aviv, Israel
| | - Yuto Maruta
- Laboratory of Membrane Trafficking Mechanisms, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Aoba-ku, AobayamaSendai, Miyagi, 980-8578, Japan
| | - Mitsunori Fukuda
- Laboratory of Membrane Trafficking Mechanisms, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Aoba-ku, AobayamaSendai, Miyagi, 980-8578, Japan
| | - Ronit Sagi-Eisenberg
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel.
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20
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Romano R, Calcagnile M, Margiotta A, Franci L, Chiariello M, Alifano P, Bucci C. RAB7A Regulates Vimentin Phosphorylation through AKT and PAK. Cancers (Basel) 2021; 13:cancers13092220. [PMID: 34066419 PMCID: PMC8125308 DOI: 10.3390/cancers13092220] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 12/21/2022] Open
Abstract
Simple Summary RAB7A (RAs-related in Brain 7A) is a master regulator of intracellular traffic controlling transport to late endosomes and lysosomes, two organelles of the endocytic pathway important for degradation. Thanks to this function, RAB7A is also involved in cellular processes linked to cancer, such as apoptosis, cytoskeletal reorganization, and cell migration. Therefore, the interest in the role of RAB7A in cancer progression is increasing. Previously, we demonstrated that RAB7A regulates phosphorylation and assembly of vimentin, a cytoskeletal intermediate filament protein, which is also an important mesenchymal marker of cancer cells. The aim of the present study is the identification of the kinases responsible for vimentin phosphorylation whose activity is affected by the modulation of RAB7A expression. We found that RAB7A is able to regulate AKT (also called protein kinase B or PKB) and PAK1 (P21-Activated Kinase 1) and several of their downstream effectors, which control proliferation, apoptosis, survival, migration, and invasion. These data suggest that RAB7A could have a key role in cancer development. Abstract RAB7A is a small GTPase that controls the late endocytic pathway but also cell migration through RAC1 (Ras-related C3 botulinum toxin substrate 1) and vimentin. In fact, RAB7A regulates vimentin phosphorylation at different sites and vimentin assembly, and, in this study, we identified vimentin domains interacting with RAB7A. As several kinases could be responsible for vimentin phosphorylation, we investigated whether modulation of RAB7A expression affects the activity of these kinases. We discovered that RAB7A regulates AKT and PAK1, and we demonstrated that increased vimentin phosphorylation at Ser38 (Serine 38), observed upon RAB7A overexpression, is due to AKT activity. As AKT and PAK1 are key regulators of several cellular events, we investigated if RAB7A could have a role in these processes by modulating AKT and PAK1 activity. We found that RAB7A protein levels affected beta-catenin and caspase 9 expression. We also observed the downregulation of cofilin-1 and decreased matrix metalloproteinase 2 (MMP2) activity upon RAB7A silencing. Altogether these results demonstrate that RAB7A regulates AKT and PAK1 kinases, affecting their downstream effectors and the processes they regulate, suggesting that RAB7A could have a role in a number of cancer hallmarks.
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Affiliation(s)
- Roberta Romano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, 73100 Lecce, Italy; (R.R.); (M.C.); (A.M.); (P.A.)
| | - Matteo Calcagnile
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, 73100 Lecce, Italy; (R.R.); (M.C.); (A.M.); (P.A.)
| | - Azzurra Margiotta
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, 73100 Lecce, Italy; (R.R.); (M.C.); (A.M.); (P.A.)
| | - Lorenzo Franci
- Istituto di Fisiologia Clinica (IFC), Consiglio Nazionale delle Ricerche (CNR), 53100 Siena, Italy; (L.F.); (M.C.)
- Core Research Laboratory (CRL), Istituto per lo Studio, La Prevenzione e la Rete Oncologica (ISPRO), 53100 Siena, Italy
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Mario Chiariello
- Istituto di Fisiologia Clinica (IFC), Consiglio Nazionale delle Ricerche (CNR), 53100 Siena, Italy; (L.F.); (M.C.)
- Core Research Laboratory (CRL), Istituto per lo Studio, La Prevenzione e la Rete Oncologica (ISPRO), 53100 Siena, Italy
| | - Pietro Alifano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, 73100 Lecce, Italy; (R.R.); (M.C.); (A.M.); (P.A.)
| | - Cecilia Bucci
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, 73100 Lecce, Italy; (R.R.); (M.C.); (A.M.); (P.A.)
- Correspondence: ; Tel.: +39-0832-298900
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21
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Oguchi ME, Homma Y, Fukuda M. The N-terminal Leu-Pro-Gln sequence of Rab34 is required for ciliogenesis in hTERT-RPE1 cells. Small GTPases 2021; 13:77-83. [PMID: 33860735 DOI: 10.1080/21541248.2021.1894910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
We have previously shown that Rab34 is an important regulator of ciliogenesis and that its unique long N-terminal region (amino acids 1-49) is essential for ciliogenesis in certain cultured mammalian cells. In the present study, we performed an in-depth deletion analysis of the N-terminal region of Rab34 together with Ala-based site-directed mutagenesis to identify the essential amino acids that are required for serum-starvation-induced ciliogenesis in hTERT-RPE1 cells. The results showed that a Rab34 mutant lacking an N-terminal 18 amino acids and a Rab34 mutant carrying an LPQ-to-AAA mutation (amino acids 16-18) failed to rescue a Rab34-KO phenotype (i.e., defect in ciliogenesis). Our findings suggest that the LPQ sequence of Rab34 is crucial for ciliogenesis in hTERT-RPE1 cells.Abbreviations: AA, amino acid(s); ac-Tub, acetylated tubulin; bsr, blasticidin S-resistant gene; HRP, horseradish peroxidase; hTERT-RPE1, human telomerase reverse transcriptase retinal pigment epithelium 1; KO, knockout; NS, not significant; PBS, phosphate-buffered saline; puro, puromycin-resistant gene.
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Affiliation(s)
- Mai E Oguchi
- Laboratory of Membrane Trafficking Mechanisms, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Yuta Homma
- Laboratory of Membrane Trafficking Mechanisms, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Mitsunori Fukuda
- Laboratory of Membrane Trafficking Mechanisms, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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22
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Hu J, Ding X, Tian S, Chu Y, Liu Z, Li Y, Li X, Wang G, Wang L, Wang Z. TRIM39 deficiency inhibits tumor progression and autophagic flux in colorectal cancer via suppressing the activity of Rab7. Cell Death Dis 2021; 12:391. [PMID: 33846303 PMCID: PMC8041807 DOI: 10.1038/s41419-021-03670-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 03/20/2021] [Accepted: 03/22/2021] [Indexed: 12/24/2022]
Abstract
The biological function of TRIM39, a member of TRIM family, remains largely unexplored in cancer, especially in colorectal cancer (CRC). In this study, we show that TRIM39 is upregulated in tumor tissues compared to adjacent normal tissues and associated with poor prognosis in CRC. Functional studies demonstrate that TRIM39 deficiency restrains CRC progression in vitro and in vivo. Our results further find that TRIM39 is a positive regulator of autophagosome–lysosome fusion. Mechanistically, TRIM39 interacts with Rab7 and promotes its activity via inhibiting its ubiquitination at lysine 191 residue. Depletion of TRIM39 inhibits CRC progression and autophagic flux in a Rab7 activity-dependent manner. Moreover, TRIM39 deficiency suppresses CRC progression through inhibiting autophagic degradation of p53. Thus, our findings uncover the roles as well as the relevant mechanisms of TRIM39 in CRC and establish a functional relationship between autophagy and CRC progression, which may provide promising approaches for the treatment of CRC.
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Affiliation(s)
- Jia Hu
- Research Center for Tissue Engineering and Regenerative Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Xueliang Ding
- Research Center for Tissue Engineering and Regenerative Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Shaobo Tian
- Research Center for Tissue Engineering and Regenerative Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Yanan Chu
- Research Center for Tissue Engineering and Regenerative Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Zhibo Liu
- Research Center for Tissue Engineering and Regenerative Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Yuqin Li
- Research Center for Tissue Engineering and Regenerative Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Xiaoqiong Li
- Research Center for Tissue Engineering and Regenerative Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Guobin Wang
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China.
| | - Lin Wang
- Research Center for Tissue Engineering and Regenerative Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China. .,Department of Clinical Laboratory, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China.
| | - Zheng Wang
- Research Center for Tissue Engineering and Regenerative Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China. .,Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China.
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23
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Nguyen JA, Yates RM. Better Together: Current Insights Into Phagosome-Lysosome Fusion. Front Immunol 2021; 12:636078. [PMID: 33717183 PMCID: PMC7946854 DOI: 10.3389/fimmu.2021.636078] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/18/2021] [Indexed: 12/15/2022] Open
Abstract
Following phagocytosis, the nascent phagosome undergoes maturation to become a phagolysosome with an acidic, hydrolytic, and often oxidative lumen that can efficiently kill and digest engulfed microbes, cells, and debris. The fusion of phagosomes with lysosomes is a principal driver of phagosomal maturation and is targeted by several adapted intracellular pathogens. Impairment of this process has significant consequences for microbial infection, tissue inflammation, the onset of adaptive immunity, and disease. Given the importance of phagosome-lysosome fusion to phagocyte function and the many virulence factors that target it, it is unsurprising that multiple molecular pathways have evolved to mediate this essential process. While the full range of these pathways has yet to be fully characterized, several pathways involving proteins such as members of the Rab GTPases, tethering factors and SNAREs have been identified. Here, we summarize the current state of knowledge to clarify the ambiguities in the field and construct a more comprehensive phagolysosome formation model. Lastly, we discuss how other cellular pathways help support phagolysosome biogenesis and, consequently, phagocyte function.
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Affiliation(s)
- Jenny A Nguyen
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Robin M Yates
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada.,Cumming School of Medicine, Snyder Institute of Chronic Disease, University of Calgary, Calgary, AB, Canada
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24
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Malik AU, Karapetsas A, Nirujogi RS, Mathea S, Chatterjee D, Pal P, Lis P, Taylor M, Purlyte E, Gourlay R, Dorward M, Weidlich S, Toth R, Polinski NK, Knapp S, Tonelli F, Alessi DR. Deciphering the LRRK code: LRRK1 and LRRK2 phosphorylate distinct Rab proteins and are regulated by diverse mechanisms. Biochem J 2021; 478:553-578. [PMID: 33459343 PMCID: PMC7886321 DOI: 10.1042/bcj20200937] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/08/2021] [Accepted: 01/18/2021] [Indexed: 01/05/2023]
Abstract
Autosomal dominant mutations in LRRK2 that enhance kinase activity cause Parkinson's disease. LRRK2 phosphorylates a subset of Rab GTPases including Rab8A and Rab10 within its effector binding motif. Here, we explore whether LRRK1, a less studied homolog of LRRK2 that regulates growth factor receptor trafficking and osteoclast biology might also phosphorylate Rab proteins. Using mass spectrometry, we found that in LRRK1 knock-out cells, phosphorylation of Rab7A at Ser72 was most impacted. This residue lies at the equivalent site targeted by LRRK2 on Rab8A and Rab10. Accordingly, recombinant LRRK1 efficiently phosphorylated Rab7A at Ser72, but not Rab8A or Rab10. Employing a novel phospho-specific antibody, we found that phorbol ester stimulation of mouse embryonic fibroblasts markedly enhanced phosphorylation of Rab7A at Ser72 via LRRK1. We identify two LRRK1 mutations (K746G and I1412T), equivalent to the LRRK2 R1441G and I2020T Parkinson's mutations, that enhance LRRK1 mediated phosphorylation of Rab7A. We demonstrate that two regulators of LRRK2 namely Rab29 and VPS35[D620N], do not influence LRRK1. Widely used LRRK2 inhibitors do not inhibit LRRK1, but we identify a promiscuous inhibitor termed GZD-824 that inhibits both LRRK1 and LRRK2. The PPM1H Rab phosphatase when overexpressed dephosphorylates Rab7A. Finally, the interaction of Rab7A with its effector RILP is not affected by LRRK1 phosphorylation and we observe that maximal stimulation of the TBK1 or PINK1 pathway does not elevate Rab7A phosphorylation. Altogether, these findings reinforce the idea that the LRRK enzymes have evolved as major regulators of Rab biology with distinct substrate specificity.
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Affiliation(s)
- Asad U. Malik
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Athanasios Karapetsas
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Raja S. Nirujogi
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Sebastian Mathea
- Structural Genomics Consortium, Institute for Pharmaceutical Chemistry and Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Deep Chatterjee
- Structural Genomics Consortium, Institute for Pharmaceutical Chemistry and Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Prosenjit Pal
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Pawel Lis
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Matthew Taylor
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Elena Purlyte
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Robert Gourlay
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Mark Dorward
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Simone Weidlich
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Rachel Toth
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Nicole K. Polinski
- Michael J Fox Foundation for Parkinson's Research, Grand Central Station, PO Box 4777, New York, NY 10163, U.S.A
| | - Stefan Knapp
- Structural Genomics Consortium, Institute for Pharmaceutical Chemistry and Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Francesca Tonelli
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Dario R. Alessi
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
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25
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Savitskiy S, Wachtel R, Pourjafar-Dehkordi D, Kang HS, Trauschke V, Lamb DC, Sattler M, Zacharias M, Itzen A. Proteolysis of Rab32 by Salmonella GtgE induces an inactive GTPase conformation. iScience 2020; 24:101940. [PMID: 33426511 PMCID: PMC7779776 DOI: 10.1016/j.isci.2020.101940] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/18/2020] [Accepted: 12/10/2020] [Indexed: 12/26/2022] Open
Abstract
Rab GTPases are central regulators of intracellular vesicular trafficking. They are frequently targeted by bacterial pathogens through post-translational modifications. Salmonella typhimurium secretes the cysteine protease GtgE during infection, leading to a regioselective proteolytic cleavage of the regulatory switch I loop in the small GTPases of the Rab32 subfamily. Here, using a combination of biochemical methods, molecular dynamics simulations, NMR spectroscopy, and single-pair Förster resonance energy transfer, we demonstrate that the cleavage of Rab32 causes a local increase of conformational flexibility in both switch regions. Cleaved Rab32 maintains its ability to interact with the GDP dissociation inhibitor (GDI). Interestingly, the Rab32 cleavage enables GDI binding also with an active GTP-bound Rab32 in vitro. Furthermore, the Rab32 proteolysis provokes disturbance in the interaction with its downstream effector VARP. Thus, the proteolysis of Rab32 is not a globally degradative mechanism but affects various biochemical and structural properties of the GTPase in a diverse manner.
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Affiliation(s)
- Sergey Savitskiy
- Department of Biochemistry and Signaltransduction, University Medical Centre Hamburg-Eppendorf (UKE), Martinistrasse 52, 20246 Hamburg, Germany.,Center for Integrated Protein Science Munich (CIPSM), Department Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Rudolf Wachtel
- Center for Integrated Protein Science Munich (CIPSM), Department Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Danial Pourjafar-Dehkordi
- Physics Department T38, Technical University of Munich, James-Franck-Strasse 1, 85748 Garching, Germany
| | - Hyun-Seo Kang
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Chemistry Department, Biomolecular NMR and Center for Integrated Protein Science Munich, Technical University of Munich, 85748 Garching, Germany
| | - Vanessa Trauschke
- Department of Chemistry, Center for Nanoscience (CeNS), NanoSystems Initiative Munich (NIM) and Center for Integrated Protein Science Munich (CIPSM), Ludwig Maximilians-Universität München, Munich Germany
| | - Don C Lamb
- Department of Chemistry, Center for Nanoscience (CeNS), NanoSystems Initiative Munich (NIM) and Center for Integrated Protein Science Munich (CIPSM), Ludwig Maximilians-Universität München, Munich Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Chemistry Department, Biomolecular NMR and Center for Integrated Protein Science Munich, Technical University of Munich, 85748 Garching, Germany
| | - Martin Zacharias
- Physics Department T38, Technical University of Munich, James-Franck-Strasse 1, 85748 Garching, Germany
| | - Aymelt Itzen
- Department of Biochemistry and Signaltransduction, University Medical Centre Hamburg-Eppendorf (UKE), Martinistrasse 52, 20246 Hamburg, Germany.,Center for Integrated Protein Science Munich (CIPSM), Department Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany.,Centre for Structural Systems Biology (CSSB), University Medical Centre Hamburg-Eppendorf (UKE), Hamburg, Germany
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26
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Keren-Kaplan T, Bonifacino JS. ARL8 Relieves SKIP Autoinhibition to Enable Coupling of Lysosomes to Kinesin-1. Curr Biol 2020; 31:540-554.e5. [PMID: 33232665 DOI: 10.1016/j.cub.2020.10.071] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 09/16/2020] [Accepted: 10/23/2020] [Indexed: 01/24/2023]
Abstract
Long-range movement of organelles within the cytoplasm relies on coupling to microtubule motors, a process that is often mediated by adaptor proteins. In many cases, this coupling involves organelle- or adaptor-induced activation of the microtubule motors by conformational reversal of an autoinhibited state. Herein, we show that a similar regulatory mechanism operates for an adaptor protein named SKIP (also known as PLEKHM2). SKIP binds to the small guanosine triphosphatase (GTPase) ARL8 on the lysosomal membrane to couple lysosomes to the anterograde microtubule motor kinesin-1. Structure-function analyses of SKIP reveal that the C-terminal region comprising three pleckstrin homology (PH) domains interacts with the N-terminal region comprising ARL8- and kinesin-1-binding sites. This interaction inhibits coupling of lysosomes to kinesin-1 and, consequently, lysosome movement toward the cell periphery. We also find that ARL8 does not just recruit SKIP to the lysosomal membrane but also relieves SKIP autoinhibition, promoting kinesin-1-driven, anterograde lysosome transport. Finally, our analyses show that the largely disordered middle region of SKIP mediates self-association and that this self-association enhances the interaction of SKIP with kinesin-1. These findings indicate that SKIP is not just a passive connector of lysosome-bound ARL8 to kinesin-1 but is itself subject to intra- and inter-molecular interactions that regulate its function. We anticipate that similar organelle- or GTPase-induced conformational changes could regulate the activity of other kinesin adaptors.
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Affiliation(s)
- Tal Keren-Kaplan
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Juan S Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
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27
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Sakurai S, Shimizu T, Ohto U. Crystal structure of the FYCO1 RUN domain suggests possible interfaces with small GTPases. Acta Crystallogr F Struct Biol Commun 2020; 76:326-333. [PMID: 32744243 PMCID: PMC7397462 DOI: 10.1107/s2053230x20009012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/02/2020] [Indexed: 01/07/2023] Open
Abstract
FYCO1 is a multidomain adaptor protein that plays an important role in autophagy by mediating the kinesin-dependent microtubule plus-end-directed transport of autophagosomes. FYCO1 contains a RUN domain, which is hypothesized to function as a specific effector for members of the Ras superfamily of small GTPases, but its role has not been well characterized and its interaction partner(s) have not been identified. Here, the crystal structure of the FYCO1 RUN domain was determined at 1.3 Å resolution. The overall structure of the FYCO1 RUN domain was similar to those of previously reported RUN domains. Detailed structural comparisons with other RUN domains and docking studies suggested a possible interaction interface of the FYCO1 RUN domain with small GTPases of the Ras superfamily.
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Affiliation(s)
- Shunya Sakurai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Toshiyuki Shimizu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Umeharu Ohto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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28
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Abstract
Autophagy (cellular self-eating) is essential for the health and survival of eukaryotic cells. Therapeutic autophagy induction is a major goal in the field. Rubicon inhibits autophagy and is a potential target for autophagy inducers. Rubicon is localized to its site of action in the cell by binding to the small GTPase Rab7. Here, we report a high-resolution structure of a large part of Rubicon, known as the Rubicon Homology (RH) domain. We show how the RH domain binds to Rab7 and show that the Rab7-binding residues of Rubicon are essential for Rubicon localization and autophagy inhibition. This provides a roadmap to block Rubicon localization and activity in order to upregulate autophagy. Rubicon is a potent negative regulator of autophagy and a potential target for autophagy-inducing therapeutics. Rubicon-mediated inhibition of autophagy requires the interaction of the C-terminal Rubicon homology (RH) domain of Rubicon with Rab7–GTP. Here we report the 2.8-Å crystal structure of the Rubicon RH domain in complex with Rab7–GTP. Our structure reveals a fold for the RH domain built around four zinc clusters. The switch regions of Rab7 insert into pockets on the surface of the RH domain in a mode that is distinct from those of other Rab–effector complexes. Rubicon residues at the dimer interface are required for Rubicon and Rab7 to colocalize in living cells. Mutation of Rubicon RH residues in the Rab7-binding site restores efficient autophagic flux in the presence of overexpressed Rubicon, validating the Rubicon RH domain as a promising therapeutic target.
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29
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The Dynein Adaptor RILP Controls Neuronal Autophagosome Biogenesis, Transport, and Clearance. Dev Cell 2020; 53:141-153.e4. [PMID: 32275887 DOI: 10.1016/j.devcel.2020.03.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 12/30/2019] [Accepted: 03/12/2020] [Indexed: 12/31/2022]
Abstract
Autophagy plays critical roles in neurodegeneration and development, but how this pathway is organized and regulated in neurons remains poorly understood. Here, we find that the dynein adaptor RILP is essential for retrograde transport of neuronal autophagosomes, and surprisingly, their biogenesis as well. We find that induction of autophagy by mTOR inhibition specifically upregulates RILP expression and its localization to autophagosomes. RILP depletion or mutations in its LC3-binding LIR motifs strongly decrease autophagosome numbers suggesting an unexpected RILP role in autophagosome biogenesis. We find that RILP also interacts with ATG5 on isolation membranes, precluding premature dynein recruitment and autophagosome transport. RILP inhibition impedes autophagic turnover and causes p62/sequestosome-1 aggregation. Together, our results identify an mTOR-responsive neuronal autophagy pathway, wherein RILP integrates the processes of autophagosome biogenesis and retrograde transport to control autophagic turnover. This pathway has important implications for understanding how autophagy contributes to neuronal function, development, and disease.
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Waschbüsch D, Purlyte E, Pal P, McGrath E, Alessi DR, Khan AR. Structural Basis for Rab8a Recruitment of RILPL2 via LRRK2 Phosphorylation of Switch 2. Structure 2020; 28:406-417.e6. [PMID: 32017888 PMCID: PMC7139218 DOI: 10.1016/j.str.2020.01.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 11/27/2019] [Accepted: 01/13/2020] [Indexed: 12/18/2022]
Abstract
Rab8a is associated with the dynamic regulation of membrane protrusions in polarized cells. Rab8a is one of several Rab GTPases that are substrates of leucine-rich repeat kinase 2 (LRRK2), a serine/threonine kinase that is linked to Parkinson's disease. Rab8a is phosphorylated at T72 (pT72) in its switch 2 helix and recruits the phospho-specific effector RILPL2, which subsequently regulates ciliogenesis. Here, we report the crystal structure of phospho-Rab8a (pRab8a) in complex with the RH2 (RILP homology) domain of RILPL2. The complex is a heterotetramer with RILPL2 forming a central α-helical dimer that bridges two pRab8a molecules. The N termini of the α helices cross over, forming an X-shaped cap (X-cap) that orients Arg residues from RILPL2 toward pT72. X-cap residues critical for pRab8a binding are conserved in JIP3 and JIP4, which also interact with LRRK2-phosphorylated Rab10. We propose a general mode of recognition for phosphorylated Rab GTPases by this family of phospho-specific effectors.
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Affiliation(s)
- Dieter Waschbüsch
- School of Biochemistry and Immunology, Trinity College, Dublin 2, Ireland
| | - Elena Purlyte
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Prosenjit Pal
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Emma McGrath
- School of Biochemistry and Immunology, Trinity College, Dublin 2, Ireland
| | - Dario R Alessi
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Amir R Khan
- School of Biochemistry and Immunology, Trinity College, Dublin 2, Ireland; Division of Newborn Medicine, Boston Children's Hospital, Boston, USA.
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Roque NR, Lage SL, Navarro R, Fazolini N, Maya-Monteiro CM, Rietdorf J, Melo RCN, D'Avila H, Bozza PT. Rab7 controls lipid droplet-phagosome association during mycobacterial infection. Biochim Biophys Acta Mol Cell Biol Lipids 2020; 1865:158703. [PMID: 32229179 DOI: 10.1016/j.bbalip.2020.158703] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 03/12/2020] [Accepted: 03/25/2020] [Indexed: 12/21/2022]
Abstract
Lipid droplets (LDs) are organelles that have multiple roles in inflammatory and infectious diseases. LD act as essential platforms for immunometabolic regulation, including as sites for lipid storage and metabolism, inflammatory lipid mediator production, and signaling pathway compartmentalization. Accumulating evidence indicates that intracellular pathogens may exploit host LDs as source of nutrients and as part of their strategy to promote immune evasion. Notably, numerous studies have demonstrated the interaction between LDs and pathogen-containing phagosomes. However, the mechanism involved in this phenomenon remains elusive. Here, we observed LDs and PLIN2 surrounding M. bovis BCG-containing phagosomes, which included observations of a bacillus cell surrounded by lipid content inside a phagosome and LAM from mycobacteria co-localizing with LDs; these results were suggestive of exchange of contents between these compartments. By using beads coated with M.tb lipids, we demonstrated that LD-phagosome associations are regulated through the mycobacterial cell wall components LAM and PIM. In addition, we demonstrated that Rab7 and RILP, but not Rab5, localizes to LDs of infected macrophages and observed the presence of Rab7 at the site of interaction with an infected phagosome. Moreover, treatment of macrophages with the Rab7 inhibitor CID1067700 significantly inhibited the association between LDs and LAM-coated beads. Altogether, our data demonstrate that LD-phagosome interactions are controlled by mycobacterial cell wall components and Rab7, which enables the exchange of contents between LDs and phagosomes and may represent a fundamental aspect of bacterial pathogenesis and immune evasion.
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Affiliation(s)
- Natalia R Roque
- Laboratório de Imunofarmacologia, IOC, Fundação Oswaldo Cruz, Rio de Janeiro, 21045-900, RJ, Brazil
| | - Silvia L Lage
- Laboratório de Imunofarmacologia, IOC, Fundação Oswaldo Cruz, Rio de Janeiro, 21045-900, RJ, Brazil
| | - Roberta Navarro
- Laboratório de Imunofarmacologia, IOC, Fundação Oswaldo Cruz, Rio de Janeiro, 21045-900, RJ, Brazil
| | - Narayana Fazolini
- Laboratório de Imunofarmacologia, IOC, Fundação Oswaldo Cruz, Rio de Janeiro, 21045-900, RJ, Brazil
| | - Clarissa M Maya-Monteiro
- Laboratório de Imunofarmacologia, IOC, Fundação Oswaldo Cruz, Rio de Janeiro, 21045-900, RJ, Brazil
| | - Jens Rietdorf
- Centro de Desenvolvimento Tecnológico em Saúde, CDTS, IOC, Fundação Oswaldo Cruz, Rio de Janeiro, 21045-900, RJ, Brazil
| | - Rossana C N Melo
- Laboratório de Biologia Celular, Departamento de Biologia, Universidade Federal de Juiz de Fora, Juiz de Fora, 36036-330, MG, Brazil
| | - Heloisa D'Avila
- Laboratório de Biologia Celular, Departamento de Biologia, Universidade Federal de Juiz de Fora, Juiz de Fora, 36036-330, MG, Brazil
| | - Patricia T Bozza
- Laboratório de Imunofarmacologia, IOC, Fundação Oswaldo Cruz, Rio de Janeiro, 21045-900, RJ, Brazil.
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de Martín Garrido N, Aylett CHS. Nutrient Signaling and Lysosome Positioning Crosstalk Through a Multifunctional Protein, Folliculin. Front Cell Dev Biol 2020; 8:108. [PMID: 32195250 PMCID: PMC7063858 DOI: 10.3389/fcell.2020.00108] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 02/10/2020] [Indexed: 12/16/2022] Open
Abstract
FLCN was identified as the gene responsible for Birt-Hogg-Dubé (BHD) syndrome, a hereditary syndrome associated with the appearance of familiar renal oncocytomas. Most mutations affecting FLCN result in the truncation of the protein, and therefore loss of its associated functions, as typical for a tumor suppressor. FLCN encodes the protein folliculin (FLCN), which is involved in numerous biological processes; mutations affecting this protein thus lead to different phenotypes depending on the cellular context. FLCN forms complexes with two large interacting proteins, FNIP1 and FNIP2. Structural studies have shown that both FLCN and FNIPs contain longin and differentially expressed in normal versus neoplastic cells (DENN) domains, typically involved in the regulation of small GTPases. Accordingly, functional studies show that FLCN regulates both the Rag and the Rab GTPases depending on nutrient availability, which are respectively involved in the mTORC1 pathway and lysosomal positioning. Although recent structural studies shed light on the precise mechanism by which FLCN regulates the Rag GTPases, which in turn regulate mTORC1, how FLCN regulates membrane trafficking through the Rab GTPases or the significance of the intriguing FLCN-FNIP-AMPK complex formation are questions that still remain unanswered. We discuss the recent progress in our understanding of FLCN regulation of both growth signaling and lysosomal positioning, as well as future approaches to establish detailed mechanisms to explain the disparate phenotypes caused by the loss of FLCN function and the development of BHD-associated and other tumors.
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Affiliation(s)
| | - Christopher H. S. Aylett
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
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Zhou Y, Liu Z, Zhang S, Zhuang R, Liu H, Liu X, Qiu X, Zhang M, Zheng Y, Li L, Hong W, Wang T. RILP Restricts Insulin Secretion Through Mediating Lysosomal Degradation of Proinsulin. Diabetes 2020; 69:67-82. [PMID: 31624142 DOI: 10.2337/db19-0086] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 10/06/2019] [Indexed: 11/13/2022]
Abstract
Insulin secretion is tightly regulated by membrane trafficking. RILP (Rab7 interacting lysosomal protein) regulates the endocytic trafficking, but its role in insulin secretion has not been investigated. In this study, we found that overexpression of RILP inhibited insulin secretion in both the β-cell lines and freshly isolated islets. Consequently, the expression of RILP in islets suppressed the ability to recover the glucose homeostasis in type 1 diabetes mice upon transplantation. Of physiological relevance is that RILP expression was upregulated in the diabetic mouse islets. Mechanistically, overexpression of RILP induced insulin granule clustering, decreased the number of proinsulin-containing granules in β-cells, and significantly promoted proinsulin degradation. Conversely, RILP depletion sustained proinsulin and increased insulin secretion. The proinsulin degradation induced by RILP expression was inhibited by lysosomal inhibitors and was Rab7-dependent. Finally, we showed that RILP interacts with insulin granule-associated Rab26 to restrict insulin secretion. This study presents a new pathway regulating insulin secretion and mechanically demonstrates a novel function of RILP in modulating insulin secretion through mediating the lysosomal degradation of proinsulin.
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Affiliation(s)
- Yuxia Zhou
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Fujian, China
| | - Zhiyu Liu
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Fujian, China
| | - Shengmei Zhang
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Fujian, China
| | - Ruijuan Zhuang
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Fujian, China
| | - Huiying Liu
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Fujian, China
| | - Xiaoqing Liu
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Fujian, China
| | - Xi Qiu
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Fujian, China
| | - Ming Zhang
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Fujian, China
| | - Yanpan Zheng
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Fujian, China
| | - Liangcheng Li
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Fujian, China
| | - Wanjin Hong
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Fujian, China
- Institute of Molecular and Cell Biology, A STAR (Agency of Science, Technology and Research), Singapore, Singapore
| | - Tuanlao Wang
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Fujian, China
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Hanafusa H, Yagi T, Ikeda H, Hisamoto N, Nishioka T, Kaibuchi K, Shirakabe K, Matsumoto K. LRRK1 phosphorylation of Rab7 at S72 links trafficking of EGFR-containing endosomes to its effector RILP. J Cell Sci 2019; 132:jcs.228809. [PMID: 31085713 DOI: 10.1242/jcs.228809] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 05/02/2019] [Indexed: 01/02/2023] Open
Abstract
Ligand-induced activation of epidermal growth factor receptor (EGFR) initiates trafficking events that re-localize the receptor from the cell surface to intracellular endocytic compartments. EGFR-containing endosomes are transported to lysosomes for degradation by the dynein-dynactin motor protein complex. However, this cargo-dependent endosomal trafficking mechanism remains largely uncharacterized. Here, we show that GTP-bound Rab7 is phosphorylated on S72 by leucine-rich repeat kinase 1 (LRRK1) at the endosomal membrane. This phosphorylation promotes the interaction of Rab7 (herein referring to Rab7a) with its effector RILP, resulting in recruitment of the dynein-dynactin complex to Rab7-positive vesicles. This, in turn, facilitates the dynein-driven transport of EGFR-containing endosomes toward the perinuclear region. These findings reveal a mechanism regulating the cargo-specific trafficking of endosomes.
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Affiliation(s)
- Hiroshi Hanafusa
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Takuya Yagi
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Haruka Ikeda
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Naoki Hisamoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Tomoki Nishioka
- Department of Cell Pharmacology, Graduate School of Medicine, Nagoya University, Showa-ku, Nagoya 466-8550, Japan
| | - Kozo Kaibuchi
- Department of Cell Pharmacology, Graduate School of Medicine, Nagoya University, Showa-ku, Nagoya 466-8550, Japan
| | - Kyoko Shirakabe
- Department of Biomedical Sciences, Graduate School of Life Sciences, Ritsumeikan University, Noji-higashi, Kusatsu 525-8577, Japan
| | - Kunihiro Matsumoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
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Feng J, Li D, Liu L, Tang Y, Du R. Interaction of the small GTP-binding protein (Rab7) with β-actin in Litopenaeus vannamei and its role in white spot syndrome virus infection. FISH & SHELLFISH IMMUNOLOGY 2019; 88:1-8. [PMID: 30826412 DOI: 10.1016/j.fsi.2019.02.053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 02/21/2019] [Accepted: 02/25/2019] [Indexed: 06/09/2023]
Abstract
In this study, GST Pull-down and mass spectrometry was applied to the precipitation and identification of the small GTP-binding protein (Rab7) interacting protein in hemocyte of Litopenaeus vannamei. According to the search in GenBank with the peptide mass fingerprint, the 45 kDa protein which was pulled down with the GST-tagged Rab7 (GST-Rab7, GTP bound form) was identified to be β-actin with 28% coverage of amino acid sequences. The interaction of Rab7 with β-actin was verified by both GST Pull-down and ELISA in vitro. Meanwhile, confocal microscopic observation showed that Rab7 could be co-localized with β-actin in hemocytes at 12 h post white spot syndrome virus (WSSV) infection (hpi). GST Pull-down and western blotting were used to analyze the cross-interaction between WSSV VP28, Rab7 and β-actin. The results showed that the GST-VP28, His-tagged Rab7 (His-Rab7) and His-β-actin formed a tripartite complex. At 12 hpi, confocal microscopic observation showed that WSSV could be co-localized with Rab7 and β-actin in hemocytes respectively. Furthermore, based on the in vivo neutralization assay, recombinant His-β-actin accelerated the infection of WSSV, conversely, recombinant His-Rab7 delayed WSSV infection in shrimp. These results suggested the interaction of Rab7 with β-actin and this interaction was involved in WSSV infection.
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Affiliation(s)
- Jixing Feng
- Laboratory of Pathology of Aquatic Animals, Yantai University, Yantai, 264005, PR China.
| | - Denglai Li
- Laboratory of Pathology of Aquatic Animals, Yantai University, Yantai, 264005, PR China
| | - Liming Liu
- Laboratory of Pathology of Aquatic Animals, Yantai University, Yantai, 264005, PR China
| | - Yongzheng Tang
- Laboratory of Pathology of Aquatic Animals, Yantai University, Yantai, 264005, PR China
| | - Rongbin Du
- Laboratory of Pathology of Aquatic Animals, Yantai University, Yantai, 264005, PR China
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Iwasawa S, Yanagi K, Kikuchi A, Kobayashi Y, Haginoya K, Matsumoto H, Kurosawa K, Ochiai M, Sakai Y, Fujita A, Miyake N, Niihori T, Shirota M, Funayama R, Nonoyama S, Ohga S, Kawame H, Nakayama K, Aoki Y, Matsumoto N, Kaname T, Matsubara Y, Shoji W, Kure S. Recurrent de novo
MAPK8IP3
variants cause neurological phenotypes. Ann Neurol 2019; 85:927-933. [DOI: 10.1002/ana.25481] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/01/2019] [Accepted: 04/03/2019] [Indexed: 01/21/2023]
Affiliation(s)
- Shinya Iwasawa
- Department of PediatricsTohoku University Graduate School of Medicine Sendai Japan
| | - Kumiko Yanagi
- National Center for Child Health and Development Tokyo Japan
| | - Atsuo Kikuchi
- Department of PediatricsTohoku University Graduate School of Medicine Sendai Japan
| | - Yasuko Kobayashi
- Department of PediatricsNational Hospital Organization Sendai‐Nishitaga Hospital Sendai Japan
- Department of Pediatric NeurologyTakuto Rehabilitation Center for Children Sendai Japan
| | - Kazuhiro Haginoya
- Department of Pediatric NeurologyTakuto Rehabilitation Center for Children Sendai Japan
- Department of Pediatric NeurologyMiyagi Children's Hospital Sendai Japan
| | - Hiroshi Matsumoto
- Department of PediatricsNational Defense Medical College Saitama Japan
| | - Kenji Kurosawa
- Division of Medical GeneticsKanagawa Children's Medical Center Yokohama Japan
| | - Masayuki Ochiai
- Department of PediatricsGraduate School of Medical Sciences, Kyushu University Fukuoka Japan
| | - Yasunari Sakai
- Department of PediatricsGraduate School of Medical Sciences, Kyushu University Fukuoka Japan
| | - Atsushi Fujita
- Department of Human GeneticsYokohama City University Graduate School of Medicine Yokohama Japan
| | - Noriko Miyake
- Department of Human GeneticsYokohama City University Graduate School of Medicine Yokohama Japan
| | - Tetsuya Niihori
- Department of Medical GeneticsTohoku University Graduate School of Medicine Sendai Japan
| | - Matsuyuki Shirota
- Division of Interdisciplinary Medical Sciences, United Centers for Advanced Research and Translational MedicineTohoku University Graduate School of Medicine Sendai Japan
| | - Ryo Funayama
- Division of Cell Proliferation, United Centers for Advanced Research and Translational MedicineTohoku University Graduate School of Medicine Sendai Japan
| | - Shigeaki Nonoyama
- Department of PediatricsNational Defense Medical College Saitama Japan
| | - Shouichi Ohga
- Department of PediatricsGraduate School of Medical Sciences, Kyushu University Fukuoka Japan
| | - Hiroshi Kawame
- Tohoku Medical Megabank organizationTohoku University Sendai Japan
| | - Keiko Nakayama
- Division of Cell Proliferation, United Centers for Advanced Research and Translational MedicineTohoku University Graduate School of Medicine Sendai Japan
| | - Yoko Aoki
- Department of Medical GeneticsTohoku University Graduate School of Medicine Sendai Japan
| | - Naomichi Matsumoto
- Department of Human GeneticsYokohama City University Graduate School of Medicine Yokohama Japan
| | - Tadashi Kaname
- National Center for Child Health and Development Tokyo Japan
| | | | - Wataru Shoji
- Frontier Research Institute for Interdisciplinary SciencesTohoku University Sendai Japan
| | - Shigeo Kure
- Department of PediatricsTohoku University Graduate School of Medicine Sendai Japan
- Tohoku Medical Megabank organizationTohoku University Sendai Japan
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USP32 regulates late endosomal transport and recycling through deubiquitylation of Rab7. Nat Commun 2019; 10:1454. [PMID: 30926795 PMCID: PMC6440979 DOI: 10.1038/s41467-019-09437-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 03/06/2019] [Indexed: 12/26/2022] Open
Abstract
The endosomal system is a highly dynamic multifunctional organelle, whose complexity is regulated in part by reversible ubiquitylation. Despite the wide-ranging influence of ubiquitin in endosomal processes, relatively few enzymes utilizing ubiquitin have been described to control endosome integrity and function. Here we reveal the deubiquitylating enzyme (DUB) ubiquitin-specific protease 32 (USP32) as a powerful player in this context. Loss of USP32 inhibits late endosome (LE) transport and recycling of LE cargos, resulting in dispersion and swelling of the late compartment. Using SILAC-based ubiquitome profiling we identify the small GTPase Rab7—the logistical centerpiece of LE biology—as a substrate of USP32. Mechanistic studies reveal that LE transport effector RILP prefers ubiquitylation-deficient Rab7, while retromer-mediated LE recycling benefits from an intact cycle of Rab7 ubiquitylation. Collectively, our observations suggest that reversible ubiquitylation helps switch Rab7 between its various functions, thereby maintaining global spatiotemporal order in the endosomal system. Though ubiquitin is known to broadly influence endosomal trafficking, few ubiquitin-utilizing enzymes targeting endosomal regulators are known. Here, the authors find that the deubiquitylating enzyme (DUB) USP32 influences endosomal membrane dynamics by deubiquitinating Rab7.
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Abstract
Cytoplasmic dynein-1 (hereafter dynein) is an essential cellular motor that drives the movement of diverse cargos along the microtubule cytoskeleton, including organelles, vesicles and RNAs. A long-standing question is how a single form of dynein can be adapted to a wide range of cellular functions in both interphase and mitosis. Recent progress has provided new insights - dynein interacts with a group of activating adaptors that provide cargo-specific and/or function-specific regulation of the motor complex. Activating adaptors such as BICD2 and Hook1 enhance the stability of the complex that dynein forms with its required activator dynactin, leading to highly processive motility toward the microtubule minus end. Furthermore, activating adaptors mediate specific interactions of the motor complex with cargos such as Rab6-positive vesicles or ribonucleoprotein particles for BICD2, and signaling endosomes for Hook1. In this Cell Science at a Glance article and accompanying poster, we highlight the conserved structural features found in dynein activators, the effects of these activators on biophysical parameters, such as motor velocity and stall force, and the specific intracellular functions they mediate.
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Affiliation(s)
- Mara A Olenick
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Erika L F Holzbaur
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
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Tong J, Tan L, Chun C, Im YJ. Structural basis of human ORP1-Rab7 interaction for the late-endosome and lysosome targeting. PLoS One 2019; 14:e0211724. [PMID: 30721249 PMCID: PMC6363164 DOI: 10.1371/journal.pone.0211724] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 01/20/2019] [Indexed: 02/07/2023] Open
Abstract
Oxysterol-binding protein (OSBP) and OSBP-related proteins (ORPs) constitute a family of lipid transfer proteins conserved in eukaryotes. ORP1 transports cholesterol at the interface between the late endosomes/lysosomes (LELs) and the endoplasmic reticulum (ER). ORP1 is targeted to the endosomal membranes by forming a tripartite complex with the LE GTPase Rab7 and its effector RILP (Rab7-interacting lysosomal protein). Here, we determined the crystal structure of human ORP1 ANK domain in complex with the GTP-bound form of Rab7. ORP1 ANK binds to the helix α3 of Rab7 located away from the switching regions, which makes the interaction independent of the nucleotide-binding state of Rab7. Thus, the effector-interacting switch regions of Rab7 are accessible for RILP binding, allowing formation of the ORP1-Rab7-RILP complex. ORP1 ANK binds to Rab7 and the Rab7-RILP complex with similar micro-molar affinities, which is consistent with the independence binding of ORP1 and RILP to Rab7. The structural model of the ORP1-Rab7-RILP complex correlates with the recruitment of ORP1 at the LEL-ER interface and the role in lipid transport and regulation.
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Affiliation(s)
- Junsen Tong
- College of Pharmacy, Chonnam National University, Gwangju, Republic of Korea
| | - Lingchen Tan
- College of Pharmacy, Chonnam National University, Gwangju, Republic of Korea
| | - ChangJu Chun
- College of Pharmacy, Chonnam National University, Gwangju, Republic of Korea
| | - Young Jun Im
- College of Pharmacy, Chonnam National University, Gwangju, Republic of Korea
- * E-mail:
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40
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Olenick MA, Dominguez R, Holzbaur ELF. Dynein activator Hook1 is required for trafficking of BDNF-signaling endosomes in neurons. J Cell Biol 2019; 218:220-233. [PMID: 30373907 PMCID: PMC6314548 DOI: 10.1083/jcb.201805016] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 09/18/2018] [Accepted: 10/15/2018] [Indexed: 01/16/2023] Open
Abstract
Axonal transport is required for neuronal development and survival. Transport from the axon to the soma is driven by the molecular motor cytoplasmic dynein, yet it remains unclear how dynein is spatially and temporally regulated. We find that the dynein effector Hook1 mediates transport of TrkB-BDNF-signaling endosomes in primary hippocampal neurons. Hook1 comigrates with a subpopulation of Rab5 endosomes positive for TrkB and BDNF, which exhibit processive retrograde motility with faster velocities than the overall Rab5 population. Knockdown of Hook1 significantly reduced the motility of BDNF-signaling endosomes without affecting the motility of other organelles. In microfluidic chambers, Hook1 depletion resulted in a significant decrease in the flux and processivity of BDNF-Qdots along the mid-axon, an effect specific for Hook1 but not Hook3. Hook1 depletion inhibited BDNF trafficking to the soma and blocked downstream BDNF- and TrkB-dependent signaling to the nucleus. Together, these studies support a model in which differential association with cargo-specific effectors efficiently regulates dynein in neurons.
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Affiliation(s)
- Mara A Olenick
- The Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Center for Engineering Mechanobiology, University of Pennsylvania, Philadelphia, PA
| | - Roberto Dominguez
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- The Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Erika L F Holzbaur
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- The Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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41
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Rosa-Ferreira C, Sweeney ST, Munro S. The small G protein Arl8 contributes to lysosomal function and long-range axonal transport in Drosophila. Biol Open 2018; 7:bio.035964. [PMID: 30115618 PMCID: PMC6176938 DOI: 10.1242/bio.035964] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The small GTPase Arl8 has emerged as a major regulatory GTPase on lysosomes. Studies in mammalian cells have shown that it regulates both fusion with late endosomes and also lysosomal motility. In its active GTP-bound state, it recruits to lysosomes the HOPS (homotypic fusion and protein sorting) endosomal tethering complex and also proteins that link lysosomes to microtubule motors such as the kinesin adaptor PLEKHM2. To gain further insights into Arl8 biology, we examined the single Drosophila ortholog. Drosophila Arl8 is essential for viability, and mitotic clones of mutant cells are able to continue to divide but show perturbation of the late endocytic pathway. Progeny-lacking Arl8 die as late larvae with movement-paralysis characteristic of defects in neuronal function. This phenotype was rescued by expression of Arl8 in motor neurons. Examination of these neurons in the mutant larvae revealed smaller synapses and axons with elevated levels of carriers containing synaptic components. Affinity chromatography revealed binding of Drosophila Arl8 to the HOPS complex, and to the Drosophila ortholog of RILP, a protein that, in mammals, recruits dynein to late endosomes, with dynein being known to be required for neuronal transport. Thus Drosophila Arl8 controls late endocytic function and transport via at least two distinct effectors. This article has an associated First Person interview with the first author of the paper. Summary:Drosophila Arl8 is essential for viability and is required for normal functioning of the late endocytic pathway and for long-range transport in axons.
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Affiliation(s)
| | - Sean T Sweeney
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Sean Munro
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
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42
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Rout AK, Wu X, Starich MR, Strub MP, Hammer JA, Tjandra N. The Structure of Melanoregulin Reveals a Role for Cholesterol Recognition in the Protein's Ability to Promote Dynein Function. Structure 2018; 26:1373-1383.e4. [PMID: 30174147 DOI: 10.1016/j.str.2018.07.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 06/12/2018] [Accepted: 07/24/2018] [Indexed: 01/24/2023]
Abstract
Melanoregulin (Mreg) is a small, highly charged, multiply palmitoylated protein present on the membrane of melanosomes. Mreg is implicated in the transfer of melanosomes from melanocytes to keratinocytes, and in promoting the microtubule minus end-directed transport of these organelles. The possible molecular function of Mreg was identified by solving its structure using nuclear magnetic resonance (NMR) spectroscopy. Mreg contains six α helices forming a fishhook-like fold in which positive and negative charges occupy opposite sides of the protein's surface and sandwich a putative, cholesterol recognition sequence (CRAC motif). Mreg containing a point mutation within its CRAC motif still targets to late endosomes/lysosomes, but no longer promotes their microtubule minus end-directed transport. Moreover, wild-type Mreg does not promote the microtubule minus end-directed transport of late endosomes/lysosomes in cells transiently depleted of cholesterol. Finally, reversing the charge of three clustered acidic residues partially inhibits Mreg's ability to drive these organelles to microtubule minus ends.
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Affiliation(s)
- Ashok K Rout
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xufeng Wu
- Cell Biology and Physiology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mary R Starich
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marie-Paule Strub
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - John A Hammer
- Cell Biology and Physiology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Nico Tjandra
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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43
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Bright LJ, Lynch M. The Rab7 subfamily across Paramecium aurelia species; evidence of high conservation in sequence and function. Small GTPases 2018; 11:421-429. [PMID: 30156960 DOI: 10.1080/21541248.2018.1502056] [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: 10/28/2022] Open
Abstract
We examined sequence conservation and signatures of selection in Rab7 proteins across 11 Paramecium aurelia species, and determined the localization patterns of two P. tetraurelia Rab7 paralogs when expressed as GFP fusions in live cells. We found that, while there is a variable number of Rab7 paralogs per genome, Rab7 genes are highly conserved in sequence and appear to be under strong purifying selection across aurelias. Additionally, and surprisingly based on earlier studies, we found that two P. tetraurelia Rab7 proteins have virtually identical localization patterns. Consistent with this, when we examined the gene family of a highly conserved Rab binding partner across aurelias (Rab-Interacting Lysosomal Protein, or RILP), we found that residues in key binding sites in RILPs were absolutely conserved in 13 of 21 proteins, representing genes from 9 of the 11 species examined. Of note, RILP gene number appears to be even more constrained than Rab7 gene number per genome. Abbreviation: WGD: Whole genome duplication.
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Affiliation(s)
- Lydia J Bright
- Department of Biology, State University of New York at New Paltz , New Paltz, NY, USA.,Department of Biology, Indiana University , Bloomington, IN, USA
| | - Michael Lynch
- Department of Biology, Indiana University , Bloomington, IN, USA.,Biodesign Institute, Arizona State University , Tempe, AZ, USA
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44
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Ma X, Liu K, Li J, Li H, Li J, Liu Y, Yang C, Liang H. A non-canonical GTPase interaction enables ORP1L-Rab7-RILP complex formation and late endosome positioning. J Biol Chem 2018; 293:14155-14164. [PMID: 30012887 DOI: 10.1074/jbc.ra118.001854] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 07/09/2018] [Indexed: 01/06/2023] Open
Abstract
Endosomal transport represents the primary mode for intracellular trafficking and signaling transduction and thus has to be tightly controlled. The molecular processes controlling the endosomal positioning utilize several large protein complexes, one of which contains the small GTPase Rab7, Rab-interacting lysosomal protein (RILP), and oxysterol-binding protein-related protein 1 (ORP1L). Rab7 is known to interact with RILP through a canonical binding site termed the effector-interacting switch region, but it is not clear how Rab7 interacts with ORP1L, limiting our understanding of the overall process. Here, we report structural and biochemical investigation of the Rab7-ORP1L interaction. We found that, contrary to prior studies, the interaction between Rab7 and the N-terminal ankyrin repeat domain (ARDN) of ORP1L is independent of Rab7's GTP- or GDP-binding state. Moreover, we show that Rab7 interacts with ORP1L ARDN via a unique region consisting of helix3 (α3) and 310-helix 2 (η2). This architecture leaves the canonical effector-interacting switch regions available for RILP binding and thus allows formation of the ORP1L-Rab7-RILP tripartite complex. Mutational disruption of the interacting interface between ORP1L and Rab7 compromised the ability of ORP1L-Rab7-RILP to regulate the late endosome positioning. Collectively, our results again manifested the versatility in the interaction between GTPase and its effector.
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Affiliation(s)
- Xinli Ma
- From the National Laboratory of Biomacromolecules, Institute of Biophysics and.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.,State Key laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.,State Key Laboratory of Utilization and Conservation of Bio-Resources in Yunnan and.,Life Science Center and School of Life Sciences, Yunnan University, Kunming 650500, China, and
| | - Jian Li
- From the National Laboratory of Biomacromolecules, Institute of Biophysics and
| | - Huanhuan Li
- From the National Laboratory of Biomacromolecules, Institute of Biophysics and.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Li
- From the National Laboratory of Biomacromolecules, Institute of Biophysics and
| | - Yingfang Liu
- From the National Laboratory of Biomacromolecules, Institute of Biophysics and.,Schools of Medicine and
| | - Chonglin Yang
- State Key laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China, .,State Key Laboratory of Utilization and Conservation of Bio-Resources in Yunnan and.,Life Science Center and School of Life Sciences, Yunnan University, Kunming 650500, China, and
| | - Huanhuan Liang
- From the National Laboratory of Biomacromolecules, Institute of Biophysics and .,Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou 510275, China
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45
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Abstract
Cytoplasmic dynein 1 is an important microtubule-based motor in many eukaryotic cells. Dynein has critical roles both in interphase and during cell division. Here, we focus on interphase cargoes of dynein, which include membrane-bound organelles, RNAs, protein complexes and viruses. A central challenge in the field is to understand how a single motor can transport such a diverse array of cargoes and how this process is regulated. The molecular basis by which each cargo is linked to dynein and its cofactor dynactin has started to emerge. Of particular importance for this process is a set of coiled-coil proteins - activating adaptors - that both recruit dynein-dynactin to their cargoes and activate dynein motility.
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46
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Kwon H, Jang D, Choi M, Lee J, Jeong K, Pak Y. Alternative translation initiation of Caveolin-2 desensitizes insulin signaling through dephosphorylation of insulin receptor by PTP1B and causes insulin resistance. Biochim Biophys Acta Mol Basis Dis 2018; 1864:2169-2182. [PMID: 29604334 DOI: 10.1016/j.bbadis.2018.03.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 03/08/2018] [Accepted: 03/26/2018] [Indexed: 12/30/2022]
Abstract
Insulin resistance, defined as attenuated sensitivity responding to insulin, impairs insulin action. Direct causes and molecular mechanisms of insulin resistance have thus far remained elusive. Here we show that alternative translation initiation (ATI) of Caveolin-2 (Cav-2) regulates insulin sensitivity. Cav-2β isoform yielded by ATI desensitizes insulin receptor (IR) via dephosphorylation by protein-tyrosine phosphatase 1B (PTP1B), and subsequent endocytosis and lysosomal degradation of IR, causing insulin resistance. Blockage of Cav-2 ATI protects against insulin resistance by preventing Cav-2β-PTP1B-directed IR desensitization, thereby normalizing insulin sensitivity and glucose uptake. Our findings show that Cav-2β is a negative regulator of IR signaling, and identify a mechanism causing insulin resistance through control of insulin sensitivity via Cav-2 ATI.
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Affiliation(s)
- Hayeong Kwon
- Division of Life Science, Graduate School of Applied Life Science (BK21 Plus Program), PMBBRC, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Donghwan Jang
- Division of Life Science, Graduate School of Applied Life Science (BK21 Plus Program), PMBBRC, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Moonjeong Choi
- Division of Life Science, Graduate School of Applied Life Science (BK21 Plus Program), PMBBRC, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jaewoong Lee
- Division of Life Science, Graduate School of Applied Life Science (BK21 Plus Program), PMBBRC, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Kyuho Jeong
- Division of Life Science, Graduate School of Applied Life Science (BK21 Plus Program), PMBBRC, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Yunbae Pak
- Division of Life Science, Graduate School of Applied Life Science (BK21 Plus Program), PMBBRC, Gyeongsang National University, Jinju 52828, Republic of Korea.
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47
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Pylypenko O, Hammich H, Yu IM, Houdusse A. Rab GTPases and their interacting protein partners: Structural insights into Rab functional diversity. Small GTPases 2018. [PMID: 28632484 DOI: 10.1080/215412481336191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023] Open
Abstract
Rab molecular switches are key players in defining membrane identity and regulating intracellular trafficking events in eukaryotic cells. In spite of their global structural similarity, Rab-family members acquired particular features that allow them to perform specific cellular functions. The overall fold and local sequence conservations enable them to utilize a common machinery for prenylation and recycling; while individual Rab structural differences determine interactions with specific partners such as GEFs, GAPs and effector proteins. These interactions orchestrate the spatiotemporal regulation of Rab localization and their turning ON and OFF, leading to tightly controlled Rab-specific functionalities such as membrane composition modifications, recruitment of molecular motors for intracellular trafficking, or recruitment of scaffold proteins that mediate interactions with downstream partners, as well as actin cytoskeleton regulation. In this review we summarize structural information on Rab GTPases and their complexes with protein partners in the context of partner binding specificity and functional outcomes of their interactions in the cell.
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Affiliation(s)
- Olena Pylypenko
- a Structural Motility, Institut Curie , PSL Research University, CNRS, UMR 144 , Paris , France
| | - Hussein Hammich
- a Structural Motility, Institut Curie , PSL Research University, CNRS, UMR 144 , Paris , France
- b Sorbonne Universités , UPMC Univ Paris 06, Sorbonne Universités, IFD , Paris , France
| | - I-Mei Yu
- a Structural Motility, Institut Curie , PSL Research University, CNRS, UMR 144 , Paris , France
| | - Anne Houdusse
- a Structural Motility, Institut Curie , PSL Research University, CNRS, UMR 144 , Paris , France
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48
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Steger M, Diez F, Dhekne HS, Lis P, Nirujogi RS, Karayel O, Tonelli F, Martinez TN, Lorentzen E, Pfeffer SR, Alessi DR, Mann M. Systematic proteomic analysis of LRRK2-mediated Rab GTPase phosphorylation establishes a connection to ciliogenesis. eLife 2017; 6:31012. [PMID: 29125462 PMCID: PMC5695910 DOI: 10.7554/elife.31012] [Citation(s) in RCA: 275] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 11/09/2017] [Indexed: 12/21/2022] Open
Abstract
We previously reported that Parkinson’s disease (PD) kinase LRRK2 phosphorylates a subset of Rab GTPases on a conserved residue in their switch-II domains (Steger et al., 2016) (PMID: 26824392). Here, we systematically analyzed the Rab protein family and found 14 of them (Rab3A/B/C/D, Rab5A/B/C, Rab8A/B, Rab10, Rab12, Rab29, Rab35 and Rab43) to be specifically phosphorylated by LRRK2, with evidence for endogenous phosphorylation for ten of them (Rab3A/B/C/D, Rab8A/B, Rab10, Rab12, Rab35 and Rab43). Affinity enrichment mass spectrometry revealed that the primary ciliogenesis regulator, RILPL1 specifically interacts with the LRRK2-phosphorylated forms of Rab8A and Rab10, whereas RILPL2 binds to phosphorylated Rab8A, Rab10, and Rab12. Induction of primary cilia formation by serum starvation led to a two-fold reduction in ciliogenesis in fibroblasts derived from pathogenic LRRK2-R1441G knock-in mice. These results implicate LRRK2 in primary ciliogenesis and suggest that Rab-mediated protein transport and/or signaling defects at cilia may contribute to LRRK2-dependent pathologies.
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Affiliation(s)
- Martin Steger
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Federico Diez
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Herschel S Dhekne
- Department of Biochemistry, Stanford University School of Medicine, Stanford, United States
| | - Pawel Lis
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Raja S Nirujogi
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Ozge Karayel
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Francesca Tonelli
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Terina N Martinez
- The Michael J. Fox Foundation for Parkinson's Research, New York, United States
| | - Esben Lorentzen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Suzanne R Pfeffer
- Department of Biochemistry, Stanford University School of Medicine, Stanford, United States
| | - Dario R Alessi
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Martinsried, Germany
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49
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Timely regulated sorting from early to late endosomes is required to maintain cerebellar long-term depression. Nat Commun 2017; 8:401. [PMID: 28864821 PMCID: PMC5581341 DOI: 10.1038/s41467-017-00518-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 07/05/2017] [Indexed: 11/16/2022] Open
Abstract
An important feature of long-term synaptic plasticity is the prolonged maintenance of plastic changes in synaptic transmission. The trafficking of AMPA-type glutamate receptors (AMPARs) is involved in the expression of many forms of synaptic plasticity, yet the subsequent events accomplishing the maintenance of plastic changes in synaptic AMPAR numbers are not fully understood. Here, we find that maintenance of cerebellar long-term depression results from a reduction in the number of AMPARs residing within endocytic recycling pathways. We then develop a genetically encoded, photosensitive inhibitor of late endosome sorting and use this to discover that initial maintenance of long-term depression relies on timely regulated late endosome sorting, which exhibits a threshold as well as switch-like behavior. Thus, our results indicate that recycling AMPAR numbers are reduced by a switching machinery of transient late endosome sorting, and that this process enables the transition from basal synaptic transmission to long-term depression maintenance. Long term depression (LTD) of the cerebellum is known to be mediated by postsynaptic trafficking of glutamate receptor AMPAR. Here, Kim and colleagues show that early- to late-endosomal sorting of AMPAR represents the switch from expression to maintenance phase of cerebellar LTD.
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50
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Ku B, You JA, Oh KJ, Yun HY, Lee HS, Shin HC, Jung J, Shin YB, Kim SJ. Crystal structures of two forms of the Acanthamoeba polyphaga mimivirus Rab GTPase. Arch Virol 2017; 162:3407-3416. [PMID: 28779233 DOI: 10.1007/s00705-017-3510-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 06/30/2017] [Indexed: 01/09/2023]
Abstract
Acanthamoeba polyphaga mimivirus (APMV) is a member of the family of giant viruses, harboring a 1,200 kbp genome within its 700 nm-diameter viral particle. The R214 gene of the APMV genome was recently shown to encode a homologue of the Rab GTPases, molecular switch proteins known to play a pivotal role in the regulation of membrane trafficking that were considered to exist only in eukaryotes. Herein, we report the first crystal structures of GDP- and GTP-bound forms of APMV Rab GTPase, both of which were determined at high resolution. An in-depth structural comparison of APMV Rab with each other and with mammalian Rab homologues led to an atomic-level elucidation of the inactive-active conformational change upon GDP/GTP exchange. APMV Rab GTPase exhibited considerable structural similarity to human Rab5, as previously predicted based on its amino acid sequence. However, it also contains unique structural features differentiating it from mammalian homologues, such as the functional substitution of a phenylalanine residue for the stabilization of the nucleotide's guanine base.
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Affiliation(s)
- Bonsu Ku
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.
- Department of Bioscience, University of Science and Technology KRIBB School, Daejeon, 34113, Republic of Korea.
| | - Jin A You
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
- Department of Bioscience, University of Science and Technology KRIBB School, Daejeon, 34113, Republic of Korea
| | - Kyoung-Jin Oh
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Hye-Yeoung Yun
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
- Department of Bioscience, University of Science and Technology KRIBB School, Daejeon, 34113, Republic of Korea
| | - Hye Seon Lee
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
- Department of Biology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Ho-Chul Shin
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Juyeon Jung
- Hazard Monitoring BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Yong-Beom Shin
- Hazard Monitoring BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Seung Jun Kim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.
- Department of Bioscience, University of Science and Technology KRIBB School, Daejeon, 34113, Republic of Korea.
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