1
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Liu Q, Meng X, Song Z, Shao Y, Zhao Y, Fang R, Huo Y, Zhang L. Insect-transmitted plant virus balances its vertical transmission through regulating Rab1-mediated receptor localization. Cell Rep 2024; 43:114571. [PMID: 39093698 DOI: 10.1016/j.celrep.2024.114571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 06/23/2024] [Accepted: 07/17/2024] [Indexed: 08/04/2024] Open
Abstract
Rice stripe virus (RSV) establishes infection in the ovaries of its vector insect, Laodelphax striatellus. We demonstrate that RSV infection delays ovarian maturation by inhibiting membrane localization of the vitellogenin receptor (VgR), thereby reducing the vitellogenin (Vg) accumulation essential for egg development. We identify the host protein L. striatellus Rab1 protein (LsRab1), which directly interacts with RSV nucleocapsid protein (NP) within nurse cells. LsRab1 is required for VgR surface localization and ovarian Vg accumulation. RSV inhibits LsRab1 function through two mechanisms: NP binding LsRab1 prevents GTP binding, and NP binding LsRab1-GTP complexes stimulates GTP hydrolysis, forming an inactive LsRab1 form. Through this dual inhibition, RSV infection prevents LsRab1 from facilitating VgR trafficking to the cell membrane, leading to inefficient Vg uptake. The Vg-VgR pathway is present in most oviparous animals, and the mechanisms detailed here provide insights into the vertical transmission of other insect-transmitted viruses of medical and agricultural importance.
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Affiliation(s)
- Qing Liu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangyi Meng
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiyu Song
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Shao
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, Shanxi Province 030801, China
| | - Yao Zhao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Rongxiang Fang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Huo
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Lili Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China.
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2
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Feathers JR, Vignogna RC, Fromme JC. Structural basis for Rab6 activation by the Ric1-Rgp1 complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.06.592747. [PMID: 38766083 PMCID: PMC11100747 DOI: 10.1101/2024.05.06.592747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Rab GTPases act as molecular switches to regulate organelle homeostasis and membrane trafficking. Rab6 plays a central role in regulating cargo flux through the Golgi and is activated via nucleotide exchange by the Ric1-Rgp1 protein complex. Ric1-Rgp1 is conserved throughout eukaryotes but the structural and mechanistic basis for its function has not been established. Here we report the cryoEM structure of a Ric1-Rgp1-Rab6 complex representing a key intermediate of the nucleotide exchange reaction. This structure reveals the overall architecture of the complex and enabled us to identify interactions critical for proper recognition and activation of Rab6 on the Golgi membrane surface. Ric1-Rgp1 interacts with the nucleotide-binding domain of Rab6 using an uncharacterized helical domain, which we establish as a novel RabGEF domain by identifying residues required for Rab6 nucleotide exchange. Unexpectedly, the complex uses an arrestin fold to interact with the Rab6 hypervariable domain, indicating that interactions with the unstructured C-terminal regions of Rab GTPases may be a common specificity mechanism used by their activators. Collectively, our findings provide a detailed mechanistic understanding of regulated Rab6 activation at the Golgi.
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Affiliation(s)
- J. Ryan Feathers
- Department of Molecular Biology & Genetics and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850 USA
- Current address: 201 Schultz Laboratory, Princeton University, Princeton, NJ 08544 USA
| | - Ryan C. Vignogna
- Department of Molecular Biology & Genetics and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850 USA
| | - J. Christopher Fromme
- Department of Molecular Biology & Genetics and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850 USA
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3
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Ying R, Li C, Li H, Zou J, Hu M, Hong Q, Shen Y, Hou L, Cheng H, Zhou R. RPGR is a guanine nucleotide exchange factor for the small GTPase RAB37 required for retinal function via autophagy regulation. Cell Rep 2024; 43:114010. [PMID: 38536817 DOI: 10.1016/j.celrep.2024.114010] [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: 07/26/2023] [Revised: 01/28/2024] [Accepted: 03/13/2024] [Indexed: 04/28/2024] Open
Abstract
Although the small GTPase RAB37 acts as an organizer of autophagosome biogenesis, the upstream regulatory mechanism of autophagy via guanosine diphosphate (GDP)-guanosine triphosphate (GTP) exchange in maintaining retinal function has not been determined. We found that retinitis pigmentosa GTPase regulator (RPGR) is a guanine nucleotide exchange factor that activates RAB37 by accelerating GDP-to-GTP exchange. RPGR directly interacts with RAB37 via the RPGR-RCC1-like domain to promote autophagy through stimulating exchange. Rpgr knockout (KO) in mice leads to photoreceptor degeneration owing to autophagy impairment in the retina. Notably, the retinopathy phenotypes of Rpgr KO retinas are rescued by the adeno-associated virus-mediated transfer of pre-trans-splicing molecules, which produce normal Rpgr mRNAs via trans-splicing in the Rpgr KO retinas. This rescue upregulates autophagy through the re-expression of RPGR in KO retinas to accelerate GDP-to-GTP exchange; thus, retinal homeostasis reverts to normal. Taken together, these findings provide an important missing link for coordinating RAB37 GDP-GTP exchange via the RPGR and retinal homeostasis by autophagy regulation.
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Affiliation(s)
- Ruhong Ying
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
| | - Cong Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
| | - Huirong Li
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Wenzhou Medical University, Wenzhou 325003, China
| | - Juan Zou
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
| | - Mengxin Hu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
| | - Qiang Hong
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
| | - Yin Shen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
| | - Ling Hou
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Wenzhou Medical University, Wenzhou 325003, China.
| | - Hanhua Cheng
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China.
| | - Rongjia Zhou
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China.
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4
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Chakraborty S, Kanade M, Gayathri P. Mechanism of GTPase activation of a prokaryotic small Ras-like GTPase MglA by an asymmetrically interacting MglB dimer. J Biol Chem 2024; 300:107197. [PMID: 38508314 PMCID: PMC11016934 DOI: 10.1016/j.jbc.2024.107197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 03/04/2024] [Indexed: 03/22/2024] Open
Abstract
Cell polarity oscillations in Myxococcus xanthus motility are driven by a prokaryotic small Ras-like GTPase, mutual gliding protein A (MglA), which switches from one cell pole to the other in response to extracellular signals. MglA dynamics is regulated by MglB, which functions both as a GTPase activating protein (GAP) and a guanine nucleotide exchange factor (GEF) for MglA. With an aim to dissect the asymmetric role of the two MglB protomers in the dual GAP and GEF activities, we generated a functional MglAB complex by coexpressing MglB with a linked construct of MglA and MglB. This strategy enabled us to generate mutations of individual MglB protomers (MglB1 or MglB2 linked to MglA) and delineate their role in GEF and GAP activities. We establish that the C-terminal helix of MglB1, but not MglB2, stimulates nucleotide exchange through a site away from the nucleotide-binding pocket, confirming an allosteric mechanism. Interaction between the N-terminal β-strand of MglB1 and β0 of MglA is essential for the optimal GEF activity of MglB. Specific residues of MglB2, which interact with Switch-I of MglA, partially contribute to its GAP activity. Thus, the role of the MglB2 protomer in the GAP activity of MglB is limited to restricting the conformation of MglA active site loops. The direct demonstration of the allosteric mechanism of GEF action provides us new insights into the regulation of small Ras-like GTPases, a feature potentially present in many uncharacterized GEFs.
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Affiliation(s)
- Sukanya Chakraborty
- Department of Biology, Indian Institute of Science Education and Research Pune, Pune, India
| | - Manil Kanade
- Department of Biology, Indian Institute of Science Education and Research Pune, Pune, India
| | - Pananghat Gayathri
- Department of Biology, Indian Institute of Science Education and Research Pune, Pune, India.
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5
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Tran LT, Akıl C, Senju Y, Robinson RC. The eukaryotic-like characteristics of small GTPase, roadblock and TRAPPC3 proteins from Asgard archaea. Commun Biol 2024; 7:273. [PMID: 38472392 DOI: 10.1038/s42003-024-05888-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 02/06/2024] [Indexed: 03/14/2024] Open
Abstract
Membrane-enclosed organelles are defining features of eukaryotes in distinguishing these organisms from prokaryotes. Specification of distinct membranes is critical to assemble and maintain discrete compartments. Small GTPases and their regulators are the signaling molecules that drive membrane-modifying machineries to the desired location. These signaling molecules include Rab and Rag GTPases, roadblock and longin domain proteins, and TRAPPC3-like proteins. Here, we take a structural approach to assess the relatedness of these eukaryotic-like proteins in Asgard archaea, the closest known prokaryotic relatives to eukaryotes. We find that the Asgard archaea GTPase core domains closely resemble eukaryotic Rabs and Rags. Asgard archaea roadblock, longin and TRAPPC3 domain-containing proteins form dimers similar to those found in the eukaryotic TRAPP and Ragulator complexes. We conclude that the emergence of these protein architectures predated eukaryogenesis, however further adaptations occurred in proto-eukaryotes to allow these proteins to regulate distinct internal membranes.
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Affiliation(s)
- Linh T Tran
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan
| | - Caner Akıl
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan
- Division of Structural Biology, University of Oxford, Oxford, England
| | - Yosuke Senju
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan
| | - Robert C Robinson
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan.
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand.
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6
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Wu XY, Dong B, Zhu XM, Cai YY, Li L, Lu JP, Yu B, Cheng JL, Xu F, Bao JD, Wang Y, Liu XH, Lin FC. SP-141 targets Trs85 to inhibit rice blast fungus infection and functions as a potential broad-spectrum antifungal agent. PLANT COMMUNICATIONS 2024; 5:100724. [PMID: 37771153 PMCID: PMC10873891 DOI: 10.1016/j.xplc.2023.100724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/12/2023] [Accepted: 09/25/2023] [Indexed: 09/30/2023]
Abstract
Rice blast is a devastating disease worldwide, threatening rice production and food security. The blast fungus Magnaporthe oryzae invades the host via the appressorium, a specialized pressure-generating structure that generates enormous turgor pressure to penetrate the host cuticle. However, owing to ongoing evolution of fungicide resistance, it is vitally important to identify new targets and fungicides. Here, we show that Trs85, a subunit of the transport protein particle III complex, is essential for appressorium-mediated infection in M. oryzae. We explain how Trs85 regulates autophagy through Ypt1 (a small guanosine triphosphatase protein) in M. oryzae. We then identify a key conserved amphipathic α helix within Trs85 that is associated with pathogenicity of M. oryzae. Through computer-aided screening, we identify a lead compound, SP-141, that affects autophagy and the Trs85-Ypt1 interaction. SP-141 demonstrates a substantial capacity to effectively inhibit infection caused by the rice blast fungus while also exhibiting wide-ranging potential as an antifungal agent with broad-spectrum activity. Taken together, our data show that Trs85 is a potential new target and that SP-141 has potential for the control of rice blast. Our findings thus provide a novel strategy that may help in the fight against rice blast.
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Affiliation(s)
- Xi-Yu Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang Province, China
| | - Bo Dong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310058, Zhejiang Province, China; Department of Pharmacology and Nutritional Science, College of Medicine, The University of Kentucky, Lexington, KY 40506, USA; Markey Cancer Center, College of Medicine, The University of Kentucky, Lexington, KY 40506, USA
| | - Xue-Ming Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310058, Zhejiang Province, China
| | - Ying-Ying Cai
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang Province, China
| | - Lin Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310058, Zhejiang Province, China
| | - Jian-Ping Lu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang Province, China
| | - Bin Yu
- Institute of Pesticide and Environmental Toxicology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, Zhejiang Province, China
| | - Jing-Li Cheng
- Institute of Pesticide and Environmental Toxicology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, Zhejiang Province, China
| | - Fei Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310058, Zhejiang Province, China
| | - Jian-Dong Bao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310058, Zhejiang Province, China
| | - Ying Wang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201106, Shanghai, China
| | - Xiao-Hong Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang Province, China.
| | - Fu-Cheng Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang Province, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310058, Zhejiang Province, China.
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7
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Justel M, Jou C, Sariego-Jamardo A, Juliá-Palacios NA, Ortez C, Poch ML, Hedrera-Fernandez A, Gomez-Martin H, Codina A, Dominguez-Carral J, Muxart J, Hernández-Laín A, Vila-Bedmar S, Zulaica M, Cancho-Candela R, Castro MDC, de la Osa-Langreo A, Peña-Valenceja A, Marcos-Vadillo E, Prieto-Matos P, Pascual-Pascual SI, López de Munain A, Camacho A, Estevez-Arias B, Musokhranova U, Olivella M, Oyarzábal A, Jimenez-Mallebrera C, Domínguez-González C, Nascimento A, García-Cazorla À, Natera-de Benito D. Expanding the phenotypic spectrum of TRAPPC11-related muscular dystrophy: 25 Roma individuals carrying a founder variant. J Med Genet 2023; 60:965-973. [PMID: 37197784 PMCID: PMC10579479 DOI: 10.1136/jmg-2022-109132] [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: 12/30/2022] [Accepted: 03/28/2023] [Indexed: 05/19/2023]
Abstract
BACKGROUND Limb-girdle muscular dystrophies (LGMD) are a heterogeneous group of genetically determined muscle disorders. TRAPPC11-related LGMD is an autosomal-recessive condition characterised by muscle weakness and intellectual disability. METHODS A clinical and histopathological characterisation of 25 Roma individuals with LGMD R18 caused by the homozygous TRAPPC11 c.1287+5G>A variant is reported. Functional effects of the variant on mitochondrial function were investigated. RESULTS The c.1287+5G>A variant leads to a phenotype characterised by early onset muscle weakness, movement disorder, intellectual disability and elevated serum creatine kinase, which is similar to other series. As novel clinical findings, we found that microcephaly is almost universal and that infections in the first years of life seem to act as triggers for a psychomotor regression and onset of seizures in several individuals with TRAPPC11 variants, who showed pseudometabolic crises triggered by infections. Our functional studies expanded the role of TRAPPC11 deficiency in mitochondrial function, as a decreased mitochondrial ATP production capacity and alterations in the mitochondrial network architecture were detected. CONCLUSION We provide a comprehensive phenotypic characterisation of the pathogenic variant TRAPPC11 c.1287+5G>A, which is founder in the Roma population. Our observations indicate that some typical features of golgipathies, such as microcephaly and clinical decompensation associated with infections, are prevalent in individuals with LGMD R18.
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Affiliation(s)
- Maria Justel
- Neuromuscular Unit, Department of Neurology, Hospital Sant Joan de Déu, Barcelona, Spain
- Department of Paediatrics, Complejo asistencial de Salamanca, Salamanca, Spain
| | - Cristina Jou
- Applied Research in Neuromuscular Diseases, Sant Joan de Deu Research Institute, Barcelona, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Department of Pathology, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Andrea Sariego-Jamardo
- Paediatric Neurology Unit, Hospital Universitario Marques de Valdecilla, Santander, Spain
| | - Natalia Alexandra Juliá-Palacios
- Neurometabolic Unit and Synaptic Metabolism Lab, Departments of Neurology, IPR (Institut Pediàtric de Recerca), CIBERER and MetabERN, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Carlos Ortez
- Neuromuscular Unit, Department of Neurology, Hospital Sant Joan de Déu, Barcelona, Spain
- Applied Research in Neuromuscular Diseases, Sant Joan de Deu Research Institute, Barcelona, Spain
| | | | | | - Hilario Gomez-Martin
- Department of Paediatrics, Complejo Asistencial Universitario de Salamanca, Salamanca, Spain
| | - Anna Codina
- Applied Research in Neuromuscular Diseases, Sant Joan de Deu Research Institute, Barcelona, Spain
| | - Jana Dominguez-Carral
- Unit of Epilepsy, Sleep and Neurophysiology, Department of Neurology, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Jordi Muxart
- Department of Radiology, Hospital Sant Joan de Déu, Barcelona, Spain
| | | | - Sara Vila-Bedmar
- Neuromuscular Unit, Department of Neurology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Miren Zulaica
- Biodonostia, Neurosciences Area, Neuromuscular Diseases Laboratory, Hospital Universitario de Donostia, San Sebastian, Spain
| | - Ramon Cancho-Candela
- Paediatric Neurology Unit, Hospital Universitario Rio Hortega de Valladolid, Valladolid, Spain
| | | | | | | | - Elena Marcos-Vadillo
- Department of Clinical Biochemistry, Complejo Asistencial Universitario de Salamanca, Salamanca, Spain
| | - Pablo Prieto-Matos
- Department of Paediatrics, Complejo asistencial de Salamanca, Salamanca, Spain
| | | | - Adolfo López de Munain
- Biodonostia, Neurosciences Area, Neuromuscular Diseases Laboratory, Hospital Universitario de Donostia, San Sebastian, Spain
| | - Ana Camacho
- Paediatric Neurology Unit, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Berta Estevez-Arias
- Neuromuscular Unit, Department of Neurology, Hospital Sant Joan de Déu, Barcelona, Spain
- Laboratory of Neurogenetics and Molecular Medicine-IPER, Sant Joan de Deu Research Institute, Barcelona, Spain
| | - Uliana Musokhranova
- Neurometabolic Unit and Synaptic Metabolism Lab, Departments of Neurology, IPR (Institut Pediàtric de Recerca), CIBERER and MetabERN, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Mireia Olivella
- Biosciences Department, Faculty of Sciences, Technology and Engineering, Universitat de Vic-Universitat Central de Catalunya, Vic, Spain
| | - Alfonso Oyarzábal
- Neurometabolic Unit and Synaptic Metabolism Lab, Departments of Neurology, IPR (Institut Pediàtric de Recerca), CIBERER and MetabERN, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Cecilia Jimenez-Mallebrera
- Applied Research in Neuromuscular Diseases, Sant Joan de Deu Research Institute, Barcelona, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Cristina Domínguez-González
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Neuromuscular Unit, Department of Neurology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Andrés Nascimento
- Neuromuscular Unit, Department of Neurology, Hospital Sant Joan de Déu, Barcelona, Spain
- Applied Research in Neuromuscular Diseases, Sant Joan de Deu Research Institute, Barcelona, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Àngels García-Cazorla
- Neurometabolic Unit and Synaptic Metabolism Lab, Departments of Neurology, IPR (Institut Pediàtric de Recerca), CIBERER and MetabERN, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Daniel Natera-de Benito
- Neuromuscular Unit, Department of Neurology, Hospital Sant Joan de Déu, Barcelona, Spain
- Applied Research in Neuromuscular Diseases, Sant Joan de Deu Research Institute, Barcelona, Spain
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8
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Wilmes S, Kümmel D. Insights into the role of the membranes in Rab GTPase regulation. Curr Opin Cell Biol 2023; 83:102177. [PMID: 37327649 DOI: 10.1016/j.ceb.2023.102177] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 06/18/2023]
Abstract
Rab GTPases are molecular switches with essential roles in mediating vesicular trafficking and establishing organelle identity. The conversion from the inactive, cytosolic to the membrane-bound, active species and back is tightly controlled by regulatory proteins. Recently, the roles of membrane properties and lipid composition of different target organelles in determining the activity state of Rabs have come to light. The investigation of several Rab guanine nucleotide exchange factors (GEFs) has revealed principles of how the recruitment via lipid interactions and the spatial confinement on the membrane surface contribute to spatiotemporal specificity in the Rab GTPase network. This paints an intricate picture of the control mechanisms in Rab activation and highlights the importance of the membrane lipid code in the organization of the endomembrane system.
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Affiliation(s)
- Stephan Wilmes
- University of Münster, Institute of Biochemistry, Corrensstraße 36, 48149 Münster, Germany
| | - Daniel Kümmel
- University of Münster, Institute of Biochemistry, Corrensstraße 36, 48149 Münster, Germany.
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9
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Sun S, Sui SF. Structural insights into assembly of TRAPPII and its activation of Rab11/Ypt32. Curr Opin Struct Biol 2023; 80:102596. [PMID: 37068358 DOI: 10.1016/j.sbi.2023.102596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 03/09/2023] [Accepted: 03/19/2023] [Indexed: 04/19/2023]
Abstract
Transport protein particle (TRAPP) complexes belong to the multisubunit tethering complex. They are guanine nucleotide exchange factors (GEFs) that play essential roles in secretory and endocytic recycling pathway and autophagy. There are two major forms of TRAPP complexes, TRAPPII and TRAPPIII, which share a core set of small subunits. TRAPPIII activates Rab1, while TRAPPII primarily activates Rab11. A steric gating mechanism has been proposed to control the substrate selection in vivo. However, the detailed mechanisms underlying the transition from TRAPPIII's GEF activity for Rab1 to TRAPPII's GEF activity for Rab11 and the roles of the complex-specific subunits in this transition are insufficiently understood. In this review, we discuss recent advances in understanding the mechanism of specific activation of Rab11/Ypt32 by TRAPPII, with a particular focus on new findings from structural studies.
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Affiliation(s)
- Shan Sun
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Sen-Fang Sui
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; School of Life Sciences, Cryo-EM Center, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
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10
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Bagde SR, Fromme JC. The TRAPP complexes: discriminating GTPases in context. FEBS Lett 2022; 597:721-733. [PMID: 36481981 PMCID: PMC10050150 DOI: 10.1002/1873-3468.14557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/23/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022]
Abstract
Correct localization of Rab GTPases in cells is critical for proper function in membrane trafficking. Guanine-nucleotide exchange factors (GEFs) act as the primary determinants of Rab localization by activating and stabilizing their Rab substrates on specific organelle and vesicle membranes. The TRAPP complexes TRAPPII and TRAPPIII are two related GEFs that use the same catalytic site to activate distinct Rabs, Rab11 and Rab1, respectively. The Rab C-terminal hypervariable domain (HVD) is an important specificity determinant for the budding yeast TRAPP complexes, with the length of the HVD playing a critical role in counter-selection. Several recent studies have used cryo-EM to illuminate how the yeast and metazoan TRAPP complexes identify and activate their substrates. This review summarizes recently characterized Rab substrate selection mechanisms and highlights how the membrane surface provides critical context for the GEF-GTPase interactions.
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Affiliation(s)
- Saket R Bagde
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - J Christopher Fromme
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
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11
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Dong X, Liang Z, Zhang J, Zhang Q, Xu Y, Zhang Z, Zhang L, Zhang B, Zhao Y. Trappc1 deficiency impairs thymic epithelial cell development by breaking endoplasmic reticulum homeostasis. Eur J Immunol 2022; 52:1789-1804. [PMID: 35908180 DOI: 10.1002/eji.202249915] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/28/2022] [Accepted: 07/26/2022] [Indexed: 11/05/2022]
Abstract
Thymic epithelial cells (TECs) are important for T cell development and immune tolerance establishment. Although comprehensive molecular regulation of TEC development has been studied, the role of transport protein particle complexes (Trappcs) in TECs is not clear. Using TEC-specific homozygous or heterozygous Trappc1 deleted mice model, we found that Trappc1 deficiency caused severe thymus atrophy with decreased cell number and blocked maturation of TECs. Mice with a TEC-specific Trappc1 deletion show poor thymic T cell output and have a greater percentage of activated/memory T cells, suffered from spontaneous autoimmune disorders. Our RNA-seq and molecular studies indicated that the decreased endoplasmic reticulum (ER) and Golgi apparatus, enhanced unfolded protein response (UPR) and subsequent Atf4-CHOP-mediated apoptosis, and reactive oxygen species (ROS)-mediated ferroptosis coordinately contributed to the reduction of Trappc1-deleted TECs. Additionally, reduced Aire+ mTECs accompanied by the decreased expression of Irf4, Irf8, and Tbx21 in Trappc1 deficiency mTECs, may further coordinately block the tissue-restricted antigen expression. In this study, we reveal that Trappc1 plays an indispensable role in TEC development and maturation and provide evidence for the importance of inter-organelle traffic and ER homeostasis in TEC development. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Xue Dong
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences.,University of Chinese Academy of Sciences
| | - Zhanfeng Liang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences.,University of Chinese Academy of Sciences.,Beijing Institute for Stem Cell and Regeneration
| | - Jiayu Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences.,University of Chinese Academy of Sciences
| | - Qian Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences.,University of Chinese Academy of Sciences
| | - Yanan Xu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences.,University of Chinese Academy of Sciences
| | - Zhaoqi Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences.,University of Chinese Academy of Sciences
| | - Lianfeng Zhang
- Key Laboratory of Human Diseases and Comparative Medicine, Ministry of Health, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences
| | - Baojun Zhang
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University
| | - Yong Zhao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences.,University of Chinese Academy of Sciences.,Beijing Institute for Stem Cell and Regeneration
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12
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Mi C, Zhang L, Huang G, Shao G, Yang F, You X, Dong MQ, Sun S, Sui SF. Structural basis for assembly of TRAPPII complex and specific activation of GTPase Ypt31/32. SCIENCE ADVANCES 2022; 8:eabi5603. [PMID: 35080977 PMCID: PMC8791620 DOI: 10.1126/sciadv.abi5603] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 12/02/2021] [Indexed: 06/14/2023]
Abstract
Transport protein particle (TRAPP) complexes belong to the multiprotein tethering complex and exist in three forms-core TRAPP/TRAPPI, TRAPPII, and TRAPPIII. TRAPPII activates GTPase Ypt31/Ypt32 as the guanine nucleotide exchange factor in the trans-Golgi network to determine the maturation of Golgi cisternae into post-Golgi carriers in yeast. Here, we present cryo-EM structures of yeast TRAPPII in apo and Ypt32-bound states. All the structures show a dimeric architecture assembled by two triangle-shaped monomers, while the monomer in the apo state exhibits both open and closed conformations, and the monomer in the Ypt32-bound form only captures the closed conformation. Located in the interior of the monomer, Ypt32 binds with both core TRAPP/TRAPPI and Trs120 via its nucleotide-binding domain and binds with Trs31 via its hypervariable domain. Combined with functional analysis, the structures provide insights into the assembly of TRAPPII and the mechanism of the specific activation of Ypt31/Ypt32 by TRAPPII.
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Affiliation(s)
- Chenchen Mi
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Li Zhang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Guoqiang Huang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Guangcan Shao
- National Institute of Biological Sciences, Beijing 102206, China
| | - Fan Yang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xin You
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
| | - Shan Sun
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Sen-Fang Sui
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
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13
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Cao S, Yang J, Fu J, Chen H, Jia H. The Dissection of SNAREs Reveals Key Factors for Vesicular Trafficking to the Endosome-like Compartment and Apicoplast via the Secretory System in Toxoplasma gondii. mBio 2021; 12:e0138021. [PMID: 34340555 PMCID: PMC8406237 DOI: 10.1128/mbio.01380-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 07/02/2021] [Indexed: 12/18/2022] Open
Abstract
Vesicular trafficking is a fundamental cellular process involved in material transport in eukaryotes, but the diversity of the intracellular compartments has prevented researchers from obtaining a clear understanding of the specific functions of vesicular trafficking factors, including SNAREs, tethers, and Rab GTPases, in Apicomplexa. In this study, we analyzed the localization of SNAREs and investigated their roles in vesicular trafficking in Toxoplasma gondii. Our results revealed the specific localizations of SNAREs in the endoplasmic reticulum (ER) (T. gondii Stx18 [TgStx18] and TgStx19), Golgi stacks (TgGS27), and endosome-like compartment (TgStx10 and TgStx12). The conditional ablation of ER- and Golgi-residing SNAREs caused severe defects in the secretory system. Most importantly, we found an R-SNARE (TgVAMP4-2) that is targeted to the apicoplast; to our knowledge, this work provides the first information showing a SNARE protein on endosymbiotic organelles and functioning in vesicular trafficking in eukaryotes. Conditional knockout of TgVAMP4-2 blocked the entrance of TgCPN60, TgACP, TgATrx2, and TgATrx1 into the apicoplast and interfered with the targeting of TgAPT1 and TgFtsH1 to the outermost membrane of the apicoplast. Together, our findings revealed the functions of SNAREs in the secretory system and the transport of nucleus-encoded proteins to an endosymbiotic organelle in a model organism of Apicomplexa. IMPORTANCE SNAREs are essential for the fusion of the transport vesicles and target membranes and, thus, provide perfect targets for obtaining a global view of the vesicle transport system. In this study, we report that a novel Qc-SNARE (TgStx19) instead of Use1 is located at the ER and acts as a partner of TgStx18 in T. gondii. TgGS27 and the tethering complex TRAPP III are conserved and critical for the biogenesis of the Golgi complex in T. gondii. A novel R-SNARE, TgVAMP4-2, is found on the outermost membrane of the apicoplast. The transport of NEAT proteins into the secondary endosymbiotic organelle depends on its function. To our knowledge, this work provides the first mention of a SNARE located on endosymbiotic organelles that functions in vesicular trafficking in eukaryotes.
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Affiliation(s)
- Shinuo Cao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Juan Yang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Jiawen Fu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Heming Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Honglin Jia
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
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14
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Harris NJ, Jenkins ML, Dalwadi U, Fleming KD, Nam SE, Parson MAH, Yip CK, Burke JE. Biochemical Insight into Novel Rab-GEF Activity of the Mammalian TRAPPIII Complex. J Mol Biol 2021; 433:167145. [PMID: 34229011 DOI: 10.1016/j.jmb.2021.167145] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/25/2021] [Accepted: 06/30/2021] [Indexed: 11/28/2022]
Abstract
Transport Protein Particle complexes (TRAPP) are evolutionarily conserved regulators of membrane trafficking, with this mediated by their guanine nucleotide exchange factor (GEF) activity towards Rab GTPases. In metazoans evidence suggests that two different TRAPP complexes exist, TRAPPII and TRAPPIII. These two complexes share a common core of subunits, with complex specific subunits (TRAPPC9 and TRAPPC10 in TRAPPII and TRAPPC8, TRAPPC11, TRAPPC12, TRAPPC13 in TRAPPIII). TRAPPII and TRAPPIII have distinct specificity for GEF activity towards Rabs, with TRAPPIII acting on Rab1, and TRAPPII acting on Rab1 and Rab11. The molecular basis for how these complex specific subunits alter GEF activity towards Rab GTPases is unknown. Here we have used a combination of biochemical assays, hydrogen deuterium exchange mass spectrometry (HDX-MS) and electron microscopy to examine the regulation of TRAPPII and TRAPPIIII complexes in solution and on membranes. GEF assays revealed that TRAPPIII has GEF activity against Rab1 and Rab43, with no detectable activity against the other 18 Rabs tested. The TRAPPIII complex had significant differences in protein dynamics at the Rab binding site compared to TRAPPII, potentially indicating an important role of accessory subunits in altering the active site of TRAPP complexes. Both the TRAPPII and TRAPPIII complexes had enhanced GEF activity on lipid membranes, with HDX-MS revealing numerous conformational changes that accompany membrane association. HDX-MS also identified a membrane binding site in TRAPPC8. Collectively, our results provide insight into the functions of TRAPP complexes and how they can achieve Rab specificity.
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Affiliation(s)
- Noah J Harris
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Meredith L Jenkins
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Udit Dalwadi
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Kaelin D Fleming
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Sung-Eun Nam
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Matthew A H Parson
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Calvin K Yip
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada; Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.
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15
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Joiner AMN, Phillips BP, Yugandhar K, Sanford EJ, Smolka MB, Yu H, Miller EA, Fromme JC. Structural basis of TRAPPIII-mediated Rab1 activation. EMBO J 2021; 40:e107607. [PMID: 34018207 PMCID: PMC8204860 DOI: 10.15252/embj.2020107607] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/07/2021] [Accepted: 04/11/2021] [Indexed: 12/17/2022] Open
Abstract
The GTPase Rab1 is a master regulator of the early secretory pathway and is critical for autophagy. Rab1 activation is controlled by its guanine nucleotide exchange factor, the multisubunit TRAPPIII complex. Here, we report the 3.7 Å cryo-EM structure of the Saccharomyces cerevisiae TRAPPIII complex bound to its substrate Rab1/Ypt1. The structure reveals the binding site for the Rab1/Ypt1 hypervariable domain, leading to a model for how the complex interacts with membranes during the activation reaction. We determined that stable membrane binding by the TRAPPIII complex is required for robust activation of Rab1/Ypt1 in vitro and in vivo, and is mediated by a conserved amphipathic α-helix within the regulatory Trs85 subunit. Our results show that the Trs85 subunit serves as a membrane anchor, via its amphipathic helix, for the entire TRAPPIII complex. These findings provide a structural understanding of Rab activation on organelle and vesicle membranes.
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Affiliation(s)
- Aaron MN Joiner
- Department of Molecular Biology and Genetics/Weill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | | | - Kumar Yugandhar
- Department of Computational Biology/Weill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | - Ethan J Sanford
- Department of Molecular Biology and Genetics/Weill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | - Marcus B Smolka
- Department of Molecular Biology and Genetics/Weill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | - Haiyuan Yu
- Department of Computational Biology/Weill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | | | - J Christopher Fromme
- Department of Molecular Biology and Genetics/Weill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
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16
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Galindo A, Planelles-Herrero VJ, Degliesposti G, Munro S. Cryo-EM structure of metazoan TRAPPIII, the multi-subunit complex that activates the GTPase Rab1. EMBO J 2021; 40:e107608. [PMID: 34018214 PMCID: PMC8204870 DOI: 10.15252/embj.2020107608] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 03/30/2021] [Accepted: 04/11/2021] [Indexed: 12/19/2022] Open
Abstract
The TRAPP complexes are nucleotide exchange factors that play essential roles in membrane traffic and autophagy. TRAPPII activates Rab11, and TRAPPIII activates Rab1, with the two complexes sharing a core of small subunits that affect nucleotide exchange but being distinguished by specific large subunits that are essential for activity in vivo. Crystal structures of core subunits have revealed the mechanism of Rab activation, but how the core and the large subunits assemble to form the complexes is unknown. We report a cryo‐EM structure of the entire Drosophila TRAPPIII complex. The TRAPPIII‐specific subunits TRAPPC8 and TRAPPC11 hold the catalytic core like a pair of tongs, with TRAPPC12 and TRAPPC13 positioned at the joint between them. TRAPPC2 and TRAPPC2L link the core to the two large arms, with the interfaces containing residues affected by disease‐causing mutations. The TRAPPC8 arm is positioned such that it would contact Rab1 that is bound to the core, indicating how the arm could determine the specificity of the complex. A lower resolution structure of TRAPPII shows a similar architecture and suggests that the TRAPP complexes evolved from a single ur‐TRAPP.
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Affiliation(s)
| | | | | | - Sean Munro
- MRC Laboratory of Molecular Biology, Cambridge, UK
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17
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Li F, Wu YW. Imaging of Spatial Cycling of Rab GTPase in the Cell. Methods Mol Biol 2021; 2293:105-115. [PMID: 34453713 DOI: 10.1007/978-1-0716-1346-7_8] [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: 12/03/2022]
Abstract
Rab GTPases (>60 members in human) function as master regulators of intracellular membrane trafficking. To fulfill their functions, Rab proteins need to localize on specific membranes in cells. It remains elusive how the distinct spatial distribution of Rab GTPases in the cell is regulated. To make a global assessment on the subcellular localization of Rab1, we determined kinetic parameters of the spatial cycling of Rab1 in live cells using photoactivatable fluorescent proteins and live cell imaging. We found that the switching between GTP- and GDP-binding states, which is governed by guanine nucleotide exchange factors (GEFs), GTPase activating proteins (GAPs), GDP dissociation inhibitor (GDI) and GDI displacement factor (GDF), is a major determinant for Rab1's ability to effectively cycle between cellular compartments and eventually for its subcellular distribution. Herein, we describe the method for monitoring Rab1 dynamics in live cells. This approach can be used to study spatial cycling of other Rab GTPases.
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Affiliation(s)
- Fu Li
- Max-Planck-Institute of Molecular Physiology, Dortmund, Germany
| | - Yao-Wen Wu
- Department of Chemistry, Uemå Centre for Microbial Research, Umeå University, Umeå, Sweden.
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18
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Jenkins ML, Harris NJ, Dalwadi U, Fleming KD, Ziemianowicz DS, Rafiei A, Martin EM, Schriemer DC, Yip CK, Burke JE. The substrate specificity of the human TRAPPII complex's Rab-guanine nucleotide exchange factor activity. Commun Biol 2020; 3:735. [PMID: 33277614 PMCID: PMC7719173 DOI: 10.1038/s42003-020-01459-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 10/13/2020] [Indexed: 12/15/2022] Open
Abstract
The TRAnsport Protein Particle (TRAPP) complexes act as Guanine nucleotide exchange factors (GEFs) for Rab GTPases, which are master regulators of membrane trafficking in eukaryotic cells. In metazoans, there are two large multi-protein TRAPP complexes: TRAPPII and TRAPPIII, with the TRAPPII complex able to activate both Rab1 and Rab11. Here we present detailed biochemical characterisation of Rab-GEF specificity of the human TRAPPII complex, and molecular insight into Rab binding. GEF assays of the TRAPPII complex against a panel of 20 different Rab GTPases revealed GEF activity on Rab43 and Rab19. Electron microscopy and chemical cross-linking revealed the architecture of mammalian TRAPPII. Hydrogen deuterium exchange MS showed that Rab1, Rab11 and Rab43 share a conserved binding interface. Clinical mutations in Rab11, and phosphomimics of Rab43, showed decreased TRAPPII GEF mediated exchange. Finally, we designed a Rab11 mutation that maintained TRAPPII-mediated GEF activity while decreasing activity of the Rab11-GEF SH3BP5, providing a tool to dissect Rab11 signalling. Overall, our results provide insight into the GTPase specificity of TRAPPII, and how clinical mutations disrupt this regulation. Here the authors reveal unique structural organization of the mammalian TRAPPII complex, which is critical in regulating membrane trafficking. They find that TRAPPII serves as a guanine nucleotide exchange factor for unexpected Rab GTPases such as Rab43 and Rab19.
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Affiliation(s)
- Meredith L Jenkins
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - Noah J Harris
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - Udit Dalwadi
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Kaelin D Fleming
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - Daniel S Ziemianowicz
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Atefeh Rafiei
- Department of Chemistry, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Emily M Martin
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 4N1, Canada.,Department of Chemistry, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Calvin K Yip
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada. .,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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19
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Al-Deri N, Okur V, Ahimaz P, Milev M, Valivullah Z, Hagen J, Sheng Y, Chung W, Sacher M, Ganapathi M. A novel homozygous variant in TRAPPC2L results in a neurodevelopmental disorder and disrupts TRAPP complex function. J Med Genet 2020; 58:592-601. [PMID: 32843486 DOI: 10.1136/jmedgenet-2020-107016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/25/2020] [Accepted: 06/26/2020] [Indexed: 11/04/2022]
Abstract
BACKGROUND Next-generation sequencing has facilitated the diagnosis of neurodevelopmental disorders with variable and non-specific clinical findings. Recently, a homozygous missense p.(Asp37Tyr) variant in TRAPPC2L, a core subunit of TRAPP complexes which function as tethering factors during membrane trafficking, was reported in two unrelated individuals with neurodevelopmental delay, post-infectious encephalopathy-associated developmental arrest, tetraplegia and accompanying rhabdomyolysis. METHODS We performed whole genome sequencing on members of an Ashkenazi Jewish pedigree to identify the underlying genetic aetiology of global developmental delay/intellectual disability in three affected siblings. To assess the effect of the identified TRAPPC2L variant, we performed biochemical and cell biological functional studies on the TRAPPC2L protein. RESULTS A rare homozygous predicted deleterious missense variant, p.(Ala2Gly), in TRAPPC2L was identified in the affected siblings and it segregated with the neurodevelopmental phenotype within the family. Using a yeast two-hybrid assay and in vitro binding, we demonstrate that the p.(Ala2Gly) variant, but not the p.(Asp37Tyr) variant, disrupted the interaction between TRAPPC2L and another core TRAPP protein, TRAPPC6a. Size exclusion chromatography suggested that this variant affects the assembly of TRAPP complexes. Employing two different membrane trafficking assays using fibroblasts from one of the affected siblings, we found a delay in traffic into and out of the Golgi. Similar to the p.(Asp37Tyr) variant, the p.(Ala2Gly) variant resulted in an increase in the levels of active RAB11. CONCLUSION Our data fill in a gap in the knowledge of TRAPP architecture with TRAPPC2L interacting with TRAPPC6a, positioning it as a putative adaptor for other TRAPP subunits. Collectively, our findings support the pathogenicity of the TRAPPC2L p.(Ala2Gly) variant.
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Affiliation(s)
- Noraldin Al-Deri
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Volkan Okur
- Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | - Priyanka Ahimaz
- Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | - Miroslav Milev
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Zaheer Valivullah
- Center for Mendelian Genomics, Broad Institute Harvard, Cambridge, Massachusetts, USA
| | - Jacob Hagen
- Department of Biomedical Sciences, Columbia University Medical Center, New York, New York, USA
| | - Yufeng Sheng
- Department of Biomedical Sciences, Columbia University Medical Center, New York, New York, USA
| | - Wendy Chung
- Department of Pediatrics, Columbia University Medical Center, New York, New York, USA.,Department of Medicine, Columbia University Medical Center, New York, New York, USA
| | - Michael Sacher
- Department of Biology, Concordia University, Montreal, Quebec, Canada .,Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
| | - Mythily Ganapathi
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, USA
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20
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Kehl A, Göser V, Reuter T, Liss V, Franke M, John C, Richter CP, Deiwick J, Hensel M. A trafficome-wide RNAi screen reveals deployment of early and late secretory host proteins and the entire late endo-/lysosomal vesicle fusion machinery by intracellular Salmonella. PLoS Pathog 2020; 16:e1008220. [PMID: 32658937 PMCID: PMC7377517 DOI: 10.1371/journal.ppat.1008220] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 07/23/2020] [Accepted: 05/19/2020] [Indexed: 12/17/2022] Open
Abstract
The intracellular lifestyle of Salmonella enterica is characterized by the formation of a replication-permissive membrane-bound niche, the Salmonella-containing vacuole (SCV). As a further consequence of the massive remodeling of the host cell endosomal system, intracellular Salmonella establish a unique network of various Salmonella-induced tubules (SIT). The bacterial repertoire of effector proteins required for the establishment for one type of these SIT, the Salmonella-induced filaments (SIF), is rather well-defined. However, the corresponding host cell proteins are still poorly understood. To identify host factors required for the formation of SIF, we performed a sub-genomic RNAi screen. The analyses comprised high-resolution live cell imaging to score effects on SIF induction, dynamics and morphology. The hits of our functional RNAi screen comprise: i) The late endo-/lysosomal SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) complex, consisting of STX7, STX8, VTI1B, and VAMP7 or VAMP8, which is, in conjunction with RAB7 and the homotypic fusion and protein sorting (HOPS) tethering complex, a complete vesicle fusion machinery. ii) Novel interactions with the early secretory GTPases RAB1A and RAB1B, providing a potential link to coat protein complex I (COPI) vesicles and reinforcing recently identified ties to the endoplasmic reticulum. iii) New connections to the late secretory pathway and/or the recycling endosome via the GTPases RAB3A, RAB8A, and RAB8B and the SNAREs VAMP2, VAMP3, and VAMP4. iv) An unprecedented involvement of clathrin-coated structures. The resulting set of hits allowed us to characterize completely new host factor interactions, and to strengthen observations from several previous studies. The facultative intracellular pathogen Salmonella enterica serovar Typhimurium induces the reorganization of the endosomal system of mammalian host cells. This activity is dependent on translocated effector proteins of the pathogen. The host cell factors required for endosomal remodeling are only partially known. To identify such factors for the formation and dynamics of endosomal compartments in Salmonella-infected cells, we performed a live cell imaging-based RNAi screen to investigate the role of 496 mammalian proteins involved in cellular logistics. We identified that endosomal remodeling by intracellular Salmonella is dependent on host factors in the following functional classes: i) the late endo-/lysosomal SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) complex, ii) the early secretory pathway, represented by regulator GTPases RAB1A and RAB1B, iii) the late secretory pathway and/or recycling endosomes represented by GTPases RAB3A, RAB8A, RAB8B, and the SNAREs VAMP2, VAMP3, and VAMP4, and iv) clathrin-coated structures. The identification of these new host factors provides further evidence for the complex manipulation of host cell transport functions by intracellular Salmonella and should enable detailed follow-up studies on the mechanisms involved.
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Affiliation(s)
- Alexander Kehl
- Division of Microbiology, University of Osnabrück, Osnabrück, Germany
- Division of Biophysics, University of Osnabrück, Osnabrück, Germany
- * E-mail: (AK); (MH)
| | - Vera Göser
- Division of Microbiology, University of Osnabrück, Osnabrück, Germany
| | - Tatjana Reuter
- Division of Microbiology, University of Osnabrück, Osnabrück, Germany
| | - Viktoria Liss
- Division of Microbiology, University of Osnabrück, Osnabrück, Germany
| | - Maximilian Franke
- Division of Microbiology, University of Osnabrück, Osnabrück, Germany
| | - Christopher John
- Division of Microbiology, University of Osnabrück, Osnabrück, Germany
| | | | - Jörg Deiwick
- Division of Microbiology, University of Osnabrück, Osnabrück, Germany
| | - Michael Hensel
- Division of Microbiology, University of Osnabrück, Osnabrück, Germany
- CellNanOs–Center for Cellular Nanoanalytics, Fachbereich Biologie/Chemie, Universität Osnabrück, Osnabrück, Germany
- * E-mail: (AK); (MH)
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21
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Pinar M, Peñalva MA. En bloc TGN recruitment of Aspergillus TRAPPII reveals TRAPP maturation as unlikely to drive RAB1-to-RAB11 transition. J Cell Sci 2020; 133:jcs241141. [PMID: 32327558 DOI: 10.1242/jcs.241141] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 04/06/2020] [Indexed: 08/31/2023] Open
Abstract
Transport protein particle (TRAPP) complexes regulate membrane traffic. TRAPPII and TRAPPIII share a core hetero-heptamer, also denoted TRAPPI. In fungi TRAPPIII and TRAPPII mediate GDP exchange on RAB1 and RAB11, respectively, regulating traffic across the Golgi, with TRAPPIII also activating RAB1 in autophagosomes. Our finding that Aspergillus nidulans TRAPPII can be assembled by addition of a TRAPPII-specific subcomplex onto core TRAPP prompted us to investigate the possibility that TRAPPI and/or TRAPPIII already residing in the Golgi matures into TRAPPII to determine a RAB1-to-RAB11 conversion as Golgi cisternae progress from early Golgi to TGN identity. By time-resolved microscopy, we determine that the TRAPPII reporter Trs120 (the homolog of metazoan TRAPPC9) is recruited to existing trans-Golgi network (TGN) cisternae slightly before RAB11 arrives, and resides for ∼45 s on them before cisternae tear off into RAB11 secretory carriers. Notably, the core TRAPP reporter Bet3 (the homolog of metazoan TRAPPC3) was not detectable in early Golgi cisternae, being instead recruited to TGN cisternae simultaneously with Trs120, indicating en bloc recruitment of TRAPPII to the Golgi and arguing strongly against the TRAPP maturation model.
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Affiliation(s)
- Mario Pinar
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Miguel A Peñalva
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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22
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Van Bergen NJ, Guo Y, Al-Deri N, Lipatova Z, Stanga D, Zhao S, Murtazina R, Gyurkovska V, Pehlivan D, Mitani T, Gezdirici A, Antony J, Collins F, Willis MJH, Coban Akdemir ZH, Liu P, Punetha J, Hunter JV, Jhangiani SN, Fatih JM, Rosenfeld JA, Posey JE, Gibbs RA, Karaca E, Massey S, Ranasinghe TG, Sleiman P, Troedson C, Lupski JR, Sacher M, Segev N, Hakonarson H, Christodoulou J. Deficiencies in vesicular transport mediated by TRAPPC4 are associated with severe syndromic intellectual disability. Brain 2020; 143:112-130. [PMID: 31794024 PMCID: PMC6935753 DOI: 10.1093/brain/awz374] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/20/2019] [Accepted: 10/07/2019] [Indexed: 12/11/2022] Open
Abstract
The conserved transport protein particle (TRAPP) complexes regulate key trafficking events and are required for autophagy. TRAPPC4, like its yeast Trs23 orthologue, is a core component of the TRAPP complexes and one of the essential subunits for guanine nucleotide exchange factor activity for Rab1 GTPase. Pathogenic variants in specific TRAPP subunits are associated with neurological disorders. We undertook exome sequencing in three unrelated families of Caucasian, Turkish and French-Canadian ethnicities with seven affected children that showed features of early-onset seizures, developmental delay, microcephaly, sensorineural deafness, spastic quadriparesis and progressive cortical and cerebellar atrophy in an effort to determine the genetic aetiology underlying neurodevelopmental disorders. All seven affected subjects shared the same identical rare, homozygous, potentially pathogenic variant in a non-canonical, well-conserved splice site within TRAPPC4 (hg19:chr11:g.118890966A>G; TRAPPC4: NM_016146.5; c.454+3A>G). Single nucleotide polymorphism array analysis revealed there was no haplotype shared between the tested Turkish and Caucasian families suggestive of a variant hotspot region rather than a founder effect. In silico analysis predicted the variant to cause aberrant splicing. Consistent with this, experimental evidence showed both a reduction in full-length transcript levels and an increase in levels of a shorter transcript missing exon 3, suggestive of an incompletely penetrant splice defect. TRAPPC4 protein levels were significantly reduced whilst levels of other TRAPP complex subunits remained unaffected. Native polyacrylamide gel electrophoresis and size exclusion chromatography demonstrated a defect in TRAPP complex assembly and/or stability. Intracellular trafficking through the Golgi using the marker protein VSVG-GFP-ts045 demonstrated significantly delayed entry into and exit from the Golgi in fibroblasts derived from one of the affected subjects. Lentiviral expression of wild-type TRAPPC4 in these fibroblasts restored trafficking, suggesting that the trafficking defect was due to reduced TRAPPC4 levels. Consistent with the recent association of the TRAPP complex with autophagy, we found that the fibroblasts had a basal autophagy defect and a delay in autophagic flux, possibly due to unsealed autophagosomes. These results were validated using a yeast trs23 temperature sensitive variant that exhibits constitutive and stress-induced autophagic defects at permissive temperature and a secretory defect at restrictive temperature. In summary we provide strong evidence for pathogenicity of this variant in a member of the core TRAPP subunit, TRAPPC4 that associates with vesicular trafficking and autophagy defects. This is the first report of a TRAPPC4 variant, and our findings add to the growing number of TRAPP-associated neurological disorders.
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Affiliation(s)
- Nicole J Van Bergen
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Yiran Guo
- Center for Applied Genomics (CAG) at the Children’s Hospital of Philadelphia (CHOP), Philadelphia, USA
| | - Noraldin Al-Deri
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Zhanna Lipatova
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Daniela Stanga
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Sarah Zhao
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Rakhilya Murtazina
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Valeriya Gyurkovska
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Alper Gezdirici
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul, 34303, Turkey
| | - Jayne Antony
- TY Nelson Department of Neurology and Neurosurgery, Children’s Hospital at Westmead, Sydney, Australia
| | - Felicity Collins
- Western Sydney Genetics Program, Children’s Hospital at Westmead, Sydney, Australia
- Medical Genomics Department, Royal Prince Alfred Hospital, Sydney, Australia
| | - Mary J H Willis
- Department of Pediatrics, Naval Medical Center San Diego, San Diego, California, USA
| | - Zeynep H Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jaya Punetha
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jill V Hunter
- Department of Radiology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Ender Karaca
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Sean Massey
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, Australia
| | - Thisara G Ranasinghe
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, Australia
| | - Patrick Sleiman
- Center for Applied Genomics (CAG) at the Children’s Hospital of Philadelphia (CHOP), Philadelphia, USA
| | - Chris Troedson
- TY Nelson Department of Neurology and Neurosurgery, Children’s Hospital at Westmead, Sydney, Australia
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children’s Hospital, Houston, Texas, 77030, USA
| | - Michael Sacher
- Department of Biology, Concordia University, Montreal, Quebec, Canada
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
| | - Nava Segev
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Hakon Hakonarson
- Center for Applied Genomics (CAG) at the Children’s Hospital of Philadelphia (CHOP), Philadelphia, USA
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
- Victorian Clinical Genetics Services, Royal Children’s Hospital, VIC, Australia
- Kids Research, The Children’s Hospital at Westmead, Sydney, NSW, Australia
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23
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Pinar M, Arias-Palomo E, de los Ríos V, Arst HN, Peñalva MA. Characterization of Aspergillus nidulans TRAPPs uncovers unprecedented similarities between fungi and metazoans and reveals the modular assembly of TRAPPII. PLoS Genet 2019; 15:e1008557. [PMID: 31869332 PMCID: PMC6946167 DOI: 10.1371/journal.pgen.1008557] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 01/07/2020] [Accepted: 12/06/2019] [Indexed: 12/22/2022] Open
Abstract
TRAnsport Protein Particle complexes (TRAPPs) are ubiquitous regulators of membrane traffic mediating nucleotide exchange on the Golgi regulatory GTPases RAB1 and RAB11. In S. cerevisiae and metazoans TRAPPs consist of two large oligomeric complexes: RAB11-activating TRAPPII and RAB1-activating TRAPPIII. These share a common core TRAPPI hetero-heptamer, absent in metazoans but detected in minor proportions in yeast, likely originating from in vitro-destabilized TRAPPII/III. Despite overall TRAPP conservation, the budding yeast genome has undergone extensive loss of genes, and lacks homologues of some metazoan TRAPP subunits. With nearly twice the total number of genes of S. cerevisiae, another ascomycete Aspergillus nidulans has also been used for studies on TRAPPs. We combined size-fractionation chromatography with single-step purification coupled to mass-spectrometry and negative-stain electron microscopy to establish the relative abundance, composition and architecture of Aspergillus TRAPPs, which consist of TRAPPII and TRAPPIII in a 2:1 proportion, plus a minor amount of TRAPPI. We show that Aspergillus TRAPPIII contains homologues of metazoan TRAPPC11, TRAPPC12 and TRAPPC13 subunits, absent in S. cerevisiae, and establish that these subunits are recruited to the complex by Tca17/TRAPPC2L, which itself binds to the ‘Trs33 side’ of the complex. Thus Aspergillus TRAPPs compositionally resemble mammalian TRAPPs to a greater extent than those in budding yeast. Exploiting the ability of constitutively-active (GEF-independent, due to accelerated GDP release) RAB1* and RAB11* alleles to rescue viability of null mutants lacking essential TRAPP subunits, we establish that the only essential role of TRAPPs is activating RAB1 and RAB11, and genetically classify each essential subunit according to their role(s) in TRAPPII (TRAPPII-specific subunits) or TRAPPII and TRAPPIII (core TRAPP subunits). Constitutively-active RAB mutant combinations allowed examination of TRAPP composition in mutants lacking essential subunits, which led to the discovery of a stable Trs120/Trs130/Trs65/Tca17 TRAPPII-specific subcomplex whose Trs20- and Trs33-dependent assembly onto core TRAPP generates TRAPPII. TRAPPs govern intracellular traffic across eukaryotes, activating the Golgi GTPases RAB1 and RAB11. Other genetically tractable fungi are emerging as alternatives to baker’s yeast for cell-biological studies. We exploit Aspergillus nidulans, a filamentous ascomycete that has a lifestyle highly demanding for exocytosis and, that unlike baker’s yeast, has not undergone extensive gene loss. We show that fungal and metazoan TRAPPs are more similar than previously thought, after identifying three A. nidulans subunits previously believed exclusive to metazoans and demonstrating that TRAPPI is very minor, if it exists at all. Also importantly we classified, using a novel genetic approach, essential TRAPP subunits according to their role in activating RAB1 and/or RAB11, which demonstrated that the only indispensable role for TRAPPs is mediating nucleotide exchange on these GTPases and led to the discovery of a stable four-subunit subcomplex that assembles onto the also stable seven-subunit core to form the TRAPPII holocomplex.
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Affiliation(s)
- Mario Pinar
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas CSIC, Madrid, Spain
| | - Ernesto Arias-Palomo
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas CSIC, Madrid, Spain
| | - Vivian de los Ríos
- Proteomics Facility, Centro de Investigaciones Biológicas CSIC, Madrid, Spain
| | - Herbert N. Arst
- Section of Microbiology, Imperial College London, London, United Kingdom
| | - Miguel A. Peñalva
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas CSIC, Madrid, Spain
- * E-mail:
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24
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Milev MP, Stanga D, Schänzer A, Nascimento A, Saint-Dic D, Ortez C, Natera-de Benito D, Barrios DG, Colomer J, Badosa C, Jou C, Gallano P, Gonzalez-Quereda L, Töpf A, Johnson K, Straub V, Hahn A, Sacher M, Jimenez-Mallebrera C. Characterization of three TRAPPC11 variants suggests a critical role for the extreme carboxy terminus of the protein. Sci Rep 2019; 9:14036. [PMID: 31575891 PMCID: PMC6773699 DOI: 10.1038/s41598-019-50415-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/11/2019] [Indexed: 12/23/2022] Open
Abstract
TRAPPC11 was identified as a component of the TRAPP III complex that functions in membrane trafficking and autophagy. Variants in TRAPPC11 have been reported to be associated with a broad spectrum of phenotypes but all affected individuals display muscular pathology. Identifying additional variants will further our understanding of the clinical spectrum of phenotypes and will reveal regions of the protein critical for its functions. Here we report three individuals from unrelated families that have bi-allellic TRAPPC11 variants. Subject 1 harbors a compound heterozygous variant (c.1287 + 5G > A and c.3379_3380insT). The former variant results in a partial deletion of the foie gras domain (p.Ala372_Ser429del), while the latter variant results in a frame-shift and extension at the carboxy terminus (p.Asp1127Valfs*47). Subjects 2 and 3 both harbour a homozygous missense variant (c.2938G > A; p.Gly980Arg). Fibroblasts from all three subjects displayed membrane trafficking defects manifested as delayed endoplasmic reticulum (ER)-to-Golgi transport and/or a delay in protein exit from the Golgi. All three individuals also show a defect in glycosylation of an ER-resident glycoprotein. However, only the compound heterozygous subject displayed an autophagic flux defect. Collectively, our characterization of these individuals with bi-allelic TRAPPC11 variants highlights the functional importance of the carboxy-terminal portion of the protein.
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Affiliation(s)
- Miroslav P Milev
- Concordia University, Department of Biology, Montreal, Quebec, Canada
| | - Daniela Stanga
- Concordia University, Department of Biology, Montreal, Quebec, Canada
| | - Anne Schänzer
- Institute of Neuropathology, Justus Liebig University Giessen, Giessen, Germany
| | - Andrés Nascimento
- Neuromuscular Unit, Neuropaediatrics Department, Hospital Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, Barcelona, Spain.,U705 and U703 Center for Biomedical Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Djenann Saint-Dic
- Concordia University, Department of Biology, Montreal, Quebec, Canada
| | - Carlos Ortez
- Neuromuscular Unit, Neuropaediatrics Department, Hospital Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Daniel Natera-de Benito
- Neuromuscular Unit, Neuropaediatrics Department, Hospital Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Desiré González Barrios
- Servicio de Pediatría, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Jaume Colomer
- Neuromuscular Unit, Neuropaediatrics Department, Hospital Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Carmen Badosa
- Neuromuscular Unit, Neuropaediatrics Department, Hospital Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Cristina Jou
- U705 and U703 Center for Biomedical Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Pathology Department and Biobank, Hospital Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Pia Gallano
- U705 and U703 Center for Biomedical Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Servicio de Genética, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Lidia Gonzalez-Quereda
- U705 and U703 Center for Biomedical Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Servicio de Genética, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Ana Töpf
- The John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle-upon-Tyne, UK
| | - Katherine Johnson
- The John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle-upon-Tyne, UK.,Institute of Cellular Medicine, Newcastle University, Newcastle-upon-Tyne, UK
| | - Volker Straub
- The John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle-upon-Tyne, UK
| | - Andreas Hahn
- Department of Child Neurology, Justus Liebig University Giessen, Giessen, Germany.
| | - Michael Sacher
- Concordia University, Department of Biology, Montreal, Quebec, Canada. .,McGill University, Department of Anatomy and Cell Biology, Montreal, Quebec, Canada.
| | - Cecilia Jimenez-Mallebrera
- Neuromuscular Unit, Neuropaediatrics Department, Hospital Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, Barcelona, Spain. .,U705 and U703 Center for Biomedical Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.
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25
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Lipatova Z, Segev N. Ypt/Rab GTPases and their TRAPP GEFs at the Golgi. FEBS Lett 2019; 593:2488-2500. [PMID: 31400292 PMCID: PMC6989042 DOI: 10.1002/1873-3468.13574] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/07/2019] [Accepted: 08/08/2019] [Indexed: 11/06/2022]
Abstract
The conserved Ypt/Rab GTPases regulate the different steps of all intracellular trafficking pathways. Ypt/Rabs are activated by their specific nucleotide exchangers termed GEFs, and when GTP bound, they recruit their downstream effectors, which mediate vesicular transport substeps. In the yeast exocytic pathway, Ypt1 and Ypt31/32 regulate traffic through the Golgi and the conserved modular TRAPP complex acts a GEF for both Ypt1 and Ypt31/32. However, the precise localization and function of these Ypts have been under debate, as is the identity of their corresponding GEFs. We have established that Ypt1 and Ypt31 reside on the two sides of the Golgi, early and late, respectively, and regulate Golgi cisternal progression. We and others have shown that whereas a single TRAPP complex, TRAPP II, activates Ypt31, three TRAPP complexes can activate Ypt1: TRAPPs I, III, and IV. We propose that TRAPP I and II activate Ypt1 and Ypt31, respectively, at the Golgi, whereas TRAPP III and IV activate Ypt1 in autophagy. Resolving these issues is important because both Rabs and TRAPPs are implicated in multiple human diseases, ranging from cancer to neurodegenerative diseases.
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Affiliation(s)
- Zhanna Lipatova
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, IL, USA
| | - Nava Segev
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, IL, USA
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26
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Otsuka Y, Satoh T, Nakayama N, Inaba R, Yamashita H, Satoh AK. Parcas is the predominant Rab11-GEF for rhodopsin transport in Drosophila photoreceptors. J Cell Sci 2019; 132:jcs.231431. [PMID: 31296556 DOI: 10.1242/jcs.231431] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 07/05/2019] [Indexed: 12/11/2022] Open
Abstract
Rab11 is essential for polarized post-Golgi vesicle trafficking to photosensitive membrane rhabdomeres in Drosophila photoreceptors. Here, we found that Parcas (Pcs), recently shown to have guanine nucleotide exchange (GEF) activity toward Rab11, co-localizes with Rab11 on the trans-side of Golgi units and post-Golgi vesicles at the base of the rhabdomeres in pupal photoreceptors. Pcs fused with the electron micrography tag APEX2 localizes on 150-300 nm vesicles at the trans-side of Golgi units, which are presumably fly recycling endosomes. Loss of Pcs impairs Rab11 localization on the trans-side of Golgi units and induces the cytoplasmic accumulation of post-Golgi vesicles bearing rhabdomere proteins, as observed in Rab11 deficiency. In contrast, loss of Rab11-specific subunits of the TRAPPII complex, another known Rab11-GEF, does not cause any defects in eye development nor the transport of rhabdomere proteins; however, simultaneous loss of TRAPPII and Pcs results in severe defects in eye development. These results indicate that both TRAPPII and Pcs are required for eye development, but Pcs functions as the predominant Rab11-GEF for post-Golgi transport to photosensitive membrane rhabdomeres.
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Affiliation(s)
- Yuna Otsuka
- Program of Life and Environmental Science, Graduate School of Integral Science for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521, Japan
| | - Takunori Satoh
- Program of Life and Environmental Science, Graduate School of Integral Science for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521, Japan
| | - Nozomi Nakayama
- Program of Life and Environmental Science, Graduate School of Integral Science for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521, Japan
| | - Ryota Inaba
- Program of Life and Environmental Science, Graduate School of Integral Science for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521, Japan
| | - Hitomi Yamashita
- Program of Life and Environmental Science, Graduate School of Integral Science for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521, Japan
| | - Akiko K Satoh
- Program of Life and Environmental Science, Graduate School of Integral Science for Life, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521, Japan
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27
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Rosquete MR, Worden N, Ren G, Sinclair RM, Pfleger S, Salemi M, Phinney BS, Domozych D, Wilkop T, Drakakaki G. AtTRAPPC11/ROG2: A Role for TRAPPs in Maintenance of the Plant Trans-Golgi Network/Early Endosome Organization and Function. THE PLANT CELL 2019; 31:1879-1898. [PMID: 31175171 PMCID: PMC6713296 DOI: 10.1105/tpc.19.00110] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/06/2019] [Accepted: 06/02/2019] [Indexed: 05/14/2023]
Abstract
The dynamic trans-Golgi network/early endosome (TGN/EE) facilitates cargo sorting and trafficking and plays a vital role in plant development and environmental response. Transport protein particles (TRAPPs) are multi-protein complexes acting as guanine nucleotide exchange factors and possibly as tethers, regulating intracellular trafficking. TRAPPs are essential in all eukaryotic cells and are implicated in a number of human diseases. It has been proposed that they also play crucial roles in plants; however, our current knowledge about the structure and function of plant TRAPPs is very limited. Here, we identified and characterized AtTRAPPC11/RESPONSE TO OLIGOGALACTURONIDE2 (AtTRAPPC11/ROG2), a TGN/EE-associated, evolutionarily conserved TRAPP protein in Arabidopsis (Arabidopsis thaliana). AtTRAPPC11/ROG2 regulates TGN integrity, as evidenced by altered TGN/EE association of several residents, including SYNTAXIN OF PLANTS61, and altered vesicle morphology in attrappc11/rog2 mutants. Furthermore, endocytic traffic and brefeldin A body formation are perturbed in attrappc11/rog2, suggesting a role for AtTRAPPC11/ROG2 in regulation of endosomal function. Proteomic analysis showed that AtTRAPPC11/ROG2 defines a hitherto uncharacterized TRAPPIII complex in plants. In addition, attrappc11/rog2 mutants are hypersensitive to salinity, indicating an undescribed role of TRAPPs in stress responses. Overall, our study illustrates the plasticity of the endomembrane system through TRAPP protein functions and opens new avenues to explore this dynamic network.
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Affiliation(s)
| | - Natasha Worden
- Department of Plant Sciences University of California, Davis, California 95616
| | - Guangxi Ren
- Department of Plant Sciences University of California, Davis, California 95616
| | - Rosalie M Sinclair
- Department of Plant Sciences University of California, Davis, California 95616
| | - Sina Pfleger
- Department of Plant Sciences University of California, Davis, California 95616
| | - Michelle Salemi
- Genome Center, University of California, Davis, California 95616
| | - Brett S Phinney
- Genome Center, University of California, Davis, California 95616
| | - David Domozych
- Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, New York 12866
| | - Thomas Wilkop
- Department of Plant Sciences University of California, Davis, California 95616
- Light Microscopy Core, University of Kentucky, Lexington, Kentucky 40536
| | - Georgia Drakakaki
- Department of Plant Sciences University of California, Davis, California 95616
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28
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Mitter AL, Schlotterhose P, Krick R. Gyp1 has a dual function as Ypt1 GAP and interaction partner of Atg8 in selective autophagy. Autophagy 2019; 15:1031-1050. [PMID: 30686108 DOI: 10.1080/15548627.2019.1569929] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Macroautophagy/autophagy is a highly conserved intracellular vesicle transport pathway that prevents accumulation of harmful materials within cells. The dynamic assembly and disassembly of the different autophagic protein complexes at the so-called phagophore assembly site (PAS) is strictly regulated. Rab GTPases are major regulators of cellular vesicle trafficking, and the Rab GTPase Ypt1 and its GEF TRAPPIII have been implicated in autophagy. We show that Gyp1 acts as a Ypt1 GTPase-activating protein (GAP) for selective autophagic variants, such as the Cvt pathway or the selective autophagic degradation of mitochondria (mitophagy). Gyp1 regulates the dynamic disassembly of the conserved Ypt1-Atg1 complex. Thereby, Gyp1 sets the stage for efficient Atg14 recruitment, and facilitates the critical step from nucleation to elongation of the phagophore. In addition, we identified Gyp1 as a new Atg8-interacting motif (AIM)-dependent Atg8 interaction partner. The Gyp1 AIM is required for efficient formation of the cargo receptor-Atg8 complexes. Our findings elucidate the molecular mechanisms of complex disassembly during phagophore formation and suggest potential dual functions of GAPs in cellular vesicle trafficking. Abbreviations AIM, Atg8-interacting motif; Atg, autophagy related; Cvt, cytoplasm-to-vacuole targeting; GAP, GTPase-activating protein; GEF, guanine-nucleotide exchange factor; GFP, green fluorescent protein; log phase, logarithmic growth phase; NHD, N-terminal helical domain; PAS, phagophore assembly site; PE, phosphatidylethanolamine; PtdIns3P, phosphatidylinositol-3-phosphate; WT, wild-type.
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Affiliation(s)
- Anne Lisa Mitter
- a Department of Cellular Biochemistry, University Medicine , Georg-August University , Goettingen , Germany
| | - Petra Schlotterhose
- a Department of Cellular Biochemistry, University Medicine , Georg-August University , Goettingen , Germany
| | - Roswitha Krick
- a Department of Cellular Biochemistry, University Medicine , Georg-August University , Goettingen , Germany
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29
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Voss S, Li F, Rätz A, Röger M, Wu YW. Spatial Cycling of Rab GTPase, Driven by the GTPase Cycle, Controls Rab's Subcellular Distribution. Biochemistry 2019; 58:276-285. [PMID: 30605611 DOI: 10.1021/acs.biochem.8b00932] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rab GTPases (>60 members in humans) function as master regulators of intracellular membrane trafficking. Correct and specific localization of Rab proteins is required for their function. How the distinct spatial distribution of Rab GTPases in the cell is regulated remains elusive. To globally assess the subcellular localization of Rab1, we determined kinetic parameters of two pathways that control the spatial cycles of Rab1, i.e., vesicular transport and GDP dissociation inhibitor (GDI)-mediated recycling. We demonstrate that the switching between GTP and GDP binding states, which is governed by guanine nucleotide exchange factors (GEFs), GTPase-activating proteins (GAPs), GDI, and GDI displacement factor (GDF), is a major determinant of Rab1's ability to effectively cycle between cellular compartments and eventually its subcellular distribution. In silico perturbations of vesicular transport, GEFs, GAPs, GDI, and GDF using a mathematical model with simplified cellular geometries showed that these regulators play an important role in the subcellular distribution and activity of Rab1.
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Affiliation(s)
- Stephanie Voss
- Chemical Genomics Centre of the Max Planck Society , Otto-Hahn-Strasse 15 , 44227 Dortmund , Germany.,Max-Planck-Institute of Molecular Physiology , Otto-Hahn-Strasse 11 , 44227 Dortmund , Germany
| | - Fu Li
- Chemical Genomics Centre of the Max Planck Society , Otto-Hahn-Strasse 15 , 44227 Dortmund , Germany.,Max-Planck-Institute of Molecular Physiology , Otto-Hahn-Strasse 11 , 44227 Dortmund , Germany.,Department of Chemistry, Umeå Centre for Microbial Research , Umeå University , 90187 Umeå , Sweden
| | - Andreas Rätz
- TU Dortmund University , Faculty of Mathematics , Vogelpothsweg 87 , 44227 Dortmund , Germany
| | - Matthias Röger
- TU Dortmund University , Faculty of Mathematics , Vogelpothsweg 87 , 44227 Dortmund , Germany
| | - Yao-Wen Wu
- Chemical Genomics Centre of the Max Planck Society , Otto-Hahn-Strasse 15 , 44227 Dortmund , Germany.,Max-Planck-Institute of Molecular Physiology , Otto-Hahn-Strasse 11 , 44227 Dortmund , Germany.,Department of Chemistry, Umeå Centre for Microbial Research , Umeå University , 90187 Umeå , Sweden
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30
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Milev MP, Graziano C, Karall D, Kuper WFE, Al-Deri N, Cordelli DM, Haack TB, Danhauser K, Iuso A, Palombo F, Pippucci T, Prokisch H, Saint-Dic D, Seri M, Stanga D, Cenacchi G, van Gassen KLI, Zschocke J, Fauth C, Mayr JA, Sacher M, van Hasselt PM. Bi-allelic mutations in TRAPPC2L result in a neurodevelopmental disorder and have an impact on RAB11 in fibroblasts. J Med Genet 2018; 55:753-764. [DOI: 10.1136/jmedgenet-2018-105441] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/18/2018] [Accepted: 07/12/2018] [Indexed: 12/28/2022]
Abstract
BackgroundThe combination of febrile illness-induced encephalopathy and rhabdomyolysis has thus far only been described in disorders that affect cellular energy status. In the absence of specific metabolic abnormalities, diagnosis can be challenging.ObjectiveThe objective of this study was to identify and characterise pathogenic variants in two individuals from unrelated families, both of whom presented clinically with a similar phenotype that included neurodevelopmental delay, febrile illness-induced encephalopathy and episodes of rhabdomyolysis, followed by developmental arrest, epilepsy and tetraplegia.MethodsWhole exome sequencing was used to identify pathogenic variants in the two individuals. Biochemical and cell biological analyses were performed on fibroblasts from these individuals and a yeast two-hybrid analysis was used to assess protein-protein interactions.ResultsProbands shared a homozygous TRAPPC2L variant (c.109G>T) resulting in a p.Asp37Tyr missense variant. TRAPPC2L is a component of transport protein particle (TRAPP), a group of multisubunit complexes that function in membrane traffic and autophagy. Studies in patient fibroblasts as well as in a yeast system showed that the p.Asp37Tyr protein was present but not functional and resulted in specific membrane trafficking delays. The human missense mutation and the analogous mutation in the yeast homologue Tca17 ablated the interaction between TRAPPC2L and TRAPPC10/Trs130, a component of the TRAPP II complex. Since TRAPP II activates the GTPase RAB11, we examined the activation state of this protein and found increased levels of the active RAB, correlating with changes in its cellular morphology.ConclusionsOur study implicates a RAB11 pathway in the aetiology of the TRAPPC2L disorder and has implications for other TRAPP-related disorders with similar phenotypes.
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31
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Stuhr M, Blank-Landeshammer B, Reymond CE, Kollipara L, Sickmann A, Kucera M, Westphal H. Disentangling thermal stress responses in a reef-calcifier and its photosymbionts by shotgun proteomics. Sci Rep 2018; 8:3524. [PMID: 29476118 PMCID: PMC5824892 DOI: 10.1038/s41598-018-21875-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 02/08/2018] [Indexed: 01/01/2023] Open
Abstract
The proliferation of key marine ecological engineers and carbonate producers often relies on their association with photosymbiotic algae. Evaluating stress responses of these organisms is important to predict their fate under future climate projections. Physiological approaches are limited in their ability to resolve the involved molecular mechanisms and attribute stress effects to the host or symbiont, while probing and partitioning of proteins cannot be applied in organisms where the host and symbiont are small and cannot be physically separated. Here we apply a label-free quantitative proteomics approach to detect changes of proteome composition in the diatom-bearing benthic foraminifera Amphistegina gibbosa experimentally exposed to three thermal-stress scenarios. We developed a workflow for protein extraction from less than ten specimens and simultaneously analysed host and symbiont proteomes. Despite little genomic data for the host, 1,618 proteins could be partially assembled and assigned. The proteomes revealed identical pattern of stress response among stress scenarios as that indicated by physiological measurements, but allowed identification of compartment-specific stress reactions. In the symbiont, stress-response and proteolysis-related proteins were up regulated while photosynthesis-related proteins declined. In contrast, host homeostasis was maintained through chaperone up-regulation associated with elevated proteosynthesis and proteolysis, and the host metabolism shifted to heterotrophy.
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Affiliation(s)
- Marleen Stuhr
- Biogeochemistry and Geology, Leibniz Centre for Tropical Marine Research (ZMT), 28359, Bremen, Germany.
| | | | - Claire E Reymond
- Biogeochemistry and Geology, Leibniz Centre for Tropical Marine Research (ZMT), 28359, Bremen, Germany
| | - Laxmikanth Kollipara
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44139, Dortmund, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44139, Dortmund, Germany.,Medizinische Fakultät, Medizinische Proteom-Center (MPC), Ruhr-Universität Bochum, 44801, Bochum, Germany.,Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, AB24 3FX, Scotland, United Kingdom
| | - Michal Kucera
- MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany
| | - Hildegard Westphal
- Biogeochemistry and Geology, Leibniz Centre for Tropical Marine Research (ZMT), 28359, Bremen, Germany.,Department of Geosciences, University of Bremen, Bremen, Germany
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32
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Rosquete MR, Davis DJ, Drakakaki G. The Plant Trans-Golgi Network: Not Just a Matter of Distinction. PLANT PHYSIOLOGY 2018; 176:187-198. [PMID: 29192030 PMCID: PMC5761815 DOI: 10.1104/pp.17.01239] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/27/2017] [Indexed: 05/18/2023]
Abstract
The trans-Golgi network in plants is a major sorting station of Golgi derived cargo while it also receives recycled material from endocytosis.
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Affiliation(s)
| | - Destiny Jade Davis
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Georgia Drakakaki
- Department of Plant Sciences, University of California, Davis, California 95616
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33
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Riedel F, Galindo A, Muschalik N, Munro S. The two TRAPP complexes of metazoans have distinct roles and act on different Rab GTPases. J Cell Biol 2017; 217:601-617. [PMID: 29273580 PMCID: PMC5800803 DOI: 10.1083/jcb.201705068] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 10/19/2017] [Accepted: 11/27/2017] [Indexed: 12/03/2022] Open
Abstract
In yeast, the TRAPP complexes activate Rab1 with TRAPPII also activating Rab11, but less is known about the two TRAPPs in metazoans. Riedel et al. show that in Drosophila melanogaster, TRAPPIII is an essential Rab1 activator, and TRAPPII activates Rab1 and Rab11 and becomes essential when an unrelated Rab11 activator is deleted. Originally identified in yeast, transport protein particle (TRAPP) complexes are Rab GTPase exchange factors that share a core set of subunits. TRAPPs were initially found to act on Ypt1, the yeast orthologue of Rab1, but recent studies have found that yeast TRAPPII can also activate the Rab11 orthologues Ypt31/32. Mammals have two TRAPP complexes, but their role is less clear, and they contain subunits that are not found in the yeast complexes but are essential for cell growth. To investigate TRAPP function in metazoans, we show that Drosophila melanogaster have two TRAPP complexes similar to those in mammals and that both activate Rab1, whereas one, TRAPPII, also activates Rab11. TRAPPII is not essential but becomes so in the absence of the gene parcas that encodes the Drosophila orthologue of the SH3BP5 family of Rab11 guanine nucleotide exchange factors (GEFs). Thus, in metazoans, Rab1 activation requires TRAPP subunits not found in yeast, and Rab11 activation is shared by TRAPPII and an unrelated GEF that is metazoan specific.
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Affiliation(s)
- Falko Riedel
- Medical Research Council Laboratory of Molecular Biology, Cambridge, England, UK
| | - Antonio Galindo
- Medical Research Council Laboratory of Molecular Biology, Cambridge, England, UK
| | - Nadine Muschalik
- Medical Research Council Laboratory of Molecular Biology, Cambridge, England, UK
| | - Sean Munro
- Medical Research Council Laboratory of Molecular Biology, Cambridge, England, UK
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34
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Lamers IJC, Reijnders MRF, Venselaar H, Kraus A, Jansen S, de Vries BBA, Houge G, Gradek GA, Seo J, Choi M, Chae JH, van der Burgt I, Pfundt R, Letteboer SJF, van Beersum SEC, Dusseljee S, Brunner HG, Doherty D, Kleefstra T, Roepman R. Recurrent De Novo Mutations Disturbing the GTP/GDP Binding Pocket of RAB11B Cause Intellectual Disability and a Distinctive Brain Phenotype. Am J Hum Genet 2017; 101:824-832. [PMID: 29106825 DOI: 10.1016/j.ajhg.2017.09.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/19/2017] [Indexed: 12/20/2022] Open
Abstract
The Rab GTPase family comprises ∼70 GTP-binding proteins, functioning in vesicle formation, transport and fusion. They are activated by a conformational change induced by GTP-binding, allowing interactions with downstream effectors. Here, we report five individuals with two recurrent de novo missense mutations in RAB11B; c.64G>A; p.Val22Met in three individuals and c.202G>A; p.Ala68Thr in two individuals. An overlapping neurodevelopmental phenotype, including severe intellectual disability with absent speech, epilepsy, and hypotonia was observed in all affected individuals. Additionally, visual problems, musculoskeletal abnormalities, and microcephaly were present in the majority of cases. Re-evaluation of brain MRI images of four individuals showed a shared distinct brain phenotype, consisting of abnormal white matter (severely decreased volume and abnormal signal), thin corpus callosum, cerebellar vermis hypoplasia, optic nerve hypoplasia and mild ventriculomegaly. To compare the effects of both variants with known inactive GDP- and active GTP-bound RAB11B mutants, we modeled the variants on the three-dimensional protein structure and performed subcellular localization studies. We predicted that both variants alter the GTP/GDP binding pocket and show that they both have localization patterns similar to inactive RAB11B. Evaluation of their influence on the affinity of RAB11B to a series of binary interactors, both effectors and guanine nucleotide exchange factors (GEFs), showed induction of RAB11B binding to the GEF SH3BP5, again similar to inactive RAB11B. In conclusion, we report two recurrent dominant mutations in RAB11B leading to a neurodevelopmental syndrome, likely caused by altered GDP/GTP binding that inactivate the protein and induce GEF binding and protein mislocalization.
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Affiliation(s)
- Ideke J C Lamers
- Department of Human Genetics, and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Margot R F Reijnders
- Department of Human Genetics, and Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands.
| | - Hanka Venselaar
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Alison Kraus
- Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds, LS7 4SA, UK
| | - Sandra Jansen
- Department of Human Genetics, and Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, and Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Gunnar Houge
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, N-5021, Norway
| | - Gyri Aasland Gradek
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, N-5021, Norway
| | - Jieun Seo
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Murim Choi
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Jong-Hee Chae
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Ineke van der Burgt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Stef J F Letteboer
- Department of Human Genetics, and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Sylvia E C van Beersum
- Department of Human Genetics, and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Simone Dusseljee
- Department of Human Genetics, and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Han G Brunner
- Department of Human Genetics, and Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands; Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, Maastricht, 6229 ER, the Netherlands
| | - Dan Doherty
- Department of Pediatrics, University of Washington and Seattle Children's Research Institute, Seattle, WA 98195, USA
| | - Tjitske Kleefstra
- Department of Human Genetics, and Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Ronald Roepman
- Department of Human Genetics, and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands.
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35
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Witkos TM, Lowe M. Recognition and tethering of transport vesicles at the Golgi apparatus. Curr Opin Cell Biol 2017; 47:16-23. [DOI: 10.1016/j.ceb.2017.02.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 02/02/2017] [Accepted: 02/08/2017] [Indexed: 12/15/2022]
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36
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Chlamydia Hijacks ARF GTPases To Coordinate Microtubule Posttranslational Modifications and Golgi Complex Positioning. mBio 2017; 8:mBio.02280-16. [PMID: 28465429 PMCID: PMC5414008 DOI: 10.1128/mbio.02280-16] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The intracellular bacterium Chlamydia trachomatis develops in a parasitic compartment called the inclusion. Posttranslationally modified microtubules encase the inclusion, controlling the positioning of Golgi complex fragments around the inclusion. The molecular mechanisms by which Chlamydia coopts the host cytoskeleton and the Golgi complex to sustain its infectious compartment are unknown. Here, using a genetically modified Chlamydia strain, we discovered that both posttranslationally modified microtubules and Golgi complex positioning around the inclusion are controlled by the chlamydial inclusion protein CT813/CTL0184/InaC and host ARF GTPases. CT813 recruits ARF1 and ARF4 to the inclusion membrane, where they induce posttranslationally modified microtubules. Similarly, both ARF isoforms are required for the repositioning of Golgi complex fragments around the inclusion. We demonstrate that CT813 directly recruits ARF GTPases on the inclusion membrane and plays a pivotal role in their activation. Together, these results reveal that Chlamydia uses CT813 to hijack ARF GTPases to couple posttranslationally modified microtubules and Golgi complex repositioning at the inclusion. Chlamydia trachomatis is an important cause of morbidity and a significant economic burden in the world. However, how Chlamydia develops its intracellular compartment, the so-called inclusion, is poorly understood. Using genetically engineered Chlamydia mutants, we discovered that the effector protein CT813 recruits and activates host ADP-ribosylation factor 1 (ARF1) and ARF4 to regulate microtubules. In this context, CT813 acts as a molecular platform that induces the posttranslational modification of microtubules around the inclusion. These cages are then used to reposition the Golgi complex during infection and promote the development of the inclusion. This study provides the first evidence that ARF1 and ARF4 play critical roles in controlling posttranslationally modified microtubules around the inclusion and that Chlamydia trachomatis hijacks this novel function of ARF to reposition the Golgi complex.
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37
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Abstract
Rab proteins are the major regulators of vesicular trafficking in eukaryotic cells. Their activity can be tightly controlled within cells: Regulated by guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs), they switch between an active GTP-bound state and an inactive GDP-bound state, interacting with downstream effector proteins only in the active state. Additionally, they can bind to membranes via C-terminal prenylated cysteine residues and they can be solubilized and shuttled between membranes by chaperone-like molecules called GDP dissociation inhibitors (GDIs). In this review we give an overview of Rab proteins with a focus on the current understanding of their regulation by GEFs, GAPs and GDI.
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Affiliation(s)
- Matthias P Müller
- a Department of Structural Biochemistry , Max Planck Institute of Molecular Physiology , Dortmund , Germany
| | - Roger S Goody
- a Department of Structural Biochemistry , Max Planck Institute of Molecular Physiology , Dortmund , Germany
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38
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Thomas LL, Fromme JC. GTPase cross talk regulates TRAPPII activation of Rab11 homologues during vesicle biogenesis. J Cell Biol 2016; 215:499-513. [PMID: 27872253 PMCID: PMC5119942 DOI: 10.1083/jcb.201608123] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/07/2016] [Accepted: 10/14/2016] [Indexed: 11/22/2022] Open
Abstract
Rab GTPases control vesicle formation and transport, but which proteins are important for their regulation is incompletely understood. Thomas and Fromme provide definitive evidence that TRAPPII is a GEF for the yeast Rab11 homologues Ypt31/32 and implicate the GTPase Arf1 in TRAPPII recruitment, suggesting that a bidirectional cross talk mechanism drives vesicle biogenesis. Rab guanosine triphosphatases (GTPases) control cellular trafficking pathways by regulating vesicle formation, transport, and tethering. Rab11 and its paralogs regulate multiple secretory and endocytic recycling pathways, yet the guanine nucleotide exchange factor (GEF) that activates Rab11 in most eukaryotic cells is unresolved. The large multisubunit transport protein particle (TRAPP) II complex has been proposed to act as a GEF for Rab11 based on genetic evidence, but conflicting biochemical experiments have created uncertainty regarding Rab11 activation. Using physiological Rab-GEF reconstitution reactions, we now provide definitive evidence that TRAPPII is a bona fide GEF for the yeast Rab11 homologues Ypt31/32. We also uncover a direct role for Arf1, a distinct GTPase, in recruiting TRAPPII to anionic membranes. Given the known role of Ypt31/32 in stimulating activation of Arf1, a bidirectional cross talk mechanism appears to drive biogenesis of secretory and endocytic recycling vesicles. By coordinating simultaneous activation of two essential GTPase pathways, this mechanism ensures recruitment of the complete set of effectors needed for vesicle formation, transport, and tethering.
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Affiliation(s)
- Laura L Thomas
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - J Christopher Fromme
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
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39
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Uemura T. Physiological Roles of Plant Post-Golgi Transport Pathways in Membrane Trafficking. PLANT & CELL PHYSIOLOGY 2016; 57:2013-2019. [PMID: 27649735 DOI: 10.1093/pcp/pcw149] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 08/12/2016] [Indexed: 05/02/2023]
Abstract
Membrane trafficking is the fundamental system through which proteins are sorted to their correct destinations in eukaryotic cells. Key regulators of this system include RAB GTPases and soluble N-ethylmaleimide sensitive factor attachment protein receptors (SNAREs). Interestingly, the numbers of RAB GTPases and SNAREs involved in post-Golgi transport pathways in plant cells are larger than those in animal and yeast cells, suggesting that plants have evolved unique and complex post-Golgi transport pathways. The trans-Golgi network (TGN) is an important organelle that acts as a sorting station in the post-Golgi transport pathways of plant cells. The TGN also functions as the early endosome, which is the first compartment to receive endocytosed proteins. Several endocytosed proteins on the plasma membrane (PM) are initially targeted to the TGN/EE, then recycled back to the PM or transported to the vacuole for degradation. The recycling and degradation of the PM localized proteins is essential for the development and environmental responses in plant. The present review describes the post-Golgi transport pathways that show unique physiological functions in plants.
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Affiliation(s)
- Tomohiro Uemura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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40
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Ishida M, E Oguchi M, Fukuda M. Multiple Types of Guanine Nucleotide Exchange Factors (GEFs) for Rab Small GTPases. Cell Struct Funct 2016; 41:61-79. [PMID: 27246931 DOI: 10.1247/csf.16008] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Rab small GTPases are highly conserved master regulators of membrane traffic in all eukaryotes. The same as the activation and inactivation of other small GTPases, the activation and inactivation of Rabs are tightly controlled by specific GEFs (guanine nucleotide exchange factors) and GAPs (GTPase-activating proteins), respectively. Although almost all Rab-GAPs reported thus far have a TBC (Tre-2/Bub2/Cdc16)/Rab-GAP domain in common, recent accumulating evidence has indicated the existence of a number of structurally unrelated types of Rab-GEFs, including DENN proteins, VPS9 proteins, Sec2 proteins, TRAPP complexes, heterodimer GEFs (Mon1-Ccz1, HPS1-HPS4 (BLOC-3 complex), Ric1-Rgp1 and Rab3GAP1/2), and other GEFs (e.g., REI-1 and RPGR). In this review article we provide an up-to-date overview of the structures and functions of all putative Rab-GEFs in mammals, with a special focus on their substrate Rabs, interacting proteins, associations with genetic diseases, and intracellular localizations.
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Affiliation(s)
- Morié Ishida
- Laboratory of Membrane Trafficking Mechanisms, Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University
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41
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Brunet S, Saint-Dic D, Milev MP, Nilsson T, Sacher M. The TRAPP Subunit Trs130p Interacts with the GAP Gyp6p to Mediate Ypt6p Dynamics at the Late Golgi. Front Cell Dev Biol 2016; 4:48. [PMID: 27252941 PMCID: PMC4877375 DOI: 10.3389/fcell.2016.00048] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 05/09/2016] [Indexed: 01/05/2023] Open
Abstract
Small GTPases of the Rab superfamily participate in virtually all vesicle-mediated trafficking events. Cycling between an active GTP-bound form and an inactive GDP-bound form is accomplished in conjunction with guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs), respectively. Rab cascades have been described in which an effector of an activated Rab is a GEF for a downstream Rab, thus ensuring activation of a pathway in an ordered fashion. Much less is known concerning crosstalk between GEFs and GAPs although regulation between these factors could also contribute to the overall physiology of a cell. Here we demonstrate that a subunit of the TRAPP II multisubunit tethering factor, a Rab GEF, participates in the recruitment of Gyp6p, a GAP for the GTPase Ypt6p, to Golgi membranes. The extreme carboxy-terminal portion of the TRAPP II subunit Trs130p is required for the interaction between TRAPP II and Gyp6p. We further demonstrate that TRAPP II mutants, but not a TRAPP III mutant, display a defect in Gyp6p interaction. A consequence of this defective interaction is the enhanced localization of Ypt6p at late Golgi membranes. Although a ypt31/32 mutant also resulted in an enhanced localization of Gyp6p at the late Golgi, the effect was not as dramatic as that seen for TRAPP II mutants, nor was Ypt31/32 detected in the same TRAPP II purification that detected Gyp6p. We propose that the interaction between TRAPP II and Gyp6p represents a parallel mechanism in addition to that mediated by Ypt31/32 for the recruitment of a GAP to the appropriate membrane, and is a novel example of crosstalk between a Rab GAP and GEF.
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Affiliation(s)
- Stephanie Brunet
- Department of Biology, Concordia University Montreal, QC, Canada
| | | | - Miroslav P Milev
- Department of Biology, Concordia University Montreal, QC, Canada
| | - Tommy Nilsson
- Department of Medicine, McGill University Montreal, QC, Canada
| | - Michael Sacher
- Department of Biology, Concordia UniversityMontreal, QC, Canada; Department of Anatomy and Cell Biology, McGill UniversityMontreal, QC, Canada
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42
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Vukašinović N, Žárský V. Tethering Complexes in the Arabidopsis Endomembrane System. Front Cell Dev Biol 2016; 4:46. [PMID: 27243010 PMCID: PMC4871884 DOI: 10.3389/fcell.2016.00046] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 05/02/2016] [Indexed: 12/30/2022] Open
Abstract
Targeting of endomembrane transport containers is of the utmost importance for proper land plant growth and development. Given the immobility of plant cells, localized membrane vesicle secretion and recycling are amongst the main processes guiding proper cell, tissue and whole plant morphogenesis. Cell wall biogenesis and modification are dependent on vectorial membrane traffic, not only during normal development, but also in stress responses and in plant defense against pathogens and/or symbiosis. It is surprising how little we know about these processes in plants, from small GTPase regulation to the tethering complexes that act as their effectors. Tethering factors are single proteins or protein complexes mediating first contact between the target membrane and arriving membrane vesicles. In this review we focus on the tethering complexes of the best-studied plant model—Arabidopsis thaliana. Genome-based predictions indicate the presence of all major tethering complexes in plants that are known from a hypothetical last eukaryotic common ancestor (LECA). The evolutionary multiplication of paralogs of plant tethering complex subunits has produced the massively expanded EXO70 family, indicating a subfunctionalization of the terminal exocytosis machinery in land plants. Interpretation of loss of function (LOF) mutant phenotypes has to consider that related, yet clearly functionally-specific complexes often share some common core subunits. It is therefore impossible to conclude with clarity which version of the complex is responsible for the phenotypic deviations observed. Experimental interest in the analysis of plant tethering complexes is growing and we hope to contribute with this review by attracting even more attention to this fascinating field of plant cell biology.
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Affiliation(s)
- Nemanja Vukašinović
- Laboratory of Cell Morphogenesis, Department of Experimental Plant Biology, Faculty of Science, Charles University Prague, Czech Republic
| | - Viktor Žárský
- Laboratory of Cell Morphogenesis, Department of Experimental Plant Biology, Faculty of Science, Charles University Prague, Czech Republic
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43
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Schroeter S, Beckmann S, Schmitt HD. Coat/Tether Interactions-Exception or Rule? Front Cell Dev Biol 2016; 4:44. [PMID: 27243008 PMCID: PMC4868844 DOI: 10.3389/fcell.2016.00044] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 04/25/2016] [Indexed: 12/02/2022] Open
Abstract
Coat complexes are important for cargo selection and vesicle formation. Recent evidence suggests that they may also be involved in vesicle targeting. Tethering factors, which form an initial bridge between vesicles and the target membrane, may bind to coat complexes. In this review, we ask whether these coat/tether interactions share some common mechanisms, or whether they are special adaptations to the needs of very specific transport steps. We compare recent findings in two multisubunit tethering complexes, the Dsl1 complex and the HOPS complex, and put them into context with the TRAPP I complex as a prominent example for coat/tether interactions. We explore where coat/tether interactions are found, compare their function and structure, and comment on a possible evolution from a common ancestor of coats and tethers.
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Affiliation(s)
- Saskia Schroeter
- Neurobiology, Max Planck Institute for Biophysical Chemistry Göttingen, Germany
| | - Sabrina Beckmann
- Neurobiology, Max Planck Institute for Biophysical Chemistry Göttingen, Germany
| | - Hans Dieter Schmitt
- Neurobiology, Max Planck Institute for Biophysical Chemistry Göttingen, Germany
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Wang N, Lee IJ, Rask G, Wu JQ. Roles of the TRAPP-II Complex and the Exocyst in Membrane Deposition during Fission Yeast Cytokinesis. PLoS Biol 2016; 14:e1002437. [PMID: 27082518 PMCID: PMC4833314 DOI: 10.1371/journal.pbio.1002437] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 03/15/2016] [Indexed: 12/27/2022] Open
Abstract
The cleavage-furrow tip adjacent to the actomyosin contractile ring is believed to be the predominant site for plasma-membrane insertion through exocyst-tethered vesicles during cytokinesis. Here we found that most secretory vesicles are delivered by myosin-V on linear actin cables in fission yeast cytokinesis. Surprisingly, by tracking individual exocytic and endocytic events, we found that vesicles with new membrane are deposited to the cleavage furrow relatively evenly during contractile-ring constriction, but the rim of the cleavage furrow is the main site for endocytosis. Fusion of vesicles with the plasma membrane requires vesicle tethers. Our data suggest that the transport particle protein II (TRAPP-II) complex and Rab11 GTPase Ypt3 help to tether secretory vesicles or tubulovesicular structures along the cleavage furrow while the exocyst tethers vesicles at the rim of the division plane. We conclude that the exocyst and TRAPP-II complex have distinct localizations at the division site, but both are important for membrane expansion and exocytosis during cytokinesis. Two putative vesicle tethers—the exocyst and TRAPP-II complexes—localize differently at the division plane to ensure efficient plasma-membrane deposition along the whole cleavage furrow during cytokinesis in the fission yeast Schizosaccharomyces pombe. Cytokinesis partitions a mother cell into two daughter cells at the end of each cell-division cycle. A significant amount of new plasma membrane is needed at the cleavage furrow during cytokinesis in many cell types. Membrane expansion is achieved through the balance of exocytosis and endocytosis. It is poorly understood where and when the membrane is deposited and retrieved during cytokinesis. By tracking individual vesicles with high spatiotemporal resolution and using electron microscopy, we found that new membrane is deposited relatively evenly along the cleavage furrow in fission yeast, while the rim of the division plane is the predominant site for endocytosis. The secretory vesicles/compartments carrying new membrane are mainly delivered along formin-nucleated actin cables by myosin-V motors. Surprisingly, we find that both exocytosis and endocytosis at the division site are ramped up before contractile-ring constriction and last until daughter-cell separation. We discovered that two putative vesicle tethers, the exocyst and TRAPP-II complexes, localize to different sites at the cleavage furrow to promote tethering of different, yet overlapping, classes of secretory vesicles/compartments for exocytosis and new membrane deposition.
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Affiliation(s)
- Ning Wang
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | - I-Ju Lee
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | - Galen Rask
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | - Jian-Qiu Wu
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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45
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Kim JJ, Lipatova Z, Segev N. TRAPP Complexes in Secretion and Autophagy. Front Cell Dev Biol 2016; 4:20. [PMID: 27066478 PMCID: PMC4811894 DOI: 10.3389/fcell.2016.00020] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 03/04/2016] [Indexed: 12/13/2022] Open
Abstract
TRAPP is a highly conserved modular multi-subunit protein complex. Originally identified as a “transport protein particle” with a role in endoplasmic reticulum-to-Golgi transport, its multiple subunits and their conservation from yeast to humans were characterized in the late 1990s. TRAPP attracted attention when it was shown to act as a Ypt/Rab GTPase nucleotide exchanger, GEF, in the 2000s. Currently, three TRAPP complexes are known in yeast, I, II, and III, and they regulate two different intracellular trafficking pathways: secretion and autophagy. Core TRAPP contains four small subunits that self assemble to a stable complex, which has a GEF activity on Ypt1. Another small subunit, Trs20/Sedlin, is an adaptor required for the association of core TRAPP with larger subunits to form TRAPP II and TRAPP III. Whereas the molecular structure of the core TRAPP complex is resolved, the architecture of the larger TRAPP complexes, including their existence as dimers and multimers, is less clear. In addition to its Ypt/Rab GEF activity, and thereby an indirect role in vesicle tethering through Ypt/Rabs, a direct role for TRAPP as a vesicle tether has been suggested. This idea is based on TRAPP interactions with vesicle coat components. While much of the basic information about TRAPP complexes comes from yeast, mutations in TRAPP subunits were connected to human disease. In this review we will summarize new information about TRAPP complexes, highlight new insights about their function and discuss current controversies and future perspectives.
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Affiliation(s)
- Jane J Kim
- Department of Biological Sciences, University of Illinois at Chicago Chicago, IL, USA
| | - Zhanna Lipatova
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago Chicago, IL, USA
| | - Nava Segev
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago Chicago, IL, USA
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Abstract
Many viruses exploit specific arms of the endomembrane system. The unique composition of each arm prompts the development of remarkably specific interactions between viruses and sub-organelles. This review focuses on the viral–host interactions occurring on the endocytic recycling compartment (ERC), and mediated by its regulatory Ras-related in brain (Rab) GTPase Rab11. This protein regulates trafficking from the ERC and the trans-Golgi network to the plasma membrane. Such transport comprises intricate networks of proteins/lipids operating sequentially from the membrane of origin up to the cell surface. Rab11 is also emerging as a critical factor in an increasing number of infections by major animal viruses, including pathogens that provoke human disease. Understanding the interplay between the ERC and viruses is a milestone in human health. Rab11 has been associated with several steps of the viral lifecycles by unclear processes that use sophisticated diversified host machinery. For this reason, we first explore the state-of-the-art on processes regulating membrane composition and trafficking. Subsequently, this review outlines viral interactions with the ERC, highlighting current knowledge on viral-host binding partners. Finally, using examples from the few mechanistic studies available we emphasize how ERC functions are adjusted during infection to remodel cytoskeleton dynamics, innate immunity and membrane composition.
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Affiliation(s)
- Sílvia Vale-Costa
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal.
| | - Maria João Amorim
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal.
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Lipatova Z, Hain AU, Nazarko VY, Segev N. Ypt/Rab GTPases: principles learned from yeast. Crit Rev Biochem Mol Biol 2015; 50:203-11. [PMID: 25702751 DOI: 10.3109/10409238.2015.1014023] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Ypt/Rab GTPases are key regulators of all membrane trafficking events in eukaryotic cells. They act as molecular switches that attach to membranes via lipid tails to recruit their multiple downstream effectors, which mediate vesicular transport. Originally discovered in yeast as Ypts, they were later shown to be conserved from yeast to humans, where Rabs are relevant to a wide array of diseases. Major principles learned from our past studies in yeast are currently accepted in the Ypt/Rab field including: (i) Ypt/Rabs are not transport-step specific, but are rather compartment specific, (ii) stimulation by nucleotide exchangers, GEFs, is critical to their function, whereas GTP hydrolysis plays a role in their cycling between membranes and the cytoplasm for multiple rounds of action, (iii) they mediate diverse functions ranging from vesicle formation to vesicle fusion and (iv) they act in GTPase cascades to regulate intracellular trafficking pathways. Our recent studies on Ypt1 and Ypt31/Ypt32 and their modular GEF complex TRAPP raise three exciting novel paradigms for Ypt/Rab function: (a) coordination of vesicular transport substeps, (b) integration of individual transport steps into pathways and (c) coordination of different transport pathways. In addition to its amenability to genetic analysis, yeast provides a superior model system for future studies on the role of Ypt/Rabs in traffic coordination due to the smaller proteome that results in a simpler traffic grid. We propose that different types of coordination are important also in human cells for fine-tuning of intracellular trafficking, and that coordination defects could result in disease.
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Affiliation(s)
- Zhanna Lipatova
- a Department of Biochemistry and Molecular Genetics , University of Illinois at Chicago , Chicago , IL , USA
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48
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Zou S, Liu Y, Zhang C, Yu S, Liang Y. Bet3 participates in autophagy through GTPase Ypt1 in Saccharomyces cerevisiae. Cell Biol Int 2015; 39:466-74. [PMID: 25581738 DOI: 10.1002/cbin.10416] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 12/13/2014] [Indexed: 11/08/2022]
Abstract
Three TRAPP (transport protein particle) complexes have been identified in Saccharomyces cerevisiae. GTPases Ypt1 and Ypt31/32 suppress autophagic defects in the mutants of TRAPPIII-specific subunit (Trs85) and TRAPPII-specific subunits (Trs130 and Trs120), respectively. However, the roles of the common TRAPP subunits (which also form the TRAPPI complex) in autophagy and their relationship to Rab GTPases in autophagy remain unclear. As Bet3 (a common TRAPP subunit) cannot be mutated together with either Trs85 or Trs130, we examined starvation-induced autophagy and the cytoplasm-to-vacuole targeting (Cvt) pathway in bet3ts cells. The results demonstrated that GFP-Atg8 was dispersed in the cytoplasm and Ape1 accumulated as a unique dot on the vacuolar membrane in bet3ts cells. Further analysis revealed that Ape1 maturation and GFP-Atg8 processing are defective in these cells. However, prApe1 (precursor form of Ape1) and GFP-Atg8 are protease-accessible in bet3ts cells under starvation, which indicates that Bet3 functions before autophagosome closure. Furthermore, active Ypt1, but not Ypt31, partly rescued the autophagic defects of bet3ts cells. We conclude that Bet3 is involved in autophagy and propose that it participates in autophagy through TRAPP complexes mostly via Ypt1 in yeast.
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Affiliation(s)
- Shenshen Zou
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
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49
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Lipatova Z, Kim JJ, Segev N. Ypt1 and TRAPP interactions: optimization of multicolor bimolecular fluorescence complementation in yeast. Methods Mol Biol 2015; 1298:107-16. [PMID: 25800836 PMCID: PMC4711993 DOI: 10.1007/978-1-4939-2569-8_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Ypt/Rab GTPases are conserved molecular switches that regulate the multiple vesicular transport steps of all intracellular trafficking pathways. They are stimulated by guanine-nucleotide exchange factors (GEFs). In yeast, Ypt1 regulates transport from the endoplasmic reticulum (ER) to two alternative pathways: secretion and autophagy. Ypt1 is activated by TRAPP, a modular multi-subunit GEF. Whereas TRAPP I activates Ypt1 to mediate transport through the Golgi, TRAPP III, which contains all the subunits of TRAPP I plus Trs85, activates Ypt1-mediated transport to autophagosomes. The functional pair Ypt31/32 regulates traffic in and out of the trans-Golgi and is activated by TRAPP II, which consists of TRAPP I plus two specific subunits, Trs120 and Trs130. To study the interaction of Ypts with specific TRAPP subunits and interactions between the different subunits of TRAPP, including the cellular sites of these interactions, we have employed a number of approaches. One approach that we have recently optimized for the use in yeast is multicolor bimolecular fluorescence complementation (BiFC). BiFC, which employs split fluorescent tags, has emerged as a powerful approach for determining protein interaction in vivo. Because proteins work in complexes, the ability to determine more than one interaction at a time using multicolor BiFC is even more powerful. Defining the sites of protein interaction is possible by co-localization of the BiFC puncta with compartmental markers. Here, we describe a set of plasmids for multicolor BiFC optimized for use in yeast. We combined their use with a set of available yeast strains that express red fluorescence compartmental markers. We have recently used these constructs to determine Ypt1 and TRAPP interactions in two different processes: intracellular trafficking and autophagy.
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Affiliation(s)
- Zhanna Lipatova
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago
| | - Jane J. Kim
- Department of Biological Sciences, University of Illinois at Chicago
| | - Nava Segev
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago,Corresponding Author: Nava Segev, Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Molecular Biology Research Building, 900 South Ashland Avenue/ Chicago, Illinois 60607, Phone: 312-355-0142; Fax 312-413-0353;
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50
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Abstract
Rab proteins represent the largest branch of the Ras-like small GTPase superfamily and there are 66 Rab genes in the human genome. They alternate between GTP- and GDP-bound states, which are facilitated by guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs), and function as molecular switches in regulation of intracellular membrane trafficking in all eukaryotic cells. Each Rab targets to an organelle and specify a transport step along exocytic, endocytic, and recycling pathways as well as the crosstalk between these pathways. Through interactions with multiple effectors temporally, a Rab can control membrane budding and formation of transport vesicles, vesicle movement along cytoskeleton, and membrane fusion at the target compartment. The large number of Rab proteins reflects the complexity of the intracellular transport system, which is essential for the localization and function of membrane and secretory proteins such as hormones, growth factors, and their membrane receptors. As such, Rab proteins have emerged as important regulators for signal transduction, cell growth, and differentiation. Altered Rab expression and/or activity have been implicated in diseases ranging from neurological disorders, diabetes to cancer.
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Affiliation(s)
- Guangpu Li
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, 975 NE 10 Street, BRC 417, Oklahoma City, OK, 73104, USA,
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