1
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Zykaj E, Abboud C, Asadi P, Warsame S, Almousa H, Milev MP, Greco BM, López-Sánchez M, Bratkovic D, Kachroo AH, Pérez-Jurado LA, Sacher M. A Humanized Yeast Model for Studying TRAPP Complex Mutations; Proof-of-Concept Using Variants from an Individual with a TRAPPC1-Associated Neurodevelopmental Syndrome. Cells 2024; 13:1457. [PMID: 39273027 PMCID: PMC11394476 DOI: 10.3390/cells13171457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2024] [Revised: 08/22/2024] [Accepted: 08/25/2024] [Indexed: 09/15/2024] Open
Abstract
Variants in membrane trafficking proteins are known to cause rare disorders with severe symptoms. The highly conserved transport protein particle (TRAPP) complexes are key membrane trafficking regulators that are also involved in autophagy. Pathogenic genetic variants in specific TRAPP subunits are linked to neurological disorders, muscular dystrophies, and skeletal dysplasias. Characterizing these variants and their phenotypes is important for understanding the general and specialized roles of TRAPP subunits as well as for patient diagnosis. Patient-derived cells are not always available, which poses a limitation for the study of these diseases. Therefore, other systems, like the yeast Saccharomyces cerevisiae, can be used to dissect the mechanisms at the intracellular level underlying these disorders. The development of CRISPR/Cas9 technology in yeast has enabled a scar-less editing method that creates an efficient humanized yeast model. In this study, core yeast subunits were humanized by replacing them with their human orthologs, and TRAPPC1, TRAPPC2, TRAPPC2L, TRAPPC6A, and TRAPPC6B were found to successfully replace their yeast counterparts. This system was used for studying the first reported individual with an autosomal recessive disorder caused by biallelic TRAPPC1 variants, a girl with a severe neurodevelopmental disorder and myopathy. We show that the maternal variant (TRAPPC1 p.(Val121Alafs*3)) is non-functional while the paternal variant (TRAPPC1 p.(His22_Lys24del)) is conditional-lethal and affects secretion and non-selective autophagy in yeast. This parallels defects seen in fibroblasts derived from this individual which also showed membrane trafficking defects and altered Golgi morphology, all of which were rescued in the human system by wild-type TRAPPC1. This study suggests that humanized yeast can be an efficient means to study TRAPP subunit variants in the absence of human cells and can assign significance to variants of unknown significance (VUS). This study lays the foundation for characterizing further TRAPP variants through this system, rapidly contributing to disease diagnosis.
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Affiliation(s)
- Erta Zykaj
- Department of Biology, Concordia University, Montreal, QC H4B1R6, Canada
| | - Chelsea Abboud
- Department of Biology, Concordia University, Montreal, QC H4B1R6, Canada
| | - Paria Asadi
- Department of Biology, Concordia University, Montreal, QC H4B1R6, Canada
| | - Simane Warsame
- Department of Biology, Concordia University, Montreal, QC H4B1R6, Canada
| | - Hashem Almousa
- Department of Biology, Concordia University, Montreal, QC H4B1R6, Canada
| | - Miroslav P Milev
- Department of Biology, Concordia University, Montreal, QC H4B1R6, Canada
| | - Brittany M Greco
- Department of Biology, Concordia University, Montreal, QC H4B1R6, Canada
| | - Marcos López-Sánchez
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Hospital del Mar, Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, 28029 Madrid, Spain
| | - Drago Bratkovic
- Women's and Children's Hospital, Metabolic Clinic, North Adelaide, SA 5006, Australia
| | - Aashiq H Kachroo
- Department of Biology, Concordia University, Montreal, QC H4B1R6, Canada
| | - Luis Alberto Pérez-Jurado
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Hospital del Mar, Hospital del Mar Research Institute (IMIM), 08003 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, 28029 Madrid, Spain
- Women's and Children's Hospital, Metabolic Clinic, North Adelaide, SA 5006, Australia
| | - Michael Sacher
- Department of Biology, Concordia University, Montreal, QC H4B1R6, Canada
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 0C7, Canada
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2
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Feathers JR, Vignogna RC, Fromme JC. Structural basis for Rab6 activation by the Ric1-Rgp1 complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.06.592747. [PMID: 38766083 PMCID: PMC11100747 DOI: 10.1101/2024.05.06.592747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Rab GTPases act as molecular switches to regulate organelle homeostasis and membrane trafficking. Rab6 plays a central role in regulating cargo flux through the Golgi and is activated via nucleotide exchange by the Ric1-Rgp1 protein complex. Ric1-Rgp1 is conserved throughout eukaryotes but the structural and mechanistic basis for its function has not been established. Here we report the cryoEM structure of a Ric1-Rgp1-Rab6 complex representing a key intermediate of the nucleotide exchange reaction. This structure reveals the overall architecture of the complex and enabled us to identify interactions critical for proper recognition and activation of Rab6 on the Golgi membrane surface. Ric1-Rgp1 interacts with the nucleotide-binding domain of Rab6 using an uncharacterized helical domain, which we establish as a novel RabGEF domain by identifying residues required for Rab6 nucleotide exchange. Unexpectedly, the complex uses an arrestin fold to interact with the Rab6 hypervariable domain, indicating that interactions with the unstructured C-terminal regions of Rab GTPases may be a common specificity mechanism used by their activators. Collectively, our findings provide a detailed mechanistic understanding of regulated Rab6 activation at the Golgi.
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Affiliation(s)
- J. Ryan Feathers
- Department of Molecular Biology & Genetics and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850 USA
- Current address: 201 Schultz Laboratory, Princeton University, Princeton, NJ 08544 USA
| | - Ryan C. Vignogna
- Department of Molecular Biology & Genetics and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850 USA
| | - J. Christopher Fromme
- Department of Molecular Biology & Genetics and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850 USA
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3
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Wiese C, Abele M, Al B, Altmann M, Steiner A, Kalbfuß N, Strohmayr A, Ravikumar R, Park CH, Brunschweiger B, Meng C, Facher E, Ehrhardt DW, Falter-Braun P, Wang ZY, Ludwig C, Assaad FF. Regulation of adaptive growth decisions via phosphorylation of the TRAPPII complex in Arabidopsis. J Cell Biol 2024; 223:e202311125. [PMID: 38558238 PMCID: PMC10983811 DOI: 10.1083/jcb.202311125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/31/2024] [Accepted: 02/15/2024] [Indexed: 04/04/2024] Open
Abstract
Plants often adapt to adverse or stress conditions via differential growth. The trans-Golgi network (TGN) has been implicated in stress responses, but it is not clear in what capacity it mediates adaptive growth decisions. In this study, we assess the role of the TGN in stress responses by exploring the previously identified interactome of the Transport Protein Particle II (TRAPPII) complex required for TGN structure and function. We identified physical and genetic interactions between AtTRAPPII and shaggy-like kinases (GSK3/AtSKs) and provided in vitro and in vivo evidence that the TRAPPII phosphostatus mediates adaptive responses to abiotic cues. AtSKs are multifunctional kinases that integrate a broad range of signals. Similarly, the AtTRAPPII interactome is vast and considerably enriched in signaling components. An AtSK-TRAPPII interaction would integrate all levels of cellular organization and instruct the TGN, a central and highly discriminate cellular hub, as to how to mobilize and allocate resources to optimize growth and survival under limiting or adverse conditions.
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Affiliation(s)
- Christian Wiese
- Biotechnology of Natural Products, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- Botany, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Miriam Abele
- Botany, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Benjamin Al
- Botany, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Melina Altmann
- Institute of Network Biology (INET), Molecular Targets and Therapeutics Center (MTTC), Helmholtz Center Munich, German Research Center for Environmental Health, Munich-Neuherberg, Germany
| | - Alexander Steiner
- Botany, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Nils Kalbfuß
- Botany, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Alexander Strohmayr
- Biotechnology of Natural Products, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- Botany, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Raksha Ravikumar
- Botany, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Chan Ho Park
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Barbara Brunschweiger
- Botany, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Eva Facher
- Systematic Botany and Mycology, Faculty of Biology, Ludwig-Maximilians-Universität (LMU) München, Planegg-Martinsried, Germany
| | - David W. Ehrhardt
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Pascal Falter-Braun
- Institute of Network Biology (INET), Molecular Targets and Therapeutics Center (MTTC), Helmholtz Center Munich, German Research Center for Environmental Health, Munich-Neuherberg, Germany
| | - Zhi-Yong Wang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Farhah F. Assaad
- Biotechnology of Natural Products, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- Botany, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
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4
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Overduin M, Bhat R. Recognition and remodeling of endosomal zones by sorting nexins. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184305. [PMID: 38408696 DOI: 10.1016/j.bbamem.2024.184305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/05/2024] [Accepted: 02/18/2024] [Indexed: 02/28/2024]
Abstract
The proteolipid code determines how cytosolic proteins find and remodel membrane surfaces. Here, we investigate how this process works with sorting nexins Snx1 and Snx3. Both proteins form sorting machines by recognizing membrane zones enriched in phosphatidylinositol 3-phosphate (PI3P), phosphatidylserine (PS) and cholesterol. This co-localized combination forms a unique "lipid codon" or lipidon that we propose is responsible for endosomal targeting, as revealed by structures and interactions of their PX domain-based readers. We outline a membrane recognition and remodeling mechanism for Snx1 and Snx3 involving this code element alongside transmembrane pH gradients, dipole moment-guided docking and specific protein-protein interactions. This generates an initial membrane-protein assembly (memtein) that then recruits retromer and additional PX proteins to recruit cell surface receptors for sorting to the trans-Golgi network (TGN), lysosome and plasma membranes. Post-translational modification (PTM) networks appear to regulate how the sorting machines form and operate at each level. The commonalities and differences between these sorting nexins show how the proteolipid code orchestrates parallel flows of molecular information from ribosome emergence to organelle genesis, and illuminates a universally applicable model of the membrane.
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Affiliation(s)
- Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada.
| | - Rakesh Bhat
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
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5
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Papaioannou P, Wallace MJ, Malhotra N, Mohler PJ, El Refaey M. Biochemical Structure and Function of TRAPP Complexes in the Cardiac System. JACC Basic Transl Sci 2023; 8:1599-1612. [PMID: 38205348 PMCID: PMC10774597 DOI: 10.1016/j.jacbts.2023.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/14/2023] [Indexed: 01/12/2024]
Abstract
Trafficking protein particle (TRAPP) is well reported to play a role in the trafficking of protein products within the Golgi and endoplasmic reticulum. Dysfunction in TRAPP has been associated with disorders in the nervous and cardiovascular systems, but the majority of literature focuses on TRAPP function in the nervous system solely. Here, we highlight the known pathways of TRAPP and hypothesize potential impacts of TRAPP dysfunction on the cardiovascular system, particularly the role of TRAPP as a guanine-nucleotide exchange factor for Rab1 and Rab11. We also review the various cardiovascular phenotypes associated with changes in TRAPP complexes and their subunits.
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Affiliation(s)
- Peter Papaioannou
- Frick Center for Heart Failure and Arrhythmia Research, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
- Division of Cardiac Surgery, Department of Surgery, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Michael J. Wallace
- Frick Center for Heart Failure and Arrhythmia Research, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Nipun Malhotra
- Frick Center for Heart Failure and Arrhythmia Research, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
- Division of Cardiac Surgery, Department of Surgery, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Peter J. Mohler
- Frick Center for Heart Failure and Arrhythmia Research, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
- Division of Cardiovascular Medicine, Department of Internal Medicine, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Mona El Refaey
- Frick Center for Heart Failure and Arrhythmia Research, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
- Division of Cardiac Surgery, Department of Surgery, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
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6
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Wiese C, Abele M, Al B, Altmann M, Steiner A, Kalbfuß N, Strohmayr A, Ravikumar R, Park CH, Brunschweiger B, Meng C, Facher E, Ehrhardt DW, Falter-Braun P, Wang ZY, Ludwig C, Assaad FF. Regulation of adaptive growth decisions via phosphorylation of the TRAPPII complex in Arabidopsis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.537966. [PMID: 37986925 PMCID: PMC10659361 DOI: 10.1101/2023.04.24.537966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Plants often adapt to adverse or stress conditions via differential growth. The trans-Golgi Network (TGN) has been implicated in stress responses, but it is not clear in what capacity it mediates adaptive growth decisions. In this study, we assess the role of the TGN in stress responses by exploring the interactome of the Transport Protein Particle II (TRAPPII) complex, required for TGN structure and function. We identified physical and genetic interactions between TRAPPII and shaggy-like kinases (GSK3/AtSKs). Kinase assays and pharmacological inhibition provided in vitro and in vivo evidence that AtSKs target the TRAPPII-specific subunit AtTRS120/TRAPPC9. GSK3/AtSK phosphorylation sites in AtTRS120/TRAPPC9 were mutated, and the resulting AtTRS120 phosphovariants subjected to a variety of single and multiple stress conditions in planta . The non-phosphorylatable TRS120 mutant exhibited enhanced adaptation to multiple stress conditions and to osmotic stress whereas the phosphomimetic version was less resilient. Higher order inducible trappii atsk mutants had a synthetically enhanced defect in root gravitropism. Our results suggest that the TRAPPII phosphostatus mediates adaptive responses to abiotic cues. AtSKs are multifunctional kinases that integrate a broad range of signals. Similarly, the TRAPPII interactome is vast and considerably enriched in signaling components. An AtSK-TRAPPII interaction would integrate all levels of cellular organization and instruct the TGN, a central and highly discriminate cellular hub, as to how to mobilize and allocate resources to optimize growth and survival under limiting or adverse conditions.
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7
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Abaji M, Mignon-Ravix C, Gorokhova S, Cacciagli P, Mortreux J, Molinari F, Chabrol B, Sigaudy S, Villard L, Riccardi F. TRAPPC2L-related disorder: first homozygous protein-truncating variant and further delineation of the phenotype. J Med Genet 2023; 60:1021-1025. [PMID: 36849228 DOI: 10.1136/jmg-2022-108677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 02/15/2023] [Indexed: 03/01/2023]
Abstract
The TRAPP (TRAfficking Protein Particle) complexes are evolutionarily conserved tethering factors involved in the intracellular transport of vesicles for secretion and autophagy processes. Pathogenic variants in 8 genes (of 14) encoding TRAPP proteins are involved in ultra-rare human diseases, called TRAPPopathies. Seven of them are autosomal recessive neurodevelopmental disorders with overlapping phenotypes. Since 2018, two homozygous missense variants in TRAPPC2L have been reported in five individuals from three unrelated families with early-onset and progressive encephalopathy, with episodic rhabdomyolysis. We now describe the first pathogenic protein-truncating variant in the TRAPPC2L gene found at a homozygous state in two affected siblings. This report provides key genetic evidence invaluable to establishing the gene-disease relationship for this gene and important insights into the TRAPPC2L phenotype. Regression, seizures and postnatal microcephaly initially described are not constant features. Acute episodes of infection do not contribute to the neurological course. HyperCKaemia is part of the clinical picture. Thus, TRAPPC2L syndrome is mainly characterised by a severe neurodevelopmental disorder and a variable degree of muscle involvement, suggesting that it belongs to the clinical entity of rare congenital muscular dystrophies.
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Affiliation(s)
- Mario Abaji
- Génétique Médicale, AP-HM, Marseille, France
- MMG, U1251, Inserm, Aix-Marseille Universite, Marseille, France
| | | | - Svetlana Gorokhova
- Génétique Médicale, AP-HM, Marseille, France
- MMG, U1251, Inserm, Aix-Marseille Universite, Marseille, France
| | - Pierre Cacciagli
- CRB, TAC, Assistance Publique Hopitaux de Marseille, Marseille, France
| | | | | | | | | | - Laurent Villard
- Génétique Médicale, AP-HM, Marseille, France
- MMG, U1251, Inserm, Aix-Marseille Universite, Marseille, France
| | - Florence Riccardi
- MMG, U1251, Inserm, Aix-Marseille Universite, Marseille, France
- Génétique Médicale, Centre Hospitalier Intercommunal Toulon - La Seyne-sur-Mer, Toulon, France
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8
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Wilmes S, Kümmel D. Insights into the role of the membranes in Rab GTPase regulation. Curr Opin Cell Biol 2023; 83:102177. [PMID: 37327649 DOI: 10.1016/j.ceb.2023.102177] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 06/18/2023]
Abstract
Rab GTPases are molecular switches with essential roles in mediating vesicular trafficking and establishing organelle identity. The conversion from the inactive, cytosolic to the membrane-bound, active species and back is tightly controlled by regulatory proteins. Recently, the roles of membrane properties and lipid composition of different target organelles in determining the activity state of Rabs have come to light. The investigation of several Rab guanine nucleotide exchange factors (GEFs) has revealed principles of how the recruitment via lipid interactions and the spatial confinement on the membrane surface contribute to spatiotemporal specificity in the Rab GTPase network. This paints an intricate picture of the control mechanisms in Rab activation and highlights the importance of the membrane lipid code in the organization of the endomembrane system.
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Affiliation(s)
- Stephan Wilmes
- University of Münster, Institute of Biochemistry, Corrensstraße 36, 48149 Münster, Germany
| | - Daniel Kümmel
- University of Münster, Institute of Biochemistry, Corrensstraße 36, 48149 Münster, Germany.
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9
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Herrmann E, Schäfer JH, Wilmes S, Ungermann C, Moeller A, Kümmel D. Structure of the metazoan Rab7 GEF complex Mon1-Ccz1-Bulli. Proc Natl Acad Sci U S A 2023; 120:e2301908120. [PMID: 37155863 PMCID: PMC10193976 DOI: 10.1073/pnas.2301908120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/14/2023] [Indexed: 05/10/2023] Open
Abstract
The endosomal system of eukaryotic cells represents a central sorting and recycling compartment linked to metabolic signaling and the regulation of cell growth. Tightly controlled activation of Rab GTPases is required to establish the different domains of endosomes and lysosomes. In metazoans, Rab7 controls endosomal maturation, autophagy, and lysosomal function. It is activated by the guanine nucleotide exchange factor (GEF) complex Mon1-Ccz1-Bulli (MCBulli) of the tri-longin domain (TLD) family. While the Mon1 and Ccz1 subunits have been shown to constitute the active site of the complex, the role of Bulli remains elusive. We here present the cryo-electron microscopy (cryo-EM) structure of MCBulli at 3.2 Å resolution. Bulli associates as a leg-like extension at the periphery of the Mon1 and Ccz1 heterodimers, consistent with earlier reports that Bulli does not impact the activity of the complex or the interactions with recruiter and substrate GTPases. While MCBulli shows structural homology to the related ciliogenesis and planar cell polarity effector (Fuzzy-Inturned-Wdpcp) complex, the interaction of the TLD core subunits Mon1-Ccz1 and Fuzzy-Inturned with Bulli and Wdpcp, respectively, is remarkably different. The variations in the overall architecture suggest divergent functions of the Bulli and Wdpcp subunits. Based on our structural analysis, Bulli likely serves as a recruitment platform for additional regulators of endolysosomal trafficking to sites of Rab7 activation.
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Affiliation(s)
- Eric Herrmann
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, 48149Münster, Germany
| | - Jan-Hannes Schäfer
- Department of Biology/Chemistry, Structural Biology section, Osnabrück University, 49076Osnabrück, Germany
| | - Stephan Wilmes
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, 48149Münster, Germany
| | - Christian Ungermann
- Department of Biology/Chemistry, Biochemistry section, Osnabrück University, 49076Osnabrück, Germany
- Center of Cellular Nanoanalytic Osnabrück, Osnabrück University, 49076Osnabrück, Germany
| | - Arne Moeller
- Department of Biology/Chemistry, Structural Biology section, Osnabrück University, 49076Osnabrück, Germany
- Center of Cellular Nanoanalytic Osnabrück, Osnabrück University, 49076Osnabrück, Germany
| | - Daniel Kümmel
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, 48149Münster, Germany
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10
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Sun S, Sui SF. Structural insights into assembly of TRAPPII and its activation of Rab11/Ypt32. Curr Opin Struct Biol 2023; 80:102596. [PMID: 37068358 DOI: 10.1016/j.sbi.2023.102596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 03/09/2023] [Accepted: 03/19/2023] [Indexed: 04/19/2023]
Abstract
Transport protein particle (TRAPP) complexes belong to the multisubunit tethering complex. They are guanine nucleotide exchange factors (GEFs) that play essential roles in secretory and endocytic recycling pathway and autophagy. There are two major forms of TRAPP complexes, TRAPPII and TRAPPIII, which share a core set of small subunits. TRAPPIII activates Rab1, while TRAPPII primarily activates Rab11. A steric gating mechanism has been proposed to control the substrate selection in vivo. However, the detailed mechanisms underlying the transition from TRAPPIII's GEF activity for Rab1 to TRAPPII's GEF activity for Rab11 and the roles of the complex-specific subunits in this transition are insufficiently understood. In this review, we discuss recent advances in understanding the mechanism of specific activation of Rab11/Ypt32 by TRAPPII, with a particular focus on new findings from structural studies.
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Affiliation(s)
- Shan Sun
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Sen-Fang Sui
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; School of Life Sciences, Cryo-EM Center, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
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11
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Kümmel D, Herrmann E, Langemeyer L, Ungermann C. Molecular insights into endolysosomal microcompartment formation and maintenance. Biol Chem 2022; 404:441-454. [PMID: 36503831 DOI: 10.1515/hsz-2022-0294] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/22/2022] [Indexed: 12/14/2022]
Abstract
Abstract
The endolysosomal system of eukaryotic cells has a key role in the homeostasis of the plasma membrane, in signaling and nutrient uptake, and is abused by viruses and pathogens for entry. Endocytosis of plasma membrane proteins results in vesicles, which fuse with the early endosome. If destined for lysosomal degradation, these proteins are packaged into intraluminal vesicles, converting an early endosome to a late endosome, which finally fuses with the lysosome. Each of these organelles has a unique membrane surface composition, which can form segmented membrane microcompartments by membrane contact sites or fission proteins. Furthermore, these organelles are in continuous exchange due to fission and fusion events. The underlying machinery, which maintains organelle identity along the pathway, is regulated by signaling processes. Here, we will focus on the Rab5 and Rab7 GTPases of early and late endosomes. As molecular switches, Rabs depend on activating guanine nucleotide exchange factors (GEFs). Over the last years, we characterized the Rab7 GEF, the Mon1-Ccz1 (MC1) complex, and key Rab7 effectors, the HOPS complex and retromer. Structural and functional analyses of these complexes lead to a molecular understanding of their function in the context of organelle biogenesis.
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Affiliation(s)
- Daniel Kümmel
- Institute of Biochemistry, University of Münster , Corrensstraße 36 , D-48149 Münster , Germany
| | - Eric Herrmann
- Institute of Biochemistry, University of Münster , Corrensstraße 36 , D-48149 Münster , Germany
| | - Lars Langemeyer
- Department of Biology/Chemistry, Biochemistry section , Osnabrück University , Barbarastraße 13 , D-49076 Osnabrück , Germany
- Center of Cellular Nanoanalytics (CellNanOs) , Osnabrück University , Barbarastraße 11 , D-49076 Osnabrück , Germany
| | - Christian Ungermann
- Department of Biology/Chemistry, Biochemistry section , Osnabrück University , Barbarastraße 13 , D-49076 Osnabrück , Germany
- Center of Cellular Nanoanalytics (CellNanOs) , Osnabrück University , Barbarastraße 11 , D-49076 Osnabrück , Germany
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Bagde SR, Fromme JC. The TRAPP complexes: discriminating GTPases in context. FEBS Lett 2022; 597:721-733. [PMID: 36481981 PMCID: PMC10050150 DOI: 10.1002/1873-3468.14557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/23/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022]
Abstract
Correct localization of Rab GTPases in cells is critical for proper function in membrane trafficking. Guanine-nucleotide exchange factors (GEFs) act as the primary determinants of Rab localization by activating and stabilizing their Rab substrates on specific organelle and vesicle membranes. The TRAPP complexes TRAPPII and TRAPPIII are two related GEFs that use the same catalytic site to activate distinct Rabs, Rab11 and Rab1, respectively. The Rab C-terminal hypervariable domain (HVD) is an important specificity determinant for the budding yeast TRAPP complexes, with the length of the HVD playing a critical role in counter-selection. Several recent studies have used cryo-EM to illuminate how the yeast and metazoan TRAPP complexes identify and activate their substrates. This review summarizes recently characterized Rab substrate selection mechanisms and highlights how the membrane surface provides critical context for the GEF-GTPase interactions.
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Affiliation(s)
- Saket R Bagde
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - J Christopher Fromme
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
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