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Vallee RB, Yi J, Quintremil S, Khobrekar N. Roles of the multivalent dynein adaptors BicD2 and RILP in neurons. Neurosci Lett 2021; 752:135796. [PMID: 33667600 DOI: 10.1016/j.neulet.2021.135796] [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] [Received: 12/24/2020] [Revised: 02/18/2021] [Accepted: 02/20/2021] [Indexed: 01/18/2023]
Abstract
Cytoplasmic dynein is responsible for all forms of retrograde transport in neurons and other cells. Work over several years has led to the identification of a class of coiled-coil domain containing "adaptor" proteins that are responsible for expanding dynein's range of cargo interactions, as well as regulating dynein motor behavior. This brief review focuses first on the BicD family of adaptor proteins, which clearly serve to expand the number of dynein cargo interactions. RILP, another adaptor protein, also interacts with multiple proteins. Surprisingly, this is to mediate a series of steps within a common pathway, higher eukaryotic autophagy. These distinct features have important implications for understanding the full range of dynein adaptor functions.
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Affiliation(s)
- Richard B Vallee
- Columbia University, Department of Pathology and Cell Biology, United States
| | - Julie Yi
- Columbia University, Department of Pathology and Cell Biology, United States
| | | | - Noopur Khobrekar
- Columbia University, Department of Pathology and Cell Biology, United States.
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2
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Abu Irqeba A, Ogilvie JM. Di-arginine and FFAT-like motifs retain a subpopulation of PRA1 at ER-mitochondria membrane contact sites. PLoS One 2020; 15:e0243075. [PMID: 33259547 PMCID: PMC7707580 DOI: 10.1371/journal.pone.0243075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 11/14/2020] [Indexed: 11/19/2022] Open
Abstract
Prenylated Rab Acceptor 1 (PRA1/Rabac1) is a four-pass transmembrane protein that has been found to localize to the Golgi and promiscuously associate with a diverse array of Rab GTPases. We have previously identified PRA1 to be among the earliest significantly down-regulated genes in the rd1 mouse model of retinitis pigmentosa, a retinal degenerative disease. Here, we show that an endogenous subpopulation of PRA1 resides within the endoplasmic reticulum (ER) at ER-mitochondria membrane contact sites in cultured mammalian cells. We also demonstrate that PRA1 contains two previously unidentified ER retention/retrieval amino acid sequences on its cytosolic N-terminal region: a membrane distal di-arginine motif and a novel membrane proximal FFAT-like motif. Using a truncation construct that lacks complete Golgi targeting information, we show that mutation of either motif leads to an increase in cell surface localization, while mutation of both motifs exhibits an additive effect. We also present evidence that illustrates that N- or C- terminal addition of a tag to full-length PRA1 leads to differential localization to either the Golgi or reticular ER, phenotypes that do not completely mirror endogenous protein localization. The presence of multiple ER retention motifs on the PRA1 N-terminal region further suggests that it has a functional role within the ER.
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Affiliation(s)
- Ameair Abu Irqeba
- Department of Biology, Saint Louis University, St. Louis, Missouri, United States of America
- * E-mail: (AAI); (JMO)
| | - Judith Mosinger Ogilvie
- Department of Biology, Saint Louis University, St. Louis, Missouri, United States of America
- * E-mail: (AAI); (JMO)
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3
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Agola JO, Sivalingam D, Cimino DF, Simons PC, Buranda T, Sklar LA, Wandinger-Ness A. Quantitative bead-based flow cytometry for assaying Rab7 GTPase interaction with the Rab-interacting lysosomal protein (RILP) effector protein. Methods Mol Biol 2015; 1298:331-54. [PMID: 25800855 PMCID: PMC6033261 DOI: 10.1007/978-1-4939-2569-8_28] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2023]
Abstract
Rab7 facilitates vesicular transport and delivery from early endosomes to late endosomes as well as from late endosomes to lysosomes. The role of Rab7 in vesicular transport is dependent on its interactions with effector proteins, among them Rab-interacting lysosomal protein (RILP), which aids in the recruitment of active Rab7 (GTP-bound) onto dynein-dynactin motor complexes to facilitate late endosomal transport on the cytoskeleton. Here we detail a novel bead-based flow cytometry assay to measure Rab7 interaction with the Rab-interacting lysosomal protein (RILP) effector protein and demonstrate its utility for quantitative assessment and studying drug-target interactions. The specific binding of GTP-bound Rab7 to RILP is readily demonstrated and shown to be dose-dependent and saturable enabling K d and B max determinations. Furthermore, binding is nearly instantaneous and temperature-dependent. In a novel application of the assay method, a competitive small molecule inhibitor of Rab7 nucleotide binding (CID 1067700 or ML282) is shown to inhibit the Rab7-RILP interaction. Thus, the assay is able to distinguish that the small molecule, rather than incurring the active conformation, instead 'locks' the GTPase in the inactive conformation. Together, this work demonstrates the utility of using a flow cytometry assay to quantitatively characterize protein-protein interactions involving small GTPases and which has been adapted to high-throughput screening. Further, the method provides a platform for testing small molecule effects on protein-protein interactions, which can be relevant to drug discovery and development.
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Affiliation(s)
- Jacob O Agola
- Department of Pathology, University of New Mexico School of Medicine, Albuquerque, NM, 87131, USA
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4
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Wandinger-Ness A, Zerial M. Rab proteins and the compartmentalization of the endosomal system. Cold Spring Harb Perspect Biol 2014; 6:a022616. [PMID: 25341920 DOI: 10.1101/cshperspect.a022616] [Citation(s) in RCA: 414] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Of the approximately 70 human Rab GTPases, nearly three-quarters are involved in endocytic trafficking. Significant plasticity in endosomal membrane transport pathways is closely coupled to receptor signaling and Rab GTPase-regulated scaffolds. Here we review current literature pertaining to endocytic Rab GTPase localizations, functions, and coordination with regulatory proteins and effectors. The roles of Rab GTPases in (1) compartmentalization of the endocytic pathway into early, recycling, late, and lysosomal routes; (2) coordination of individual transport steps from vesicle budding to fusion; (3) effector interactomes; and (4) integration of GTPase and signaling cascades are discussed.
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Affiliation(s)
- Angela Wandinger-Ness
- Department of Pathology MSC08 4640, University of New Mexico HSC, Albuquerque, New Mexico 87131
| | - Marino Zerial
- Max Planck Institute of Molecular and Cell Biology and Genetics, 01307 Dresden, Germany
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5
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Ishigami T, Abe K, Aoki I, Minegishi S, Ryo A, Matsunaga S, Matsuoka K, Takeda H, Sawasaki T, Umemura S, Endo Y. Anti‐interleukin‐5 and multiple autoantibodies are associated with human atherosclerotic diseases and serum interleukin‐5 levels. FASEB J 2013; 27:3437-45. [DOI: 10.1096/fj.12-222653] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Tomoaki Ishigami
- Department of Medical Science and Cardiorenal MedicineYokohama City University Graduate School of MedicineYokohamaJapan
| | - Kaito Abe
- Department of Medical Science and Cardiorenal MedicineYokohama City University Graduate School of MedicineYokohamaJapan
| | - Ichiro Aoki
- Department of Molecular PathologyYokohama City University Graduate School of MedicineYokohamaJapan
| | - Shintaro Minegishi
- Department of Medical Science and Cardiorenal MedicineYokohama City University Graduate School of MedicineYokohamaJapan
| | - Akihide Ryo
- Department of MicrobiologyYokohama City University Graduate School of MedicineYokohamaJapan
| | - Satoko Matsunaga
- Department of MicrobiologyYokohama City University Graduate School of MedicineYokohamaJapan
| | - Kazuhiro Matsuoka
- Ehime University Cell‐Free Science and Technology Research Center Division of Proteomedical Sciences; EhimeJapan
| | - Hiroyuki Takeda
- Ehime University Cell‐Free Science and Technology Research Center Division of Proteomedical Sciences; EhimeJapan
| | - Tatsuya Sawasaki
- Ehime University Cell‐Free Science and Technology Research Center Division of Proteomedical Sciences; EhimeJapan
| | - Satoshi Umemura
- Department of Medical Science and Cardiorenal MedicineYokohama City University Graduate School of MedicineYokohamaJapan
| | - Yaeta Endo
- Ehime University Cell‐Free Science and Technology Research Center Division of Proteomedical Sciences; EhimeJapan
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6
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Alvim Kamei CL, Boruc J, Vandepoele K, Van den Daele H, Maes S, Russinova E, Inzé D, De Veylder L. The PRA1 gene family in Arabidopsis. PLANT PHYSIOLOGY 2008; 147:1735-49. [PMID: 18583532 PMCID: PMC2492607 DOI: 10.1104/pp.108.122226] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2008] [Accepted: 06/25/2008] [Indexed: 05/18/2023]
Abstract
Prenylated Rab acceptor 1 (PRA1) domain proteins are small transmembrane proteins that regulate vesicle trafficking as receptors of Rab GTPases and the vacuolar soluble N-ethylmaleimide-sensitive factor attachment receptor protein VAMP2. However, little is known about PRA1 family members in plants. Sequence analysis revealed that higher plants, compared with animals and primitive plants, possess an expanded family of PRA1 domain-containing proteins. The Arabidopsis (Arabidopsis thaliana) PRA1 (AtPRA1) proteins were found to homodimerize and heterodimerize in a manner corresponding to their phylogenetic distribution. Different AtPRA1 family members displayed distinct expression patterns, with a preference for vascular cells and expanding or developing tissues. AtPRA1 genes were significantly coexpressed with Rab GTPases and genes encoding vesicle transport proteins, suggesting an involvement in the vesicle trafficking process similar to that of their animal counterparts. Correspondingly, AtPRA1 proteins were localized in the endoplasmic reticulum, Golgi apparatus, and endosomes/prevacuolar compartments, hinting at a function in both secretory and endocytic intracellular trafficking pathways. Taken together, our data reveal a high functional diversity of AtPRA1 proteins, probably dealing with the various demands of the complex trafficking system.
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Affiliation(s)
- Claire Lessa Alvim Kamei
- Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-590, Brazil
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7
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Colucci AMR, Campana MC, Bellopede M, Bucci C. The Rab-interacting lysosomal protein, a Rab7 and Rab34 effector, is capable of self-interaction. Biochem Biophys Res Commun 2005; 334:128-33. [PMID: 15996637 DOI: 10.1016/j.bbrc.2005.06.067] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2005] [Accepted: 06/14/2005] [Indexed: 11/28/2022]
Abstract
Rab-interacting lysosomal protein (RILP) has been identified as an interacting partner of the small GTPases Rab7 and Rab34. Active Rab7 recruits RILP on the late endosomal/lysosomal membrane and RILP then functions as a Rab7 effector controlling transport to degradative compartments. Indeed, RILP induces recruitment of dynein-dynactin motor complexes to Rab7-containing late endosomes and lysosomes. Recently, Rab7 and RILP have been found to be key proteins also for the biogenesis of phagolysosomes. Therefore, RILP represents probably an important factor for all endocytic routes to lysosomes. In this study, we show, using the yeast two-hybrid system, that RILP is able to interact with itself. The data obtained with the two-hybrid system were confirmed using co-immunoprecipitation in HeLa cells. The data together indicate that RILP, as already demonstrated for several other Rab effector proteins, is capable of self-association, thus probably forming a homo-dimer.
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Affiliation(s)
- Anna Maria Rosaria Colucci
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università degli Studi di Lecce, Via Monteroni, 73100 Lecce, Italy
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8
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Abstract
Rab7, a member of the Rab family of small G proteins, has been shown to regulate late endocytic traffic and lysosome biogenesis, but the exact roles and the mode of actions of Rab7 are still undetermined. Accumulating evidence suggests that each Rab protein has multiple target proteins and works together with them to coordinate the individual step of vesicle traffic. Rabring7 (Rab7-interacting ring finger protein) is a Rab7 target protein that has been isolated using a CytoTrap system. This protein shows no homology with RILP, which has been reported as another Rab7 target protein. Rabring7 is recruited efficiently to late endosome/lysosome by the GTP-bound form of Rab7. Exogenous expression of Rabring7 not only affects epidermal growth factor degradation but also induces the perinuclear aggregation of lysosomes and the increased acidity in the lysosomes. This chapter describes the procedures for the isolation of Rabring7 with a CytoTrap system, the analysis of the Rab7-Rabring7 interactions, and the properties of Rabring7.
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9
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Abstract
Rab proteins are master regulators of vesicular membrane traffic of endocytic and exocytic pathways. They basically serve to recruit proteins and lipids required for vesicle formation, docking, and fusion. Each Rab protein is able to recruit one or more effectors, and, through the action of effectors, it drives its specific downstream functions. The Rab interacting lysosomal protein (RILP) is a common effector of Rab7 and Rab34, two Rab proteins implicated in the biogenesis of lysosomes. RILP is recruited onto late endosomal/lysosomal membranes by Rab7-GTP where it induces the recruitment of the dynein-dynactin motor complexes. Therefore, through the timed and selective dynein motor recruitment onto late endosomes and lysosomes, Rab7 and RILP control transport to endocytic degradative compartments. A similar role for Rab7 and RILP has been demonstrated also for phagosomes. Indeed, RILP recruits dynein-dynactin motors on Rab7-GTP-positive phagosomes and the recruitment not only displaces phagosomes centripetally, but also promotes the extension of phagosomal tubules toward late endocytic compartments. RILP is therefore a key protein for the biogenesis of lysosomes and phagolysosomes. This chapter describes how to express wild-type or mutated RILP in mammalian cells, and how to test the effects caused by RILP dysfunction. In particular, we report assays to monitor the interaction between RILP and Rab7, morphology and distribution of endosomes, and to measure degradation of endocytic markers.
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10
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Houlden H, King RHM, Muddle JR, Warner TT, Reilly MM, Orrell RW, Ginsberg L. A novel RAB7 mutation associated with ulcero-mutilating neuropathy. Ann Neurol 2004; 56:586-90. [PMID: 15455439 DOI: 10.1002/ana.20281] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
There are two known autosomal dominant genes for the hereditary ulcero-mutilating neuropathies: SPTLC1 (hereditary sensory neuropathy type 1) and RAB7 (Charcot-Marie-Tooth disease type 2B). We report a family with autosomal dominant ulcero-mutilating neuropathy, developing in the teens and characterized by ulcers, amputations, sensory involvement in the feet but no motor features. Sequencing the RAB7 gene showed a novel heterozygous A to C mutation, changing asparagine to threonine at codon 161. The mutation is situated adjacent to a previously identified valine to methionine mutation at codon 162, implying a hotspot for mutations in the highly conserved C terminus of RAB7.
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Affiliation(s)
- Henry Houlden
- University Department of Clinical Neurosciences, Royal Free Campus, Royal Free and University College Medical School, University College London, United Kingdom
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11
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Abstract
Regulation of membrane trafficking requires the concerted actions of rab proteins, their effectors and several phosphatidylinositol 3'-kinases. Rab7 is required for late endosomal transport and here we establish that the phosphatidylinositol 3'-kinase hVPS34 and its adaptor protein p150 are rab7 interacting partners. The hVPS34/p150 complex colocalized with rab7 on late endosomes and hVPS34 activity was dependent on nucleotide cycling of rab7. In addition, total cellular phosphatidylinositol 3'-phosphate levels were modulated by rab7 expression, suggesting that rab7 activation impacted kinase cycling to early endosomes. The data identify rab7 as an important regulator of late endosomal hVPS34 function and link rab7 to the regulation of phosphatidylinositol 3'-kinase cycling between early and late endosomes.
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Affiliation(s)
- Mary-Pat Stein
- Molecular Trafficking Laboratory, Department of Pathology, University of New Mexico School of Medicine, Albuquerque, New Mexico 87131, USA
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12
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Mizuno K, Kitamura A, Sasaki T. Rabring7, a novel Rab7 target protein with a RING finger motif. Mol Biol Cell 2003; 14:3741-52. [PMID: 12972561 PMCID: PMC196564 DOI: 10.1091/mbc.e02-08-0495] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Rab7, a member of the Rab family small G proteins, has been shown to regulate intracellular vesicle traffic to late endosome/lysosome and lysosome biogenesis, but the exact roles of Rab7 are still undetermined. Accumulating evidence suggests that each Rab protein has multiple target proteins that function in the exocytic/endocytic pathway. We have isolated a new Rab7 target protein, Rabring7 (Rab7-interacting RING finger protein), using a CytoTrap system. It contains an H2 type RING finger motif at the C termini. Rabring7 shows no homology with RILP, which has been reported as another Rab7 target protein. GST pull-down and coimmunoprecipitation assays demonstrate that Rabring7 specifically binds the GTP-bound form of Rab7 at the N-terminal portion. Rabring7 is found mainly in the cytosol and is recruited efficiently to late endosomes/lysosomes by the GTP-bound form of Rab7 in BHK cells. Overexpression of Rabring7 not only affects epidermal growth factor degradation but also causes the perinuclear aggregation of lysosomes, in which the accumulation of the acidotropic probe LysoTracker is remarkably enhanced. These results suggest that Rabring7 plays crucial roles as a Rab7 target protein in vesicle traffic to late endosome/lysosome and lysosome biogenesis.
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Affiliation(s)
- Kouichi Mizuno
- Department of Biochemistry, The University of Tokushima Graduate School of Medicine, Tokushima 770-8503, Japan
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13
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Calero M, Collins RN. Saccharomyces cerevisiae Pra1p/Yip3p interacts with Yip1p and Rab proteins. Biochem Biophys Res Commun 2002; 290:676-81. [PMID: 11785952 DOI: 10.1006/bbrc.2001.6242] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The regulation of membrane traffic involves the Rab family of Ras-related GTPases, of which there are a total of 11 members in the yeast Saccharomyces cerevisiae. Previous work has identified PRA1 as a dual prenylated Rab GTPase and VAMP2 interacting protein [Martinic et al. (1999) J. Biol. Chem. 272, 26991-26998]. In this study we demonstrate that the yeast counterpart of PRA1 interacts with Rab proteins and with Yip1p, a membrane protein of unknown function that has been reported to interact specifically with the Rab proteins Ypt1p and Ypt31p. Yeast Pra1p/Yip3p is a factor capable of biochemical interaction with a panel of different Rab proteins and does not show in vitro specificity for any particular Rab. The interactions between Pra1p/Yip3p and Rab proteins are dependent on the presence of the Rab protein C-terminal cysteines and require C-terminal prenylation.
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Affiliation(s)
- Monica Calero
- Department of Molecular Medicine, Cornell University, Ithaca, New York 14853-6401, USA
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