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Almousa H, Lewis SA, Bakhtiari S, Nordlie SH, Pagnozzi A, Magee H, Efthymiou S, Heim JA, Cornejo P, Zaki MS, Anwar N, Maqbool S, Rahman F, Neilson DE, Vemuri A, Jin SC, Yang XR, Heidari A, van Gassen K, Trimouille A, Thauvin-Robinet C, Liu J, Bruel AL, Tomoum H, Shata MO, Hashem MO, Toosi MB, Karimiani EG, Yeşil G, Lingappa L, Baruah D, Ebrahimzadeh F, Van-Gils J, Faivre L, Zamani M, Galehdari H, Sadeghian S, Shariati G, Mohammad R, van der Smagt J, Qari A, Vincent JB, Innes AM, Dursun A, Özgül RK, Akar HT, Bilguvar K, Mignot C, Keren B, Raveli C, Burglen L, Afenjar A, Kaat LD, van Slegtenhorst M, Alkuraya F, Houlden H, Padilla-Lopez S, Maroofian R, Sacher M, Kruer MC. TRAPPC6B biallelic variants cause a neurodevelopmental disorder with TRAPP II and trafficking disruptions. Brain 2024; 147:311-324. [PMID: 37713627 PMCID: PMC10766242 DOI: 10.1093/brain/awad301] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/11/2023] [Accepted: 08/10/2023] [Indexed: 09/17/2023] Open
Abstract
Highly conserved transport protein particle (TRAPP) complexes regulate subcellular trafficking pathways. Accurate protein trafficking has been increasingly recognized to be critically important for normal development, particularly in the nervous system. Variants in most TRAPP complex subunits have been found to lead to neurodevelopmental disorders with diverse but overlapping phenotypes. We expand on limited prior reports on TRAPPC6B with detailed clinical and neuroradiologic assessments, and studies on mechanisms of disease, and new types of variants. We describe 29 additional patients from 18 independent families with biallelic variants in TRAPPC6B. We identified seven homozygous nonsense (n = 12 patients) and eight canonical splice-site variants (n = 17 patients). In addition, we identified one patient with compound heterozygous splice-site/missense variants with a milder phenotype and one patient with homozygous missense variants. Patients displayed non-progressive microcephaly, global developmental delay/intellectual disability, epilepsy and absent expressive language. Movement disorders including stereotypies, spasticity and dystonia were also observed. Brain imaging revealed reductions in cortex, cerebellum and corpus callosum size with frequent white matter hyperintensity. Volumetric measurements indicated globally diminished volume rather than specific regional losses. We identified a reduced rate of trafficking into the Golgi apparatus and Golgi fragmentation in patient-derived fibroblasts that was rescued by wild-type TRAPPC6B. Molecular studies revealed a weakened interaction between mutant TRAPPC6B (c.454C>T, p.Q152*) and its TRAPP binding partner TRAPPC3. Patient-derived fibroblasts from the TRAPPC6B (c.454C>T, p.Q152*) variant displayed reduced levels of TRAPPC6B as well as other TRAPP II complex-specific members (TRAPPC9 and TRAPPC10). Interestingly, the levels of the TRAPPC6B homologue TRAPPC6A were found to be elevated. Moreover, co-immunoprecipitation experiments showed that TRAPPC6A co-precipitates equally with TRAPP II and TRAPP III, while TRAPPC6B co-precipitates significantly more with TRAPP II, suggesting enrichment of the protein in the TRAPP II complex. This implies that variants in TRAPPC6B may preferentially affect TRAPP II functions compared to TRAPP III functions. Finally, we assessed phenotypes in a Drosophila TRAPPC6B-deficiency model. Neuronal TRAPPC6B knockdown impaired locomotion and led to wing posture defects, supporting a role for TRAPPC6B in neuromotor function. Our findings confirm the association of damaging biallelic TRAPPC6B variants with microcephaly, intellectual disability, language impairments, and epilepsy. A subset of patients also exhibited dystonia and/or spasticity with impaired ambulation. These features overlap with disorders arising from pathogenic variants in other TRAPP subunits, particularly components of the TRAPP II complex. These findings suggest that TRAPPC6B is essential for brain development and function, and TRAPP II complex activity may be particularly relevant for mediating this function.
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Affiliation(s)
- Hashem Almousa
- Department of Biology, Concordia University, Montreal, Quebec H4B1R6, Canada
| | - Sara A Lewis
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Departments of Child Health, Cellular and Molecular Medicine, Genetics, and Neurology, University of Arizona College of Medicine—Phoenix, Phoenix, AZ 85004, USA
| | - Somayeh Bakhtiari
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Departments of Child Health, Cellular and Molecular Medicine, Genetics, and Neurology, University of Arizona College of Medicine—Phoenix, Phoenix, AZ 85004, USA
| | - Sandra Hinz Nordlie
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Departments of Child Health, Cellular and Molecular Medicine, Genetics, and Neurology, University of Arizona College of Medicine—Phoenix, Phoenix, AZ 85004, USA
| | - Alex Pagnozzi
- CSIRO Health and Biosecurity, The Australian e-Health Research Centre, Brisbane 4029, Australia
| | - Helen Magee
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Departments of Child Health, Cellular and Molecular Medicine, Genetics, and Neurology, University of Arizona College of Medicine—Phoenix, Phoenix, AZ 85004, USA
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Jennifer A Heim
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
| | - Patricia Cornejo
- Pediatric Neuroradiology Division, Pediatric Radiology, Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Department of Child Health, University of Arizona College of Medicine, Phoenix, AZ 85004, USA
- Department of Radiology, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo 12622, Egypt
- Genetics Department, Armed Forces College of Medicine (AFCM), Cairo 4460015, Egypt
| | - Najwa Anwar
- Department of Developmental-Behavioural Paediatrics, The Children's Hospital and Institute of Child Health, Lahore 54000, Pakistan
| | - Shazia Maqbool
- Department of Developmental-Behavioural Paediatrics, The Children's Hospital and Institute of Child Health, Lahore 54000, Pakistan
| | - Fatima Rahman
- Department of Developmental-Behavioural Paediatrics, The Children's Hospital and Institute of Child Health, Lahore 54000, Pakistan
| | - Derek E Neilson
- Genetics and Metabolism, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
| | - Anusha Vemuri
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Sheng Chih Jin
- Department of Genetics, Washington University, St.Louis, MO 63110, USA
| | - Xiao-Ru Yang
- Department of Medical Genetics and Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, S.W. Calgary, AB T2N 4N1, Canada
| | - Abolfazl Heidari
- Reference Laboratory, Qazvin Medical University, Qazvin 34148-33245, Iran
| | - Koen van Gassen
- Division of Laboratories, Pharmacy and Biomedical Genetics, Section of Clinical Genetics, University Medical Center Utrecht (UMCU), 3584 CX Utrecht, Netherlands
| | - Aurélien Trimouille
- Laboratoire de Génétique Moléculaire, Service de Génétique Médicale, CHU Bordeaux—Hôpital Pellegrin, Place Amélie Raba Léon, 33000 Bordeaux, France
| | - Christel Thauvin-Robinet
- Department of Genetics and Reference Center for Development Disorders and Intellectual Disabilities, FHU TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
- Unité Fontctionnelle d’Innovation diagnostiques des maladies rares, FHU TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
- GAD ‘Génétique des Anomalies du Développement’, INSERM-Université de Bourgogne UMR1231, 21078 Dijon, France
| | - James Liu
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Departments of Child Health, Cellular and Molecular Medicine, Genetics, and Neurology, University of Arizona College of Medicine—Phoenix, Phoenix, AZ 85004, USA
| | - Ange-Line Bruel
- Unité Fontctionnelle d’Innovation diagnostiques des maladies rares, FHU TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
- GAD ‘Génétique des Anomalies du Développement’, INSERM-Université de Bourgogne UMR1231, 21078 Dijon, France
| | - Hoda Tomoum
- Department of Pediatrics, Ain Shams University, Cairo 11516, Egypt
| | | | - Mais O Hashem
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Mehran Beiraghi Toosi
- Pediatric Neurology Department, Ghaem Hospital, Mashhad University of Medical Sciences, Mashhad 13944-91388, Iran
- Neuroscience Research Center, Mashhad University of Medical Science, Mashhad 13944-91388, Iran
| | - Ehsan Ghayoor Karimiani
- Molecular and Clinical Sciences Institute, St.George’s, University of London, London SW17 0RE, UK
| | - Gözde Yeşil
- Istanbul Medical Faculty Department of Medical Genetics, Istanbul University, Istanbul 34452, Turkey
| | - Lokesh Lingappa
- Pediatric Neurology, Rainbow Children Hospital, Hyderabad 500034, India
| | - Debangana Baruah
- Pediatric Neurology, Rainbow Children Hospital, Hyderabad 500034, India
| | - Farnoosh Ebrahimzadeh
- Department of Internal Medicine, Mashhad University of Medical Sciences, Mashhad 13944-91388, Iran
| | - Julien Van-Gils
- Division of Laboratories, Pharmacy and Biomedical Genetics, Section of Clinical Genetics, University Medical Center Utrecht (UMCU), 3584 CX Utrecht, Netherlands
| | - Laurence Faivre
- Department of Genetics and Reference Center for Development Disorders and Intellectual Disabilities, FHU TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
| | - Mina Zamani
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz 6135783151, Iran
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz 6155889467, Iran
| | - Hamid Galehdari
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz 6135783151, Iran
| | - Saeid Sadeghian
- Department of Pediatric Neurology, Golestan Medical, Educational, and Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz 6135733118, Iran
| | - Gholamreza Shariati
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz 6155889467, Iran
- Department of Medical Genetics, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz 6135733118, Iran
| | - Rahema Mohammad
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Jasper van der Smagt
- Division of Laboratories, Pharmacy and Biomedical Genetics, Section of Clinical Genetics, University Medical Center Utrecht (UMCU), 3584 CX Utrecht, Netherlands
| | - Alya Qari
- Medical Genomics Department, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - John B Vincent
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON M6J 1H4, Canada
| | - A Micheil Innes
- Department of Medical Genetics and Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, S.W. Calgary, AB T2N 4N1, Canada
| | - Ali Dursun
- Department of Pediatric Metabolism, Hacettepe University, Faculty of Medicine & Institute of Child Health, Ankara 06800, Turkey
| | - R Köksal Özgül
- Department of Pediatric Metabolism, Hacettepe University, Faculty of Medicine & Institute of Child Health, Ankara 06800, Turkey
| | - Halil Tuna Akar
- Department of Pediatric Metabolism, Hacettepe University, Faculty of Medicine & Institute of Child Health, Ankara 06800, Turkey
| | - Kaya Bilguvar
- Department of Medical Genetics, Acibadem Mehmet Ali Aydinlar University, Istanbul 34752, Turkey
- Department of Neurosurgery and Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Cyril Mignot
- Département de Génétique, APHP Sorbonne Université, Hôpital Trousseau & Groupe Hospitalier Pitié-Salpêtrière, 75013 Paris, France
- Centre de Référence Déficiences Intellectuelles de Causes Rares, 75012 Paris, France
| | - Boris Keren
- Département de Génétique, APHP Sorbonne Université, Hôpital Trousseau & Groupe Hospitalier Pitié-Salpêtrière, 75013 Paris, France
| | - Claudia Raveli
- APHP Sorbonne Université, Service de Neuropédiatrie, Hôpital Trousseau, 75012 Paris, France
| | - Lydie Burglen
- Département de Génétique, Centre de référence des malformations et maladies congénitales du cervelet, APHP. Sorbonne Université, Hôpital Trousseau, 75012 Paris, France
| | - Alexandra Afenjar
- Département de Génétique, Centre de référence des malformations et maladies congénitales du cervelet, APHP. Sorbonne Université, Hôpital Trousseau, 75012 Paris, France
| | - Laura Donker Kaat
- Department of Clinical Genetics, Erasmus Medical Center, 3000 Rotterdam, The Netherlands
| | | | - Fowzan Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Sergio Padilla-Lopez
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Departments of Child Health, Cellular and Molecular Medicine, Genetics, and Neurology, University of Arizona College of Medicine—Phoenix, Phoenix, AZ 85004, USA
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Michael Sacher
- Department of Biology, Concordia University, Montreal, Quebec H4B1R6, Canada
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A0C7, Canada
| | - Michael C Kruer
- Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
- Departments of Child Health, Cellular and Molecular Medicine, Genetics, and Neurology, University of Arizona College of Medicine—Phoenix, Phoenix, AZ 85004, USA
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Epigenetic impact of a 1-week intensive multimodal group program for adolescents with multiple adverse childhood experiences. Sci Rep 2022; 12:17177. [PMID: 36266402 PMCID: PMC9585146 DOI: 10.1038/s41598-022-21246-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/26/2022] [Indexed: 01/04/2023] Open
Abstract
Adverse childhood experiences (ACEs, i.e., abuse, neglect, household dysfunction) represent a potential risk factor for a wide range of long-lasting diseases and shorter life expectancy. We recently described a 1-week residential group program, based on mindfulness training, artistic expression and EMDR group therapy, that significantly reduced PTSD-related symptoms and increased attention/awareness-related outcomes in adolescent girls with multiple ACEs in a randomized controlled study. Since epigenetic mechanisms (i.e., DNA methylation) have been associated with the long-lasting effects of ACEs, the present report extends these prior findings by exploring genome-wide DNA methylation changes following the program. Saliva samples from all participants (n = 44) were collected and genomic DNA was extracted prior (T1) and following (T2) the intervention. Genome-wide DNA methylation analysis using the MethylationEPIC beadchip array (Illumina) revealed 49 differentially methylated loci (DML; p value < 0.001; methylation change > 10%) that were annotated to genes with roles in biological processes linked to early childhood adversity (i.e., neural, immune, and endocrine pathways, cancer and cardiovascular disease). DNA sequences flanking these DML showed significant enrichment of transcription factor binding sites involved in inflammation, cancer, cardiovascular disease, and brain development. Methylation changes in SIRT5 and TRAPPC2L genes showed associations with changes in trauma-related psychological measures. Results presented here suggest that this multimodal group program for adolescents with multiple victimization modulates the DNA methylome at sites of potential relevance for health and behavioral disorders associated with ACEs.
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3
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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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4
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Vit G, Duro J, Rajendraprasad G, Hertz EPT, Holland LKK, Weisser MB, McEwan BC, Lopez‐Mendez B, Sotelo‐Parrilla P, Jeyaprakash AA, Montoya G, Mailand N, Maeda K, Kettenbach A, Barisic M, Nilsson J. Chemogenetic profiling reveals PP2A-independent cytotoxicity of proposed PP2A activators iHAP1 and DT-061. EMBO J 2022; 41:e110611. [PMID: 35695070 PMCID: PMC9289710 DOI: 10.15252/embj.2022110611] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 01/01/2023] Open
Abstract
Protein phosphatase 2A (PP2A) is an abundant phosphoprotein phosphatase that acts as a tumor suppressor. For this reason, compounds able to activate PP2A are attractive anticancer agents. The compounds iHAP1 and DT-061 have recently been reported to selectively stabilize specific PP2A-B56 complexes to mediate cell killing. We were unable to detect direct effects of iHAP1 and DT-061 on PP2A-B56 activity in biochemical assays and composition of holoenzymes. Therefore, we undertook genome-wide CRISPR-Cas9 synthetic lethality screens to uncover biological pathways affected by these compounds. We found that knockout of mitotic regulators is synthetic lethal with iHAP1 while knockout of endoplasmic reticulum (ER) and Golgi components is synthetic lethal with DT-061. Indeed we showed that iHAP1 directly blocks microtubule assembly both in vitro and in vivo and thus acts as a microtubule poison. In contrast, DT-061 disrupts both the Golgi apparatus and the ER and lipid synthesis associated with these structures. Our work provides insight into the biological pathways perturbed by iHAP1 and DT-061 causing cellular toxicity and argues that these compounds cannot be used for dissecting PP2A-B56 biology.
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Affiliation(s)
- Gianmatteo Vit
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Joana Duro
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Girish Rajendraprasad
- Cell Division and CytoskeletonDanish Cancer Society Research CenterCopenhagenDenmark
| | - Emil P T Hertz
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Lya Katrine Kauffeldt Holland
- Cell Death and Metabolism UnitCenter for Autophagy, Recycling and Disease (CARD)Danish Cancer Society Research Center (DCRC)CopenhagenDenmark
| | - Melanie Bianca Weisser
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Brennan C McEwan
- Department of Biochemistry and Cell BiologyGeisel School of Medicine at Dartmouth CollegeHanoverNHUSA,Norris Cotton Cancer CenterLebanonNHUSA
| | - Blanca Lopez‐Mendez
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | | | | | - Guillermo Montoya
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Niels Mailand
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Kenji Maeda
- Cell Death and Metabolism UnitCenter for Autophagy, Recycling and Disease (CARD)Danish Cancer Society Research Center (DCRC)CopenhagenDenmark
| | - Arminja Kettenbach
- Department of Biochemistry and Cell BiologyGeisel School of Medicine at Dartmouth CollegeHanoverNHUSA
| | - Marin Barisic
- Cell Division and CytoskeletonDanish Cancer Society Research CenterCopenhagenDenmark,Department of Cellular and Molecular MedicineFaculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Jakob Nilsson
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
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Tang BL. Defects in early secretory pathway transport machinery components and neurodevelopmental disorders. Rev Neurosci 2021; 32:851-869. [PMID: 33781010 DOI: 10.1515/revneuro-2021-0020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/12/2021] [Indexed: 12/23/2022]
Abstract
The early secretory pathway, provisionally comprising of vesicular traffic between the endoplasmic reticulum (ER) and the Golgi apparatus, occurs constitutively in mammalian cells. Critical for a constant supply of secretory and plasma membrane (PM) materials, the pathway is presumably essential for general cellular function and survival. Neurons exhibit a high intensity in membrane dynamics and protein/lipid trafficking, with differential and polarized trafficking towards the somatodendritic and axonal PM domains. Mutations in genes encoding early secretory pathway membrane trafficking machinery components are known to result in neurodevelopmental or neurological disorders with disease manifestation in early life. Here, such rare disorders associated with autosomal recessive mutations in coat proteins, membrane tethering complexes and membrane fusion machineries responsible for trafficking in the early secretory pathway are summarily discussed. These mutations affected genes encoding subunits of coat protein complex I and II, subunits of transport protein particle (TRAPP) complexes, members of the YIP1 domain family (YIPF) and a SNAP receptor (SNARE) family member. Why the ubiquitously present and constitutively acting early secretory pathway machinery components could specifically affect neurodevelopment is addressed, with the plausible underlying disease etiologies and neuropathological mechanisms resulting from these mutations explored.
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Affiliation(s)
- Bor Luen Tang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore117597, Singapore
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6
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Milev MP, Saint-Dic D, Zardoui K, Klopstock T, Law C, Distelmaier F, Sacher M. The phenotype associated with variants in TANGO2 may be explained by a dual role of the protein in ER-to-Golgi transport and at the mitochondria. J Inherit Metab Dis 2021; 44:426-437. [PMID: 32909282 DOI: 10.1002/jimd.12312] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 08/13/2020] [Accepted: 08/31/2020] [Indexed: 12/17/2022]
Abstract
TANGO2 variants result in a complex disease phenotype consisting of recurrent crisis-induced rhabdomyolysis, encephalopathy, seizures, lactic acidosis, hypoglycemia, and cardiac arrhythmias. Although first described in a fruit fly model as a protein necessary for some aspect of Golgi function and organization, its role in the cell at a fundamental level has not been addressed. Such studies are necessary to better counsel families regarding treatment options and nutrition management to mitigate the metabolic aspects of the disease. The few studies performed to address the pathway(s) in which TANGO2 functions have led to enigmatic results, with some suggesting defects in membrane traffic while others suggest unknown mitochondrial defects. Here, we have performed a robust membrane trafficking assay on fibroblasts derived from three different individuals harboring TANGO2 variants and show that there is a significant delay in the movement of cargo between the endoplasmic reticulum and the Golgi. Importantly, this delay was attributed to a defect in TANGO2 function. We further show that a portion of TANGO2 protein localizes to the mitochondria through a necessary but not sufficient stretch of amino acids at the amino terminus of the protein. Fibroblasts from affected individuals also displayed changes in mitochondrial morphology. We conclude that TANGO2 functions in both membrane trafficking and in some as yet undetermined role in mitochondria physiology. The phenotype of affected individuals can be partially explained by this dual involvement of the protein.
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Affiliation(s)
- Miroslav P Milev
- Department of Biology, Concordia University, Montreal Quebec, Canada
| | - Djenann Saint-Dic
- Department of Biology, Concordia University, Montreal Quebec, Canada
| | - Khashayar Zardoui
- Department of Biology, Concordia University, Montreal Quebec, Canada
| | - Thomas Klopstock
- Department of Neurology, Friedrich-Baur-Institute, Ludwig-Maximilians-University, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Christopher Law
- Centre for Microscopy and Cellular Imaging, Concordia University, Quebec, Canada
| | - Felix Distelmaier
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children's Hospital Düsseldorf, Medical faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Michael Sacher
- Department of Biology, Concordia University, Montreal Quebec, Canada
- Department of Anatomy and Cell Biology, McGill University, Quebec, Canada
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7
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Grinev VV, Barneh F, Ilyushonak IM, Nakjang S, Smink J, van Oort A, Clough R, Seyani M, McNeill H, Reza M, Martinez-Soria N, Assi SA, Ramanouskaya TV, Bonifer C, Heidenreich O. RUNX1/RUNX1T1 mediates alternative splicing and reorganises the transcriptional landscape in leukemia. Nat Commun 2021; 12:520. [PMID: 33483506 PMCID: PMC7822815 DOI: 10.1038/s41467-020-20848-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 12/14/2020] [Indexed: 01/30/2023] Open
Abstract
The fusion oncogene RUNX1/RUNX1T1 encodes an aberrant transcription factor, which plays a key role in the initiation and maintenance of acute myeloid leukemia. Here we show that the RUNX1/RUNX1T1 oncogene is a regulator of alternative RNA splicing in leukemic cells. The comprehensive analysis of RUNX1/RUNX1T1-associated splicing events identifies two principal mechanisms that underlie the differential production of RNA isoforms: (i) RUNX1/RUNX1T1-mediated regulation of alternative transcription start site selection, and (ii) direct or indirect control of the expression of genes encoding splicing factors. The first mechanism leads to the expression of RNA isoforms with alternative structure of the 5'-UTR regions. The second mechanism generates alternative transcripts with new junctions between internal cassettes and constitutive exons. We also show that RUNX1/RUNX1T1-mediated differential splicing affects several functional groups of genes and produces proteins with unique conserved domain structures. In summary, this study reveals alternative splicing as an important component of transcriptome re-organization in leukemia by an aberrant transcriptional regulator.
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Affiliation(s)
- Vasily V. Grinev
- grid.17678.3f0000 0001 1092 255XDepartment of Genetics, Faculty of Biology, Belarusian State University, 220030 Minsk, Republic of Belarus
| | - Farnaz Barneh
- grid.487647.ePrincess Maxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
| | - Ilya M. Ilyushonak
- grid.17678.3f0000 0001 1092 255XDepartment of Genetics, Faculty of Biology, Belarusian State University, 220030 Minsk, Republic of Belarus
| | - Sirintra Nakjang
- grid.1006.70000 0001 0462 7212Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Job Smink
- grid.487647.ePrincess Maxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
| | - Anita van Oort
- grid.487647.ePrincess Maxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
| | - Richard Clough
- grid.1006.70000 0001 0462 7212Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Michael Seyani
- grid.1006.70000 0001 0462 7212Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Hesta McNeill
- grid.1006.70000 0001 0462 7212Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Mojgan Reza
- grid.1006.70000 0001 0462 7212Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Natalia Martinez-Soria
- grid.1006.70000 0001 0462 7212Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Salam A. Assi
- grid.6572.60000 0004 1936 7486Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Tatsiana V. Ramanouskaya
- grid.17678.3f0000 0001 1092 255XDepartment of Genetics, Faculty of Biology, Belarusian State University, 220030 Minsk, Republic of Belarus
| | - Constanze Bonifer
- grid.6572.60000 0004 1936 7486Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Olaf Heidenreich
- grid.487647.ePrincess Maxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands ,grid.1006.70000 0001 0462 7212Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE1 7RU UK ,grid.1006.70000 0001 0462 7212Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
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8
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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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9
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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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10
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Taheri F, Taghizadeh E, Pour MJR, Rostami D, Renani PG, Rastgar-Moghadam A, Hayat SMG. Limb-girdle Muscular Dystrophy and Therapy: Insights into Cell and Gene-based Approaches. Curr Gene Ther 2020; 19:386-394. [PMID: 32067617 DOI: 10.2174/1566523220666200218113526] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/11/2020] [Accepted: 02/04/2020] [Indexed: 12/17/2022]
Abstract
The Limb-Girdle Muscular Dystrophies (LGMD) are genetically heterogeneous disorders, responsible for muscle wasting and severe form of dystrophies. Despite the critical developments in the insight and information of pathomechanisms of limb-girdle muscular dystrophy, any definitive treatments do not exist, and current strategies are only based on the improvement of the signs of disorder and to enhance the life quality without resolving an underlying cause. There is a crucial relationship between pharmacological therapy and different consequences; therefore, other treatment strategies will be required. New approaches, such as gene replacement, gene transfer, exon skipping, siRNA knockdown, and anti-myostatin therapy, which can target specific cellular or molecular mechanism of LGMD, could be a promising avenue for the treatment. Recently, genome engineering strategies with a focus on molecular tools such as CRISPR-Cas9 are used to different types of neuromuscular disorders and show the highest potential for clinical translation of these therapies. Thus, recent advancements and challenges in the field will be reviewed in this paper.
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Affiliation(s)
- Forough Taheri
- Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Eskandar Taghizadeh
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran.,Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad J R Pour
- Department of Biology, Faculty of Sciences, Mashhad-Branch, Islamic Azad University, Mashhad, Iran
| | - Daryoush Rostami
- Department of School Allied, Zabol University of Medical Sciences, Zabol, Iran
| | - Pedram G Renani
- Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Azam Rastgar-Moghadam
- Department of Genetics, Tehran Medical Sciences Branch, Islamic Azad University, Tehran, Iran
| | - Seyed M G Hayat
- Department of Medical Genetics, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
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11
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Dube U, Ibanez L, Budde JP, Benitez BA, Davis AA, Harari O, Iles MM, Law MH, Brown KM, Cruchaga C. Overlapping genetic architecture between Parkinson disease and melanoma. Acta Neuropathol 2020; 139:347-364. [PMID: 31845298 PMCID: PMC7379325 DOI: 10.1007/s00401-019-02110-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 11/29/2019] [Accepted: 12/04/2019] [Indexed: 12/15/2022]
Abstract
Epidemiologic studies have reported inconsistent results regarding an association between Parkinson disease (PD) and cutaneous melanoma (melanoma). Identifying shared genetic architecture between these diseases can support epidemiologic findings and identify common risk genes and biological pathways. Here, we apply polygenic, linkage disequilibrium-informed methods to the largest available case-control, genome-wide association study summary statistic data for melanoma and PD. We identify positive and significant genetic correlation (correlation: 0.17, 95% CI 0.10-0.24; P = 4.09 × 10-06) between melanoma and PD. We further demonstrate melanoma and PD-inferred gene expression to overlap across tissues (correlation: 0.14, 95% CI 0.06 to 0.22; P = 7.87 × 10-04) and highlight seven genes including PIEZO1, TRAPPC2L, and SOX6 as potential mediators of the genetic correlation between melanoma and PD. These findings demonstrate specific, shared genetic architecture between PD and melanoma that manifests at the level of gene expression.
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Affiliation(s)
- Umber Dube
- Medical Scientist Training Program, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO, 63110, USA
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, 63110, USA
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
- Department of Psychiatry, NeuroGenomics and Informatics, Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO, 63110, USA
| | - Laura Ibanez
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, 63110, USA
- Department of Psychiatry, NeuroGenomics and Informatics, Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO, 63110, USA
| | - John P Budde
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, 63110, USA
- Department of Psychiatry, NeuroGenomics and Informatics, Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO, 63110, USA
| | - Bruno A Benitez
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, 63110, USA
- Department of Psychiatry, NeuroGenomics and Informatics, Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO, 63110, USA
| | - Albert A Davis
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | - Oscar Harari
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, 63110, USA
- Department of Psychiatry, NeuroGenomics and Informatics, Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO, 63110, USA
| | - Mark M Iles
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
| | - Matthew H Law
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Kevin M Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Ave. CB8134, St. Louis, MO, 63110, USA.
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA.
- Department of Psychiatry, NeuroGenomics and Informatics, Washington University School of Medicine, 660 S. Euclid Ave. B8111, St. Louis, MO, 63110, USA.
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12
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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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13
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Kalde M, Elliott L, Ravikumar R, Rybak K, Altmann M, Klaeger S, Wiese C, Abele M, Al B, Kalbfuß N, Qi X, Steiner A, Meng C, Zheng H, Kuster B, Falter-Braun P, Ludwig C, Moore I, Assaad FF. Interactions between Transport Protein Particle (TRAPP) complexes and Rab GTPases in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:279-297. [PMID: 31264742 DOI: 10.1111/tpj.14442] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/15/2019] [Accepted: 06/11/2019] [Indexed: 05/23/2023]
Abstract
Transport Protein Particle II (TRAPPII) is essential for exocytosis, endocytosis, protein sorting and cytokinesis. In spite of a considerable understanding of its biological role, little information is known about Arabidopsis TRAPPII complex topology and molecular function. In this study, independent proteomic approaches initiated with TRAPP components or Rab-A GTPase variants converge on the TRAPPII complex. We show that the Arabidopsis genome encodes the full complement of 13 TRAPPC subunits, including four previously unidentified components. A dimerization model is proposed to account for binary interactions between TRAPPII subunits. Preferential binding to dominant negative (GDP-bound) versus wild-type or constitutively active (GTP-bound) RAB-A2a variants discriminates between TRAPPII and TRAPPIII subunits and shows that Arabidopsis complexes differ from yeast but resemble metazoan TRAPP complexes. Analyzes of Rab-A mutant variants in trappii backgrounds provide genetic evidence that TRAPPII functions upstream of RAB-A2a, allowing us to propose that TRAPPII is likely to behave as a guanine nucleotide exchange factor (GEF) for the RAB-A2a GTPase. GEFs catalyze exchange of GDP for GTP; the GTP-bound, activated, Rab then recruits a diverse local network of Rab effectors to specify membrane identity in subsequent vesicle fusion events. Understanding GEF-Rab interactions will be crucial to unravel the co-ordination of plant membrane traffic.
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Affiliation(s)
- Monika Kalde
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Liam Elliott
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Raksha Ravikumar
- Plant Science Department, Botany, Technische Universität München, Freising, 85354, Germany
| | - Katarzyna Rybak
- Plant Science Department, Botany, Technische Universität München, Freising, 85354, Germany
| | - Melina Altmann
- Institute of Network Biology (INET), Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, 85764, Germany
| | - Susan Klaeger
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, 85354, Germany
| | - Christian Wiese
- Plant Science Department, Botany, Technische Universität München, Freising, 85354, Germany
| | - Miriam Abele
- Plant Science Department, Botany, Technische Universität München, Freising, 85354, Germany
| | - Benjamin Al
- Plant Science Department, Botany, Technische Universität München, Freising, 85354, Germany
| | - Nils Kalbfuß
- Plant Science Department, Botany, Technische Universität München, Freising, 85354, Germany
| | - Xingyun Qi
- Department of Biology, McGill University, Montreal, H3B 1A1, Canada
| | - Alexander Steiner
- Plant Science Department, Botany, Technische Universität München, Freising, 85354, Germany
| | - Chen Meng
- BayBioMS, Bavarian Center for Biomolecular Mass Spectrometry, Technische Universität München, Freising, 85354, Germany
| | - Huanquan Zheng
- Department of Biology, McGill University, Montreal, H3B 1A1, Canada
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, 85354, Germany
| | - Pascal Falter-Braun
- Institute of Network Biology (INET), Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, 85764, Germany
- Faculty of Biology, Microbe-Host-Interactions, Ludwig-Maximilians-Universität (LMU) München, Planegg-Martinsried, 82152, Germany
| | - Christina Ludwig
- BayBioMS, Bavarian Center for Biomolecular Mass Spectrometry, Technische Universität München, Freising, 85354, Germany
| | - Ian Moore
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Farhah F Assaad
- Plant Science Department, Botany, Technische Universität München, Freising, 85354, Germany
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14
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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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15
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Sacher M, Shahrzad N, Kamel H, Milev MP. TRAPPopathies: An emerging set of disorders linked to variations in the genes encoding transport protein particle (TRAPP)-associated proteins. Traffic 2018; 20:5-26. [PMID: 30152084 DOI: 10.1111/tra.12615] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 08/23/2018] [Accepted: 08/26/2018] [Indexed: 02/06/2023]
Abstract
The movement of proteins between cellular compartments requires the orchestrated actions of many factors including Rab family GTPases, Soluble NSF Attachment protein REceptors (SNAREs) and so-called tethering factors. One such tethering factor is called TRAnsport Protein Particle (TRAPP), and in humans, TRAPP proteins are distributed into two related complexes called TRAPP II and III. Although thought to act as a single unit within the complex, in the past few years it has become evident that some TRAPP proteins function independently of the complex. Consistent with this, variations in the genes encoding these proteins result in a spectrum of human diseases with diverse, but partially overlapping, phenotypes. This contrasts with other tethering factors such as COG, where variations in the genes that encode its subunits all result in an identical phenotype. In this review, we present an up-to-date summary of all the known disease-related variations of genes encoding TRAPP-associated proteins and the disorders linked to these variations which we now call TRAPPopathies.
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Affiliation(s)
- Michael Sacher
- Department of Biology, Concordia University, Montreal, Quebec, Canada.,Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
| | - Nassim Shahrzad
- Department of Medicine, University of California, San Francisco, California
| | - Hiba Kamel
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Miroslav P Milev
- Department of Biology, Concordia University, Montreal, Quebec, Canada
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16
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Mbimba T, Hussein NJ, Najeed A, Safadi FF. TRAPPC9: Novel insights into its trafficking and signaling pathways in health and disease (Review). Int J Mol Med 2018; 42:2991-2997. [PMID: 30272317 DOI: 10.3892/ijmm.2018.3889] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/14/2018] [Indexed: 11/06/2022] Open
Abstract
Trafficking protein particle complex 9 (TRAPPC9) is a protein subunit of the transport protein particle II (TRAPPII), which has been reported to be important in the trafficking of cargo from the endoplasmic reticulum (ER) to the Golgi, and in intra‑Golgi and endosome‑to‑Golgi transport in yeast cells. In mammalian cells, TRAPPII has been shown to be important in Golgi vesicle tethering and intra‑Golgi transport. TRAPPC9 is considered to be a novel molecule capable of modulating the activation of nuclear factor‑κB (NF‑κB). Mutations in TRAPPC9 have been linked to a rare consanguineous hereditary form of mental retardation, as part of the NF‑κB pathways. In addition, TRAPPC9 has been reported to be involved in breast and colon cancer and liver diseases. The present review highlights the most recent publications on the structure, expression and function of TRAPPC9, and its association with various human diseases.
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Affiliation(s)
- Thomas Mbimba
- Department of Anatomy and Neurobiology, College of Medicine, Northeast Ohio Medical University, Rootstown, OH 44272, USA
| | - Nazar J Hussein
- Department of Anatomy and Neurobiology, College of Medicine, Northeast Ohio Medical University, Rootstown, OH 44272, USA
| | - Ayesha Najeed
- Department of Anatomy and Neurobiology, College of Medicine, Northeast Ohio Medical University, Rootstown, OH 44272, USA
| | - Fayez F Safadi
- Department of Anatomy and Neurobiology, College of Medicine, Northeast Ohio Medical University, Rootstown, OH 44272, USA
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17
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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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18
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Mutations in TRAPPC12 Manifest in Progressive Childhood Encephalopathy and Golgi Dysfunction. Am J Hum Genet 2017; 101:291-299. [PMID: 28777934 DOI: 10.1016/j.ajhg.2017.07.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 07/06/2017] [Indexed: 12/23/2022] Open
Abstract
Progressive childhood encephalopathy is an etiologically heterogeneous condition characterized by progressive central nervous system dysfunction in association with a broad range of morbidity and mortality. The causes of encephalopathy can be either non-genetic or genetic. Identifying the genetic causes and dissecting the underlying mechanisms are critical to understanding brain development and improving treatments. Here, we report that variants in TRAPPC12 result in progressive childhood encephalopathy. Three individuals from two unrelated families have either a homozygous deleterious variant (c.145delG [p.Glu49Argfs∗14]) or compound-heterozygous variants (c.360dupC [p.Glu121Argfs∗7] and c.1880C>T [p. Ala627Val]). The clinical phenotypes of the three individuals are strikingly similar: severe disability, microcephaly, hearing loss, spasticity, and characteristic brain imaging findings. Fibroblasts derived from all three individuals showed a fragmented Golgi that could be rescued by expression of wild-type TRAPPC12. Protein transport from the endoplasmic reticulum to and through the Golgi was delayed. TRAPPC12 is a member of the TRAPP protein complex, which functions in membrane trafficking. Variants in several other genes encoding members of the TRAPP complex have been associated with overlapping clinical presentations, indicating shared and distinct functions for each complex member. Detailed understanding of the TRAPP-opathies will illuminate the role of membrane protein transport in human disease.
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19
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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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20
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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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21
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Liang WC, Zhu W, Mitsuhashi S, Noguchi S, Sacher M, Ogawa M, Shih HH, Jong YJ, Nishino I. Congenital muscular dystrophy with fatty liver and infantile-onset cataract caused by TRAPPC11 mutations: broadening of the phenotype. Skelet Muscle 2015; 5:29. [PMID: 26322222 PMCID: PMC4551700 DOI: 10.1186/s13395-015-0056-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 08/07/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Transport protein particle (TRAPP) is a multiprotein complex involved in endoplasmic reticulum-to-Golgi trafficking. Zebrafish with a mutation in the TRAPPC11 orthologue showed hepatomegaly with steatosis and defects in visual system development. In humans, TRAPPC11 mutations have been reported in only three families showing limb-girdle muscular dystrophy (LGMD) or myopathy with movement disorders and intellectual disability. METHODS We screened muscular dystrophy genes using next-generation sequencing and performed associated molecular and biochemical analyses in a patient with fatty liver and cataract in addition to infantile-onset muscle weakness. RESULTS We identified the first Asian patient with TRAPPC11 mutations. Muscle pathology demonstrated typical dystrophic changes and liver biopsy revealed steatosis. The patient carried compound heterozygous mutations of a previously reported missense and a novel splice-site mutation. The splice-site change produced two aberrantly-spliced transcripts that were both predicted to result in translational frameshift and truncated proteins. Full-length TRAPPC11 protein was undetectable on immunoblotting. CONCLUSION This report widens the phenotype of TRAPPC11-opathy as the patient showed the following: (1) congenital muscular dystrophy phenotype rather than LGMD; (2) steatosis and infantile-onset cataract, both not observed in previously reported patients; but (3) no ataxia or abnormal movement, clearly indicating that TRAPPC11 plays a physiological role in multiple tissues in human.
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Affiliation(s)
- Wen-Chen Liang
- Departments of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Pediatrics, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wenhua Zhu
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan.,Department of Genome Medicine Development, Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo, Japan.,Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - Satomi Mitsuhashi
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan.,Department of Genome Medicine Development, Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Satoru Noguchi
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan.,Department of Genome Medicine Development, Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Michael Sacher
- Department of Biology, Concordia University, Montreal, QC H4B 1R6 Canada.,Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 2B2 Canada
| | - Megumu Ogawa
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Hsiang-Hung Shih
- Departments of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Pediatrics, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yuh-Jyh Jong
- Departments of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Biological Science and Technology, College of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan.,Department of Genome Medicine Development, Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo, Japan
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Affiliation(s)
- Miroslav P Milev
- Concordia University, Department of Biology, Montreal, Quebec, Canada
| | - Michael Sacher
- Concordia University, Department of Biology, Montreal, Quebec, Canada.,McGill University, Department of Anatomy and Cell Biology, Montreal, Quebec, Canada
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23
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Brunet S, Noueihed B, Shahrzad N, Saint-Dic D, Hasaj B, Guan TL, Moores A, Barlowe C, Sacher M. The SMS domain of Trs23p is responsible for the in vitro appearance of the TRAPP I complex in Saccharomyces cerevisiae. CELLULAR LOGISTICS 2014; 2:28-42. [PMID: 22645708 PMCID: PMC3355973 DOI: 10.4161/cl.19414] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Saccharomyces cerevisiae transport protein particle (TRAPP) is a family of related multisubunit complexes required for endoplasmic reticulum-to-Golgi transport (TRAPP I), endosome-to-Golgi transport (TRAPP II) or cytosol to vacuole targeting (TRAPP III). To gain insight into the relationship between these complexes, we generated random and targeted mutations in the Trs23p core subunit. Remarkably, at physiological salt concentrations only two peaks (TRAPP I and a high molecular weight peak) are detected in wild-type cells. As the salt was raised, the high molecular weight peak resolved into TRAPP II and III peaks. Deletion of a Saccharomycotina-specific domain of Trs23p resulted in destabilization of TRAPP I but had no effect on TRAPP II or III. This mutation had no observable growth phenotype, normal levels of Ypt1p-directed guanine nucleotide exchange factor activity in vivo and did not display any in vivo nor in vitro blocks in membrane traffic. Biochemical analysis indicated that TRAPP I could be produced from the TRAPP II/III peak in vitro by increasing the salt concentration. Our data suggest that the SMS domain of Trs23p is responsible for the in vitro appearance of TRAPP I in S. cerevisiae. The implications of these findings are discussed.
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24
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Wang C, Gohlke U, Roske Y, Heinemann U. Crystal structure of the yeast TRAPP-associated protein Tca17. FEBS J 2014; 281:4195-206. [PMID: 24961828 DOI: 10.1111/febs.12888] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 05/28/2014] [Accepted: 06/19/2014] [Indexed: 11/28/2022]
Abstract
UNLABELLED The transport protein particle (TRAPP) is a hetero-multimeric complex involved in the trafficking of COP II (coat protein complex II) vesicles. TRAPP is present in different eukaryotes from yeast to vertebrates and occurs in three distinct modifications with function in different intracellular transport steps. All forms contain a core of five essential subunits, and the different species of TRAPP are formed by the addition of various subunits. A recently identified TRAPP-associated protein, Tca17, is supposed to be involved in the regulation of the transport complex. We have determined the three-dimensional structure of yeast Tca17 by X-ray crystallography at a resolution of 1.8 Å. It adopts the longin fold characteristic for the Bet5 family of TRAPP subunits, and it also shares a binding motif of these for the interaction with other members of the complex. Two alternative models of the localization of Tca17 within TRAPP as well as its potential role in the regulation of TRAPP function by transient integration into the complex are discussed. DATABASE Structural data are available in the Protein Databank under accession number 3PR6.
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Affiliation(s)
- Chengcheng Wang
- Macromolecular Structure and Interaction Group, Max-Delbrück-Center for Molecular Medicine, and Chemistry and Biochemistry Institute, Freie Universität, Berlin, Germany
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25
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Brunet S, Sacher M. In Sickness and in Health: The Role of TRAPP and Associated Proteins in Disease. Traffic 2014; 15:803-18. [PMID: 24917561 DOI: 10.1111/tra.12183] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 06/06/2014] [Accepted: 06/06/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Stephanie Brunet
- Department of Biology; Concordia University; 7141 Sherbrooke Street West, SP-457.01 Montreal QC H4B 1R6 Canada
| | - Michael Sacher
- Department of Biology; Concordia University; 7141 Sherbrooke Street West, SP-457.01 Montreal QC H4B 1R6 Canada
- Department of Anatomy and Cell Biology; McGill University; 845 Sherbrooke Street West Montreal QC H3A 0G4 Canada
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26
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Vacaru AM, Unlu G, Spitzner M, Mione M, Knapik EW, Sadler KC. In vivo cell biology in zebrafish - providing insights into vertebrate development and disease. J Cell Sci 2014; 127:485-95. [PMID: 24481493 PMCID: PMC4007761 DOI: 10.1242/jcs.140194] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Over the past decades, studies using zebrafish have significantly advanced our understanding of the cellular basis for development and human diseases. Zebrafish have rapidly developing transparent embryos that allow comprehensive imaging of embryogenesis combined with powerful genetic approaches. However, forward genetic screens in zebrafish have generated unanticipated findings that are mirrored by human genetic studies: disruption of genes implicated in basic cellular processes, such as protein secretion or cytoskeletal dynamics, causes discrete developmental or disease phenotypes. This is surprising because many processes that were assumed to be fundamental to the function and survival of all cell types appear instead to be regulated by cell-specific mechanisms. Such discoveries are facilitated by experiments in whole animals, where zebrafish provides an ideal model for visualization and manipulation of organelles and cellular processes in a live vertebrate. Here, we review well-characterized mutants and newly developed tools that underscore this notion. We focus on the secretory pathway and microtubule-based trafficking as illustrative examples of how studying cell biology in vivo using zebrafish has broadened our understanding of the role fundamental cellular processes play in embryogenesis and disease.
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Affiliation(s)
- Ana M. Vacaru
- Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA
- Department of Medicine/Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA
| | - Gokhan Unlu
- Division of Genetic Medicine, Department of Medicine, and Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Marie Spitzner
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Marina Mione
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Ela W. Knapik
- Division of Genetic Medicine, Department of Medicine, and Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kirsten C. Sadler
- Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA
- Department of Medicine/Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA
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27
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De Franceschi N, Wild K, Schlacht A, Dacks JB, Sinning I, Filippini F. Longin and GAF domains: structural evolution and adaptation to the subcellular trafficking machinery. Traffic 2013; 15:104-21. [PMID: 24107188 DOI: 10.1111/tra.12124] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 09/18/2013] [Accepted: 09/23/2013] [Indexed: 11/28/2022]
Abstract
Endomembrane trafficking is one of the most prominent cytological features of eukaryotes. Given their widespread distribution and specialization, coiled-coil domains, coatomer domains, small GTPases and Longin domains are considered primordial 'building blocks' of the membrane trafficking machineries. Longin domains are conserved across eukaryotes and were likely to be present in the Last Eukaryotic Common Ancestor. The Longin fold is based on the α-β-α sandwich architecture and a unique topology, possibly accounting for the special adaptation to the eukaryotic trafficking machinery. The ancient Per ARNT Sim (PAS) and cGMP-specific phosphodiesterases, Adenylyl cyclases and FhlA (GAF) family domains show a similar architecture, and the identification of prokaryotic counterparts of GAF domains involved in trafficking provides an additional connection for the endomembrane system back into the pre-eukaryotic world. Proteome-wide, comparative bioinformatic analyses of the domains reveal three binding regions (A, B and C) mediating either specific or conserved protein-protein interactions. While the A region mediates intra- and inter-molecular interactions, the B region is involved in binding small GTPases, thus providing an evolutionary connection among major building blocks in the endomembrane system. Finally, we propose that the peculiar interaction surface of the C region of the Longin domain allowed it to extensively integrate into the endomembrane trafficking machinery in the earliest stages of building the eukaryotic cell.
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Affiliation(s)
- Nicola De Franceschi
- Molecular Biology and Bioinformatics Unit, Department of Biology, University of Padova, Padova, Italy; Current address: Centre for Biotechnology, University of Turku, Turku, Finland
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Brunet S, Shahrzad N, Saint-Dic D, Dutczak H, Sacher M. Atrs20Mutation That Mimics an SEDT-Causing Mutation Blocks Selective and Non-Selective Autophagy: A Model for TRAPP III Organization. Traffic 2013; 14:1091-104. [DOI: 10.1111/tra.12095] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 07/28/2013] [Accepted: 07/30/2013] [Indexed: 02/04/2023]
Affiliation(s)
- Stephanie Brunet
- Department of Biology; Concordia University; Montreal; Quebec; Canada
| | - Nassim Shahrzad
- Department of Biology; Concordia University; Montreal; Quebec; Canada
| | - Djenann Saint-Dic
- Department of Biology; Concordia University; Montreal; Quebec; Canada
| | - Hartley Dutczak
- Department of Biology; Concordia University; Montreal; Quebec; Canada
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Taussig D, Lipatova Z, Kim JJ, Zhang X, Segev N. Trs20 is required for TRAPP II assembly. Traffic 2013; 14:678-90. [PMID: 23465091 DOI: 10.1111/tra.12065] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 02/22/2013] [Accepted: 03/07/2013] [Indexed: 11/28/2022]
Abstract
The modular TRAPP complexes act as nucleotide exchangers to activate the Golgi Ypt/Rab GTPases, Ypt1 and Ypt31/Ypt32. In yeast, TRAPP I acts at the cis-Golgi and its assembly and structure are well characterized. In contrast, TRAPP II acts at the trans-Golgi and is poorly understood. Especially puzzling is the role of Trs20, an essential TRAPP I/II subunit required neither for the assembly of TRAPP I nor for its Ypt1-exchange activity. Mutations in Sedlin, the human functional ortholog of Trs20, cause the cartilage-specific disorder SEDT. Here we show that Trs20 interacts with the TRAPP II-specific subunit Trs120. Furthermore, the Trs20-Trs120 interaction is required for assembly of TRAPP II and for its Ypt32-exchange activity. Finally, Trs20-D46Y, with a single-residue substitution equivalent to a SEDT-causing mutation in Sedlin, interacts with TRAPP I, but the resulting TRAPP complex cannot interact with Trs120 and TRAPP II cannot be assembled. These results indicate that Trs20 is crucial for assembly of TRAPP II, and the defective assembly caused by a SEDT-linked mutation suggests that this role is conserved.
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Affiliation(s)
- David Taussig
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA
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Yu S, Liang Y. A trapper keeper for TRAPP, its structures and functions. Cell Mol Life Sci 2012; 69:3933-44. [PMID: 22669257 PMCID: PMC11114727 DOI: 10.1007/s00018-012-1024-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 04/20/2012] [Accepted: 05/02/2012] [Indexed: 12/22/2022]
Abstract
During biosynthesis many membrane and secreted proteins are transported from the endoplasmic reticulum, through the Golgi and on to the plasma membrane in small transport vesicles. These transport vesicles have to undergo budding, movement, tethering, docking, and fusion at each organelle of the biosynthetic pathway. The transport protein particle (TRAPP) complex was initially identified as the tethering factor for endoplasmic reticulum (ER)-derived COPII vesicles, but the functions of TRAPP may extend to other areas of biology. Three forms of TRAPP complexes have been discovered to date, and recent advances in research have provided new insights on the structures and functions of TRAPP. Here we provide a comprehensive review of the recent findings in TRAPP biology.
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Affiliation(s)
- Sidney Yu
- School of Biomedical Sciences and Epithelial Cell Biology Research Center, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, People's Republic of China,
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Venditti R, Scanu T, Santoro M, Di Tullio G, Spaar A, Gaibisso R, Beznoussenko GV, Mironov AA, Mironov A, Zelante L, Piemontese MR, Notarangelo A, Malhotra V, Vertel BM, Wilson C, De Matteis MA. Sedlin controls the ER export of procollagen by regulating the Sar1 cycle. Science 2012; 337:1668-72. [PMID: 23019651 DOI: 10.1126/science.1224947] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Newly synthesized proteins exit the endoplasmic reticulum (ER) via coat protein complex II (COPII) vesicles. Procollagen (PC), however, forms prefibrils that are too large to fit into typical COPII vesicles; PC thus needs large transport carriers, which we term megacarriers. TANGO1 assists PC packing, but its role in promoting the growth of megacarriers is not known. We found that TANGO1 recruited Sedlin, a TRAPP component that is defective in spondyloepiphyseal dysplasia tarda (SEDT), and that Sedlin was required for the ER export of PC. Sedlin bound and promoted efficient cycling of Sar1, a guanosine triphosphatase that can constrict membranes, and thus allowed nascent carriers to grow and incorporate PC prefibrils. This joint action of TANGO1 and Sedlin sustained the ER export of PC, and its derangement may explain the defective chondrogenesis underlying SEDT.
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Mahfouz H, Ragnini-Wilson A, Venditti R, De Matteis MA, Wilson C. Mutational analysis of the yeast TRAPP subunit Trs20p identifies roles in endocytic recycling and sporulation. PLoS One 2012; 7:e41408. [PMID: 23049729 PMCID: PMC3458868 DOI: 10.1371/journal.pone.0041408] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 06/22/2012] [Indexed: 11/20/2022] Open
Abstract
Trs20p is a subunit of the evolutionarily conserved TRAPP (TRAnsport Protein Particle) complex that mediates various aspects of membrane trafficking. Three TRAPP complexes have been identified in yeast with roles in ER-to-Golgi trafficking, post-Golgi and endosomal-to-Golgi transport and in autophagy. The role of Trs20p, which is essential for viability and a component of all three complexes, and how it might function within each TRAPP complex, has not been clarified to date. To begin to address the role of Trs20p we generated different mutants by random mutagenesis but, surprisingly, no defects were observed in diverse anterograde transport pathways or general secretion in Trs20 temperature-sensitive mutants. Instead, mutation of Trs20 led to defects in endocytic recycling and a block in sporulation/meiosis. The phenotypes of different mutants appear to be separable suggesting that the mutations affect the function of Trs20 in different TRAPP complexes.
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Affiliation(s)
- Hichem Mahfouz
- Consorzio Mario Negri Sud, Santa Maria Imbaro, Chieti, Italy
| | - Antonella Ragnini-Wilson
- Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
- Consorzio Mario Negri Sud, Santa Maria Imbaro, Chieti, Italy
| | | | | | - Cathal Wilson
- Telethon Institute of Genetics and Medicine, Naples, Italy
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Zong M, Wu XG, Chan CWL, Choi MY, Chan HC, Tanner JA, Yu S. The adaptor function of TRAPPC2 in mammalian TRAPPs explains TRAPPC2-associated SEDT and TRAPPC9-associated congenital intellectual disability. PLoS One 2011; 6:e23350. [PMID: 21858081 PMCID: PMC3156116 DOI: 10.1371/journal.pone.0023350] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 07/13/2011] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The TRAPP (Transport protein particle) complex is a conserved protein complex functioning at various steps in vesicle transport. Although yeast has three functionally and structurally distinct forms, TRAPPI, II and III, emerging evidence suggests that mammalian TRAPP complex may be different. Mutations in the TRAPP complex subunit 2 (TRAPPC2) cause X-linked spondyloepiphyseal dysplasia tarda, while mutations in the TRAPP complex subunit 9 (TRAPPC9) cause postnatal mental retardation with microcephaly. The structural interplay between these subunits found in mammalian equivalent of TRAPPI and those specific to TRAPPII and TRAPPIII remains largely unknown and we undertook the present study to examine the interaction between these subunits. Here, we reveal that the mammalian equivalent of the TRAPPII complex is structurally distinct from the yeast counterpart thus leading to insight into mechanism of disease. PRINCIPAL FINDINGS We analyzed how TRAPPII- or TRAPPIII- specific subunits interact with the six-subunit core complex of TRAPP by co-immunoprecipitation in mammalian cells. TRAPPC2 binds to TRAPPII-specific subunit TRAPPC9, which in turn binds to TRAPPC10. Unexpectedly, TRAPPC2 can also bind to the putative TRAPPIII-specific subunit, TRAPPC8. Endogenous TRAPPC9-positive TRAPPII complex does not contain TRAPPC8, suggesting that TRAPPC2 binds to either TRAPPC9 or TRAPPC8 during the formation of the mammalian equivalents of TRAPPII or TRAPPIII, respectively. Therefore, TRAPPC2 serves as an adaptor for the formation of these complexes. A disease-causing mutation of TRAPPC2, D47Y, failed to interact with either TRAPPC9 or TRAPPC8, suggesting that aspartate 47 in TRAPPC2 is at or near the site of interaction with TRAPPC9 or TRAPPC8, mediating the formation of TRAPPII and/or TRAPPIII. Furthermore, disease-causing deletional mutants of TRAPPC9 all failed to interact with TRAPPC2 and TRAPPC10. CONCLUSIONS TRAPPC2 serves as an adaptor for the formation of TRAPPII or TRAPPIII in mammalian cells. The mammalian equivalent of TRAPPII is likely different from the yeast TRAPPII structurally.
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Affiliation(s)
- Min Zong
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, People's Republic of China
| | - Xing-gang Wu
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, People's Republic of China
| | - Cecilia W. L. Chan
- Department of Biochemistry, University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China
| | - Mei Y. Choi
- Department of Biochemistry, University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China
| | - Hsiao Chang Chan
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, People's Republic of China
- Epithelial Cell Biology Research Center, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, People's Republic of China
| | - Julian A. Tanner
- Department of Biochemistry, University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China
| | - Sidney Yu
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, People's Republic of China
- Epithelial Cell Biology Research Center, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, People's Republic of China
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Duarte DT, Hul S, Sacher M. A yeast two hybrid screen identifies SPATA4 as a TRAPP interactor. FEBS Lett 2011; 585:2676-81. [PMID: 21827752 DOI: 10.1016/j.febslet.2011.07.040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 07/25/2011] [Accepted: 07/26/2011] [Indexed: 11/17/2022]
Abstract
The TRAPP vesicle-tethering complex consists of more than 10 distinct polypeptides and is involved in protein transport. Using the C2 subunit as bait we identified SPATA4, a spermatocyte-specific protein of unknown function, as an interacting partner in a yeast two hybrid screen. Further studies indicate SPATA4 interacts with the C2 portion of the TRAPP complex. SPATA4 fractionates with both cytosolic and nuclear fractions suggesting it may have several distinct functions. SPATA4 is one of only three human proteins that contain a DUF1042 domain and we show that C2 does not interact with another one of the DUF1042 domain-containing proteins. Our results suggest a role for SPATA4 in membrane traffic and a specialized function for TRAPP in spermatocytes.
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Scrivens PJ, Noueihed B, Shahrzad N, Hul S, Brunet S, Sacher M. C4orf41 and TTC-15 are mammalian TRAPP components with a role at an early stage in ER-to-Golgi trafficking. Mol Biol Cell 2011; 22:2083-93. [PMID: 21525244 PMCID: PMC3113772 DOI: 10.1091/mbc.e10-11-0873] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
TRAPP is a multisubunit tethering complex implicated in multiple vesicle trafficking steps in Saccharomyces cerevisiae and conserved throughout eukarya, including humans. Here we confirm the role of TRAPPC2L as a stable component of mammalian TRAPP and report the identification of four novel components of the complex: C4orf41, TTC-15, KIAA1012, and Bet3L. Two of the components, KIAA1012 and Bet3L, are mammalian homologues of Trs85p and Bet3p, respectively. The remaining two novel TRAPP components, C4orf41 and TTC-15, have no homologues in S. cerevisiae. With this work, human homologues of all the S. cerevisiae TRAPP proteins, with the exception of the Saccharomycotina-specific subunit Trs65p, have now been reported. Through a multidisciplinary approach, we demonstrate that the novel proteins are bona fide components of human TRAPP and implicate C4orf41 and TTC-15 (which we call TRAPPC11 and TRAPPC12, respectively) in ER-to-Golgi trafficking at a very early stage. We further present a binary interaction map for all known mammalian TRAPP components and evidence that TRAPP oligomerizes. Our data are consistent with the absence of a TRAPP I-equivalent complex in mammalian cells, suggesting that the fundamental unit of mammalian TRAPP is distinct from that characterized in S. cerevisiae.
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Affiliation(s)
- P James Scrivens
- Department of Biology, Concordia University, Montreal, Quebec, Canada
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Choi C, Davey M, Schluter C, Pandher P, Fang Y, Foster LJ, Conibear E. Organization and Assembly of the TRAPPII Complex. Traffic 2011; 12:715-25. [DOI: 10.1111/j.1600-0854.2011.01181.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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TRAPP complexes in membrane traffic: convergence through a common Rab. Nat Rev Mol Cell Biol 2010; 11:759-63. [PMID: 20966969 DOI: 10.1038/nrm2999] [Citation(s) in RCA: 133] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Transport protein particle (TRAPP; also known as trafficking protein particle), a multimeric guanine nucleotide-exchange factor for the yeast GTPase Ypt1 and its mammalian homologue, RAB1, regulates multiple membrane trafficking pathways. TRAPP complexes exist in three forms, each of which activates Ypt1 or RAB1 through a common core of subunits and regulates complex localization through distinct subunits. Whereas TRAPPI and TRAPPII tether coated vesicles during endoplasmic reticulum to Golgi and intra-Golgi traffic, respectively, TRAPPIII has recently been shown to be required for autophagy. These advances illustrate how the TRAPP complexes link Ypt1 and RAB1 activation to distinct membrane-tethering events.
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Yip CK, Berscheminski J, Walz T. Molecular architecture of the TRAPPII complex and implications for vesicle tethering. Nat Struct Mol Biol 2010; 17:1298-304. [PMID: 20972447 PMCID: PMC2988884 DOI: 10.1038/nsmb.1914] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Accepted: 08/19/2010] [Indexed: 01/04/2023]
Abstract
Multi-subunit tethering complexes participate in the process of vesicle tethering, the initial interaction between transport vesicles and their acceptor compartments. TRAPPII is a highly conserved tethering complex that functions in the late Golgi and consists of all TRAPPI and three specific subunits. We have purified native yeast TRAPPII and characterized its structure and subunit organization by single-particle electron microscopy. Our data show that the nine TRAPPII components form a core complex that dimerizes into a three-layered, diamond-shaped structure. The TRAPPI subunits assemble into TRAPPI complexes that form the outer layers. The three TRAPPII-specific subunits cap the ends of TRAPPI and form the middle layer responsible for dimerization. TRAPPII binds Ypt1 and likely uses the TRAPPI catalytic core to promote guanine nucleotide exchange. We discuss implications of the TRAPPII structure for coat interaction and TRAPPII-associated human pathologies.
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Affiliation(s)
- Calvin K Yip
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA.
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