1
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Borroto MC, Patel H, Srivastava S, Swanson LC, Keren B, Whalen S, Mignot C, Wang X, Chen Q, Rosenfeld JA, McLean S, Littlejohn RO, Emrick L, Burrage LC, Attali R, Lesca G, Acquaviva-Bourdain C, Sarret C, Seaver LH, Platzer K, Bartolomaeus T, Wünsch C, Fischer S, Rodriguez Barreto AM, Granadillo JL, Schreiner E, Brunet T, Schatz UA, Thiffault I, Mullegama SV, Michaud JL, Hamdan FF, Rossignol E, Campeau PM. Cohort Expansion and Genotype-Phenotype Analysis of RAB11A-Associated Neurodevelopmental Disorder. Pediatr Neurol 2024; 160:45-53. [PMID: 39181022 DOI: 10.1016/j.pediatrneurol.2024.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 11/07/2023] [Accepted: 07/13/2024] [Indexed: 08/27/2024]
Abstract
BACKGROUND GTPases of the Rab family are important orchestrators of membrane trafficking, and their dysregulation has been linked to a variety of neuropathologies. In 2017, we established a causal link between RAB11A variants and developmental and epileptic encephalopathy. In this study, we expand the phenotype of RAB11A-associated neurodevelopmental disorder and explore genotype-phenotype correlations. METHODS We assessed 16 patients with pathogenic or likely pathogenic RAB11A variants, generally de novo, heterozygous missense variants. One individual had a homozygous nonsense variant, although concomitant with a pathogenic LAMA2 variant, which made their respective contributions to the phenotype difficult to discriminate. RESULTS We reinforce the finding that certain RAB11A missense variants lead to intellectual disability and developmental delays. Other clinical features might include gait disturbances, hypotonia, magnetic resonance imaging abnormalities, visual anomalies, dysmorphisms, early adrenarche, and obesity. Epilepsy seems to be less common and linked to variants outside the binding sites. Individuals with variants in the binding sites seem to have a more multisystemic, nonepileptic phenotype. CONCLUSIONS Similar to other Rab-related disorders, RAB11A-associated neurodevelopmental disorder can also impact gait, tonus, brain anatomy and physiology, vision, adrenarche, and body weight and structure. Epilepsy seems to affect the minority of patients with variants outside the binding sites.
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Affiliation(s)
| | - Heena Patel
- Centre de recherche Azrieli du CHU Sainte-Justine, Montreal, Québec, Canada
| | - Siddharth Srivastava
- Department of Neurology, Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Lindsay C Swanson
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts
| | - Boris Keren
- Département de génétique, APHP-Sorbonne Université, Hôpital de la Pitié-Salpêtrière, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Sandra Whalen
- UF de Génétique Clinique et Centre de Reference Anomalies du Développement et Syndromes Malformatifs, APHP, Sorbonne Université, Hôpital Trousseau, Paris, France
| | - Cyril Mignot
- Département de Génétique, Centre de Référence Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié-Salpêtrière and Hôpital Trousseau, APHP, Sorbonne Université, Paris, France
| | | | - Qian Chen
- Children's Hospital, Capital Institute of Pediatrics, Beijing, China
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Scott McLean
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas; Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas
| | - Rebecca O Littlejohn
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas; Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas
| | - Lisa Emrick
- Section of Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Ruben Attali
- Genomic Research Department, Emedgene, an Illumina Company, Tel Aviv, Israel
| | - Gaetan Lesca
- Department of Medical Genetics, Lyon University Hospital, University Claude Bernard Lyon 1, Lyon, France
| | - Cecile Acquaviva-Bourdain
- Hospices civils de Lyon, service biochimie et biologie moléculaire, UF maladies héréditaires du métabolisme, Bron, France
| | - Catherine Sarret
- CHU Estaing, Pôle Pédiatrie, Service de Génétique, Clermont-Ferrand, France
| | - Laurie H Seaver
- Corewell Health Helen DeVos Children's Hospital, Grand Rapids, Michigan; Department of Pediatrics and Human Development, Michigan State University College of Human Medicine, Grand Rapids, Michigan
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Tobias Bartolomaeus
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Cornelia Wünsch
- Sozialpädiatrisches Zentrum Leipzig - Frühe Hilfe Leipzig e.V., Leipzig, Germany
| | - Susann Fischer
- Sozialpädiatrisches Zentrum Leipzig - Frühe Hilfe Leipzig e.V., Leipzig, Germany
| | | | - Jorge L Granadillo
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Elisabeth Schreiner
- Diagnostic and Research Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Theresa Brunet
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany; Department of Pediatric Neurology and Developmental Medicine, Dr. v. Hauner Children's Hospital, LMU - University of Munich, Munich, Germany
| | - Ulrich A Schatz
- Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | - Isabelle Thiffault
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, Missouri; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, Missouri
| | | | - Jacques L Michaud
- Centre de recherche Azrieli du CHU Sainte-Justine, Montreal, Québec, Canada; Departments of Pediatrics and Neurosciences, Université de Montréal, Montreal, Québec, Canada
| | - Fadi F Hamdan
- Centre de recherche Azrieli du CHU Sainte-Justine, Montreal, Québec, Canada; Department of Pediatrics, University of Montreal, Montreal, Québec, Canada
| | - Elsa Rossignol
- Centre de recherche Azrieli du CHU Sainte-Justine, Montreal, Québec, Canada
| | - Philippe M Campeau
- Centre de recherche Azrieli du CHU Sainte-Justine, Montreal, Québec, Canada; Department of Pediatrics, University of Montreal, Montreal, Québec, Canada.
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2
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Wang Y, Wang X, Bai B, Shaha A, He X, He Y, Ye Z, Shah VH, Kang N. Targeting Src SH3 domain-mediated glycolysis of HSC suppresses transcriptome, myofibroblastic activation, and colorectal liver metastasis. Hepatology 2024; 80:578-594. [PMID: 38271673 PMCID: PMC11266532 DOI: 10.1097/hep.0000000000000763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 12/27/2023] [Indexed: 01/27/2024]
Abstract
BACKGROUND AND AIMS Transforming growth factor-beta 1 (TGFβ1) induces HSC activation into metastasis-promoting cancer-associated fibroblasts (CAFs), but how the process is fueled remains incompletely understood. We studied metabolic reprogramming induced by TGFβ1 in HSCs. APPROACHES AND RESULTS Activation of cultured primary human HSCs was assessed by the expression of myofibroblast markers. Glucose transporter 1 (Glut1) of murine HSC was disrupted by Cre recombinase/LoxP sequence derived from bacteriophage P1 recombination (Cre/LoxP). Plasma membrane (PM) Glut1 and glycolysis were studied by biotinylation assay and the Angilent Seahorse XFe96 Analyzer. S.c. HSC/tumor co-implantation and portal vein injection of MC38 colorectal cancer cells into HSC-specific Glut1 knockout mice were performed to determine in vivo relevance. Transcriptome was obtained by RNA sequencing of HSCs and spatialomics with MC38 liver metastases. TGFβ1-induced CAF activation of HSCs was accompanied by elevation of PM Glut1, glucose uptake, and glycolysis. Targeting Glut1 or Src by short hairpin RNA, pharmacologic inhibition, or a Src SH3 domain deletion mutant abrogated TGFβ1-stimulated PM accumulation of Glut1, glycolysis, and CAF activation. Mechanistically, binding of the Src SH3 domain to SH3 domain-binding protein 5 led to a Src/SH3 domain-binding protein 5/Rab11/Glut1 complex that activated Rab11-dependent Glut1 PM transport under TGFβ1 stimulation. Deleting the Src SH3 domain or targeting Glut1 of HSCs by short hairpin RNA or Cre recombinase/LoxP sequence derived from bacteriophage P1 recombination suppressed CAF activation in mice and MC38 colorectal liver metastasis. Multi-omics revealed that Glut1 deficiency in HSCs/CAFs suppressed HSC expression of tumor-promoting factors and altered MC38 transcriptome, contributing to reduced MC38 liver metastases. CONCLUSION The Src SH3 domain-facilitated metabolic reprogramming induced by TGFβ1 represents a target to inhibit CAF activation and the pro-metastatic liver microenvironment.
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Affiliation(s)
- Yuanguo Wang
- Tumor Microenvironment and Metastasis, the Hormel Institute, University of Minnesota, Austin, Minnesota, USA
| | - Xianghu Wang
- Tumor Microenvironment and Metastasis, the Hormel Institute, University of Minnesota, Austin, Minnesota, USA
- The School of Medicine, Taizhou University, Taizhou, Zhejiang, China
| | - Bing Bai
- Tumor Microenvironment and Metastasis, the Hormel Institute, University of Minnesota, Austin, Minnesota, USA
| | - Aurpita Shaha
- Tumor Microenvironment and Metastasis, the Hormel Institute, University of Minnesota, Austin, Minnesota, USA
| | - Xipu He
- Tumor Microenvironment and Metastasis, the Hormel Institute, University of Minnesota, Austin, Minnesota, USA
- The School of Chemistry and Chemical Engineering, Nanning, Guangxi, China
| | - Yingzi He
- Tumor Microenvironment and Metastasis, the Hormel Institute, University of Minnesota, Austin, Minnesota, USA
- The School of Environmental and Life Sciences, Nanning Normal University, Nanning, Guangxi, China
| | - Zhenqing Ye
- Department of Population Health Science, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Vijay H. Shah
- GI Research Unit and Cancer Cell Biology Program, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Ningling Kang
- Tumor Microenvironment and Metastasis, the Hormel Institute, University of Minnesota, Austin, Minnesota, USA
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Moreno-Corona NC, de León-Bautista MP, León-Juárez M, Hernández-Flores A, Barragán-Gálvez JC, López-Ortega O. Rab GTPases, Active Members in Antigen-Presenting Cells, and T Lymphocytes. Traffic 2024; 25:e12950. [PMID: 38923715 DOI: 10.1111/tra.12950] [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: 01/07/2024] [Revised: 04/25/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024]
Abstract
Processes such as cell migration, phagocytosis, endocytosis, and exocytosis refer to the intense exchange of information between the internal and external environment in the cells, known as vesicular trafficking. In eukaryotic cells, these essential cellular crosstalks are controlled by Rab GTPases proteins through diverse adaptor proteins like SNAREs complex, coat proteins, phospholipids, kinases, phosphatases, molecular motors, actin, or tubulin cytoskeleton, among others, all necessary for appropriate mobilization of vesicles and distribution of molecules. Considering these molecular events, Rab GTPases are critical components in specific biological processes of immune cells, and many reports refer primarily to macrophages; therefore, in this review, we address specific functions in immune cells, concretely in the mechanism by which the GTPase contributes in dendritic cells (DCs) and, T/B lymphocytes.
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Affiliation(s)
| | - Mercedes Piedad de León-Bautista
- Escuela de Medicina, Universidad Vasco de Quiroga, Morelia, Mexico
- Human Health, Laboratorio de Enfermedades Infecciosas y Genómica (INEX LAB), Morelia, Mexico
| | - Moises León-Juárez
- Laboratorio de Virología Perinatal y Diseño Molecular de Antígenos y Biomarcadores, Departamento de Inmunobioquimica, Instituto Nacional de Perinatología, Ciudad de México, Mexico
| | | | - Juan Carlos Barragán-Gálvez
- División de Ciencias Naturales y Exactas, Departamento de Farmacia, Universidad de Guanajuato, Guanajuato, Mexico
| | - Orestes López-Ortega
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institute Necker Enfants Malades, Paris, France
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4
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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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5
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Li GL, Han YQ, Su BQ, Yu HS, Zhang S, Yang GY, Wang J, Liu F, Ming SL, Chu BB. Porcine reproductive and respiratory syndrome virus 2 hijacks CMA-mediated lipolysis through upregulation of small GTPase RAB18. PLoS Pathog 2024; 20:e1012123. [PMID: 38607975 PMCID: PMC11014436 DOI: 10.1371/journal.ppat.1012123] [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: 08/25/2023] [Accepted: 03/14/2024] [Indexed: 04/14/2024] Open
Abstract
RAB GTPases (RABs) control intracellular membrane trafficking with high precision. In the present study, we carried out a short hairpin RNA (shRNA) screen focused on a library of 62 RABs during infection with porcine reproductive and respiratory syndrome virus 2 (PRRSV-2), a member of the family Arteriviridae. We found that 13 RABs negatively affect the yield of PRRSV-2 progeny virus, whereas 29 RABs have a positive impact on the yield of PRRSV-2 progeny virus. Further analysis revealed that PRRSV-2 infection transcriptionally regulated RAB18 through RIG-I/MAVS-mediated canonical NF-κB activation. Disrupting RAB18 expression led to the accumulation of lipid droplets (LDs), impaired LDs catabolism, and flawed viral replication and assembly. We also discovered that PRRSV-2 co-opts chaperone-mediated autophagy (CMA) for lipolysis via RAB18, as indicated by the enhanced associations between RAB18 and perlipin 2 (PLIN2), CMA-specific lysosomal associated membrane protein 2A (LAMP2A), and heat shock protein family A (Hsp70) member 8 (HSPA8/HSC70) during PRRSV-2 infection. Knockdown of HSPA8 and LAMP2A impacted on the yield of PRRSV-2 progeny virus, implying that the virus utilizes RAB18 to promote CMA-mediated lipolysis. Importantly, we determined that the C-terminal domain (CTD) of HSPA8 could bind to the switch II domain of RAB18, and the CTD of PLIN2 was capable of associating with HSPA8, suggesting that HSPA8 facilitates the interaction between RAB18 and PLIN2 in the CMA process. In summary, our findings elucidate how PRRSV-2 hijacks CMA-mediated lipid metabolism through innate immune activation to enhance the yield of progeny virus, offering novel insights for the development of anti-PRRSV-2 treatments.
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Affiliation(s)
- Guo-Li Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province, China
- Key Laboratory of Animal Biochemistry and Nutrition, Zhengzhou, Henan Province, Ministry of Agriculture and Rural Affairs of the People’s Republic of China
- Key Laboratory of Veterinary Biotechnology of Henan Province, Zhengzhou, Henan Province, China
| | - Ying-Qian Han
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province, China
- Key Laboratory of Animal Biochemistry and Nutrition, Zhengzhou, Henan Province, Ministry of Agriculture and Rural Affairs of the People’s Republic of China
- Key Laboratory of Veterinary Biotechnology of Henan Province, Zhengzhou, Henan Province, China
| | - Bing-Qian Su
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province, China
- Key Laboratory of Animal Biochemistry and Nutrition, Zhengzhou, Henan Province, Ministry of Agriculture and Rural Affairs of the People’s Republic of China
- Key Laboratory of Veterinary Biotechnology of Henan Province, Zhengzhou, Henan Province, China
| | - Hai-Shen Yu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province, China
- Key Laboratory of Animal Biochemistry and Nutrition, Zhengzhou, Henan Province, Ministry of Agriculture and Rural Affairs of the People’s Republic of China
- Key Laboratory of Veterinary Biotechnology of Henan Province, Zhengzhou, Henan Province, China
| | - Shuang Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province, China
- Key Laboratory of Animal Biochemistry and Nutrition, Zhengzhou, Henan Province, Ministry of Agriculture and Rural Affairs of the People’s Republic of China
- Key Laboratory of Veterinary Biotechnology of Henan Province, Zhengzhou, Henan Province, China
| | - Guo-Yu Yang
- Key Laboratory of Animal Biochemistry and Nutrition, Zhengzhou, Henan Province, Ministry of Agriculture and Rural Affairs of the People’s Republic of China
- Key Laboratory of Veterinary Biotechnology of Henan Province, Zhengzhou, Henan Province, China
| | - Jiang Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province, China
- Key Laboratory of Animal Biochemistry and Nutrition, Zhengzhou, Henan Province, Ministry of Agriculture and Rural Affairs of the People’s Republic of China
- Key Laboratory of Veterinary Biotechnology of Henan Province, Zhengzhou, Henan Province, China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou, Henan Province, China
| | - Fang Liu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province, China
| | - Sheng-Li Ming
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province, China
- Key Laboratory of Animal Biochemistry and Nutrition, Zhengzhou, Henan Province, Ministry of Agriculture and Rural Affairs of the People’s Republic of China
- Key Laboratory of Veterinary Biotechnology of Henan Province, Zhengzhou, Henan Province, China
| | - Bei-Bei Chu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province, China
- Key Laboratory of Animal Biochemistry and Nutrition, Zhengzhou, Henan Province, Ministry of Agriculture and Rural Affairs of the People’s Republic of China
- Key Laboratory of Veterinary Biotechnology of Henan Province, Zhengzhou, Henan Province, China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou, Henan Province, China
- International Joint Research Center of National Animal Immunology, Henan Agricultural University, Zhengzhou, Henan Province, China
- Longhu Advanced Immunization Laboratory, Zhengzhou, Henan Province, China
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Win S, Than TA, Kaplowitz N. Mitochondrial P-JNK target, SAB (SH3BP5), in regulation of cell death. Front Cell Dev Biol 2024; 12:1359152. [PMID: 38559813 PMCID: PMC10978662 DOI: 10.3389/fcell.2024.1359152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/19/2024] [Indexed: 04/04/2024] Open
Abstract
Cell death occurs in various circumstances, such as homeostasis, stress response, and defense, via specific pathways and mechanisms that are regulated by specific activator-induced signal transductions. Among them, Jun N-terminal kinases (JNKs) participate in various aspects, and the recent discovery of JNKs and mitochondrial protein SAB interaction in signal regulation of cell death completes our understanding of the mechanism of sustained activation of JNK (P-JNK), which leads to triggering of the machinery of cell death. This understanding will lead the investigators to discover the modulators facilitating or preventing cell death for therapeutic application in acute or chronic diseases and cancer. We discuss here the mechanism and modulators of the JNK-SAB-ROS activation loop, which is the core component of mitochondria-dependent cell death, specifically apoptosis and mitochondrial permeability transition (MPT)-driven necrosis, and which may also contribute to cell death mechanisms of ferroptosis and pyroptosis. The discussion here is based on the results and evidence discovered from liver disease models, but the JNK-SAB-ROS activation loop to sustain JNK activation is universally applicable to various disease models where mitochondria and reactive oxygen species contribute to the mechanism of disease.
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Affiliation(s)
- Sanda Win
- *Correspondence: Sanda Win, ; Neil Kaplowitz,
| | | | - Neil Kaplowitz
- Department of Medicine, Division of Gastroenterology and Liver Diseases, University of Southern California, Los Angeles, CA, United States
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7
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Fukatsu S, Sashi H, Shirai R, Takagi N, Oizumi H, Yamamoto M, Ohbuchi K, Miyamoto Y, Yamauchi J. Rab11a Controls Cell Shape via C9orf72 Protein: Possible Relationships to Frontotemporal Dementia/Amyotrophic Lateral Sclerosis (FTDALS) Type 1. PATHOPHYSIOLOGY 2024; 31:100-116. [PMID: 38390945 PMCID: PMC10885063 DOI: 10.3390/pathophysiology31010008] [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: 12/08/2023] [Revised: 01/24/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024] Open
Abstract
Abnormal nucleotide insertions of C9orf72, which forms a complex with Smith-Magenis syndrome chromosomal region candidate gene 8 (SMCR8) protein and WD repeat-containing protein 41 (WDR41) protein, are associated with an autosomal-dominant neurodegenerative frontotemporal dementia and/or amyotrophic lateral sclerosis type 1 (FTDALS1). The differentially expressed in normal and neoplastic cells (DENN) domain-containing C9orf72 and its complex with SMCR8 and WDR41 function as a guanine-nucleotide exchange factor for Rab GTP/GDP-binding proteins (Rab GEF, also called Rab activator). Among Rab proteins serving as major effectors, there exists Rab11a. However, it remains to be established which Rab protein is related to promoting or sustaining neuronal morphogenesis or homeostasis. In this study, we describe that the knockdown of Rab11a decreases the expression levels of neuronal differentiation marker proteins, as well as the elongation of neurite-like processes, using N1E-115 cells, a well-utilized neuronal differentiation model. Similar results were obtained in primary cortical neurons. In contrast, the knockdown of Rab11b, a Rab11a homolog, did not significantly affect their cell morphological changes. It is of note that treatment with hesperetin, a citrus flavonoid (also known as Vitamin P), recovered the neuronal morphological phenotypes induced by Rab11a knockdown. Also, the knockdown of Rab11a or Rab11b led to a decrease in glial marker expression levels and in morphological changes in FBD-102b cells, which serve as the oligodendroglial differentiation model. Rab11a is specifically involved in the regulation of neuronal morphological differentiation. The knockdown effect mimicking the loss of function of C9orf72 is reversed by treatment with hesperetin. These findings may reveal a clue for identifying one of the potential molecular and cellular phenotypes underlying FTDALS1.
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Affiliation(s)
- Shoya Fukatsu
- Laboratory of Molecular Neurology, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan
| | - Hinami Sashi
- Laboratory of Applied Biochemistry, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan
| | - Remina Shirai
- Laboratory of Molecular Neurology, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan
| | - Norio Takagi
- Laboratory of Applied Biochemistry, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan
| | - Hiroaki Oizumi
- Tsumura Research Laboratories, Tsumura & Co., Inashiki 200-1192, Japan
| | - Masahiro Yamamoto
- Tsumura Research Laboratories, Tsumura & Co., Inashiki 200-1192, Japan
| | - Katsuya Ohbuchi
- Tsumura Research Laboratories, Tsumura & Co., Inashiki 200-1192, Japan
| | - Yuki Miyamoto
- Laboratory of Molecular Neurology, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan
- Laboratory of Molecular Pharmacology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Junji Yamauchi
- Laboratory of Molecular Neurology, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan
- Laboratory of Molecular Pharmacology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
- Diabetic Neuropathy Project, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
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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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Wilson B, Flett C, Gemperle J, Lawless C, Hartshorn M, Hinde E, Harrison T, Chastney M, Taylor S, Allen J, Norman JC, Zacharchenko T, Caswell PT. Proximity labelling identifies pro-migratory endocytic recycling cargo and machinery of the Rab4 and Rab11 families. J Cell Sci 2023; 136:jcs260468. [PMID: 37232246 PMCID: PMC10323252 DOI: 10.1242/jcs.260468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 05/18/2023] [Indexed: 05/27/2023] Open
Abstract
Endocytic recycling controls the return of internalised cargoes to the plasma membrane to coordinate their positioning, availability and downstream signalling. The Rab4 and Rab11 small GTPase families regulate distinct recycling routes, broadly classified as fast recycling from early endosomes (Rab4) and slow recycling from perinuclear recycling endosomes (Rab11), and both routes handle a broad range of overlapping cargoes to regulate cell behaviour. We adopted a proximity labelling approach, BioID, to identify and compare the protein complexes recruited by Rab4a, Rab11a and Rab25 (a Rab11 family member implicated in cancer aggressiveness), revealing statistically robust protein-protein interaction networks of both new and well-characterised cargoes and trafficking machinery in migratory cancer cells. Gene ontological analysis of these interconnected networks revealed that these endocytic recycling pathways are intrinsically connected to cell motility and cell adhesion. Using a knock-sideways relocalisation approach, we were further able to confirm novel links between Rab11, Rab25 and the ESCPE-1 and retromer multiprotein sorting complexes, and identify new endocytic recycling machinery associated with Rab4, Rab11 and Rab25 that regulates cancer cell migration in the 3D matrix.
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Affiliation(s)
- Beverley Wilson
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, M13 9PT, UK
| | - Chloe Flett
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, M13 9PT, UK
| | - Jakub Gemperle
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, M13 9PT, UK
| | - Craig Lawless
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, M13 9PT, UK
| | - Matthew Hartshorn
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, M13 9PT, UK
| | - Eleanor Hinde
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, M13 9PT, UK
| | - Tess Harrison
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, M13 9PT, UK
| | - Megan Chastney
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, M13 9PT, UK
| | - Sarah Taylor
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, M13 9PT, UK
| | - Jennifer Allen
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, M13 9PT, UK
| | - Jim C. Norman
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - Thomas Zacharchenko
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, M13 9PT, UK
| | - Patrick T. Caswell
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, M13 9PT, UK
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10
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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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11
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Wang X, Li X, Wang J, Wang J, Hu C, Zeng J, Shi A, Lin L. SMGL-1/NBAS acts as a RAB-8 GEF to regulate unconventional protein secretion. J Cell Biol 2022; 221:213235. [PMID: 35604368 PMCID: PMC9129922 DOI: 10.1083/jcb.202111125] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 04/13/2022] [Accepted: 05/04/2022] [Indexed: 01/07/2023] Open
Abstract
Unconventional protein secretion (UPS) pathways are conserved across species. However, the underlying mechanisms that regulate Golgi-bypassing UPS of integral proteins remain elusive. In this study, we show that RAB-8 and SMGL-1/NBAS are required for the UPS of integral proteins in C. elegans intestine. SMGL-1 resides in the ER-Golgi intermediate compartment and adjacent RAB-8-positive structures, and NRZ complex component CZW-1/ZW10 is required for this residency. Notably, SMGL-1 acts as a guanine nucleotide exchange factor for RAB-8, ensuring UPS of integral proteins by driving the activation of RAB-8. Furthermore, we show that Pseudomonas aeruginosa infection elevated the expression of SMGL-1 and RAB-8. Loss of SMGL-1 or RAB-8 compromised resistance to environmental colchicine, arsenite, and pathogenic bacteria. These results suggest that the SMGL-1/RAB-8-mediated UPS could integrate environmental signals to serve as a host defense response. Together, by establishing the C. elegans intestine as a multicellular model, our findings provide insights into RAB-8-dependent Golgi-bypassing UPS, especially in the context of epithelia in vivo.
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Affiliation(s)
- Xianghong Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xinxin Li
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Junkai Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jiabin Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Can Hu
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jia Zeng
- Department of Biochemistry and Molecular Biology, Guizhou Medical University, Guiyang, Guizhou, China
| | - Anbing Shi
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China,Cell Architecture Research Center, Huazhong University of Science and Technology, Wuhan, Hubei, China,Correspondence to Anbing Shi:
| | - Long Lin
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China,Cell Architecture Research Center, Huazhong University of Science and Technology, Wuhan, Hubei, China,Long Lin:
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12
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Harris NJ, Jenkins ML, Dalwadi U, Fleming KD, Nam SE, Parson MAH, Yip CK, Burke JE. Biochemical Insight into Novel Rab-GEF Activity of the Mammalian TRAPPIII Complex. J Mol Biol 2021; 433:167145. [PMID: 34229011 DOI: 10.1016/j.jmb.2021.167145] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/25/2021] [Accepted: 06/30/2021] [Indexed: 11/28/2022]
Abstract
Transport Protein Particle complexes (TRAPP) are evolutionarily conserved regulators of membrane trafficking, with this mediated by their guanine nucleotide exchange factor (GEF) activity towards Rab GTPases. In metazoans evidence suggests that two different TRAPP complexes exist, TRAPPII and TRAPPIII. These two complexes share a common core of subunits, with complex specific subunits (TRAPPC9 and TRAPPC10 in TRAPPII and TRAPPC8, TRAPPC11, TRAPPC12, TRAPPC13 in TRAPPIII). TRAPPII and TRAPPIII have distinct specificity for GEF activity towards Rabs, with TRAPPIII acting on Rab1, and TRAPPII acting on Rab1 and Rab11. The molecular basis for how these complex specific subunits alter GEF activity towards Rab GTPases is unknown. Here we have used a combination of biochemical assays, hydrogen deuterium exchange mass spectrometry (HDX-MS) and electron microscopy to examine the regulation of TRAPPII and TRAPPIIII complexes in solution and on membranes. GEF assays revealed that TRAPPIII has GEF activity against Rab1 and Rab43, with no detectable activity against the other 18 Rabs tested. The TRAPPIII complex had significant differences in protein dynamics at the Rab binding site compared to TRAPPII, potentially indicating an important role of accessory subunits in altering the active site of TRAPP complexes. Both the TRAPPII and TRAPPIII complexes had enhanced GEF activity on lipid membranes, with HDX-MS revealing numerous conformational changes that accompany membrane association. HDX-MS also identified a membrane binding site in TRAPPC8. Collectively, our results provide insight into the functions of TRAPP complexes and how they can achieve Rab specificity.
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Affiliation(s)
- Noah J Harris
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Meredith L Jenkins
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Udit Dalwadi
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Kaelin D Fleming
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Sung-Eun Nam
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Matthew A H Parson
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Calvin K Yip
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada; Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.
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13
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Abstract
CNNM/CorB proteins are a broadly conserved family of integral membrane proteins with close to 90,000 protein sequences known. They are associated with Mg2+ transport but it is not known if they mediate transport themselves or regulate other transporters. Here, we determine the crystal structure of an archaeal CorB protein in two conformations (apo and Mg2+-ATP bound). The transmembrane DUF21 domain exists in an inward-facing conformation with a Mg2+ ion coordinated by a conserved π-helix. In the absence of Mg2+-ATP, the CBS-pair domain adopts an elongated dimeric configuration with previously unobserved domain-domain contacts. Hydrogen-deuterium exchange mass spectrometry, analytical ultracentrifugation, and molecular dynamics experiments support a role of the structural rearrangements in mediating Mg2+-ATP sensing. Lastly, we use an in vitro, liposome-based assay to demonstrate direct Mg2+ transport by CorB proteins. These structural and functional insights provide a framework for understanding function of CNNMs in Mg2+ transport and associated diseases.
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14
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Stariha JTB, Hoffmann RM, Hamelin DJ, Burke JE. Probing Protein-Membrane Interactions and Dynamics Using Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS). Methods Mol Biol 2021; 2263:465-485. [PMID: 33877613 DOI: 10.1007/978-1-0716-1197-5_22] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cellular membranes are a central hub for initiation and execution of many signaling processes. Integral to these processes being accomplished appropriately is the highly controlled recruitment and assembly of proteins at membrane surfaces. The study of the molecular mechanisms that mediate protein-membrane interactions can be facilitated by utilizing hydrogen-deuterium exchange mass spectrometry (HDX-MS). HDX-MS is a robust analytical technique that allows for the measurement of the exchange rate of backbone amide hydrogens with solvent to make inferences about protein structure and conformation. This chapter discusses the use of HDX-MS as a tool to study the conformational changes that occur within peripheral membrane proteins upon association with membrane. Particular reference will be made to the analysis of the protein kinase Akt and its activation upon binding phosphatidylinositol (3,4,5) tris-phosphate (PIP3)-containing membranes to illustrate specific methodological principles.
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Affiliation(s)
- Jordan T B Stariha
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Reece M Hoffmann
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - David J Hamelin
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada. .,Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, Canada.
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15
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Chandrakumar AA, Coyaud É, Marshall CB, Ikura M, Raught B, Rottapel R. Tankyrase regulates epithelial lumen formation via suppression of Rab11 GEFs. J Cell Biol 2021; 220:212384. [PMID: 34128958 PMCID: PMC8221736 DOI: 10.1083/jcb.202008037] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 02/24/2021] [Accepted: 03/05/2021] [Indexed: 01/08/2023] Open
Abstract
Rab11 GTPase proteins are required for cytokinesis, ciliogenesis, and lumenogenesis. Rab11a is critical for apical delivery of podocalyxin (PODXL) during lumen formation in epithelial cells. SH3BP5 and SH3BP5L are guanine nucleotide exchange factors (GEFs) for Rab11. We show that SH3BP5 and SH3BP5L are required for activation of Rab11a and cyst lumen formation. Using proximity-dependent biotin identification (BioID) interaction proteomics, we have identified SH3BP5 and its paralogue SH3BP5L as new substrates of the poly-ADP-ribose polymerase Tankyrase and the E3 ligase RNF146. We provide data demonstrating that epithelial polarity via cyst lumen formation is governed by Tankyrase, which inhibits Rab11a activation through the suppression of SH3BP5 and SH3BP5L. RNF146 reduces Tankyrase protein abundance and restores Rab11a activation and lumen formation. Thus, Rab11a activation is controlled by a signaling pathway composed of the sequential inhibition of SH3BP5 paralogues by Tankyrase, which is itself suppressed by RNF146.
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Affiliation(s)
- Arun A Chandrakumar
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Étienne Coyaud
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | | | - Mitsuhiko Ikura
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Brian Raught
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Robert Rottapel
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada.,Department of Immunology, University of Toronto, Toronto, Ontario, Canada.,Division of Rheumatology, St. Michael's Hospital, Toronto, Ontario, Canada
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16
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Chung IYW, Li L, Tyurin O, Gagarinova A, Wibawa R, Li P, Hartland EL, Cygler M. Structural and functional study of Legionella pneumophila effector RavA. Protein Sci 2021; 30:940-955. [PMID: 33660322 DOI: 10.1002/pro.4057] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/15/2021] [Accepted: 02/20/2021] [Indexed: 01/20/2023]
Abstract
Legionella pneumophila is an intracellular pathogen that causes Legionnaire's disease in humans. This bacterium can be found in freshwater environments as a free-living organism, but it is also an intracellular parasite of protozoa. Human infection occurs when inhaled aerosolized pathogen comes into contact with the alveolar mucosa and replicates in alveolar macrophages. Legionella enters the host cell by phagocytosis and redirects the Legionella-containing phagosomes from the phagocytic maturation pathway. These nascent phagosomes fuse with ER-derived secretory vesicles and membranes forming the Legionella-containing vacuole. Legionella subverts many host cellular processes by secreting over 300 effector proteins into the host cell via the Dot/Icm type IV secretion system. The cellular function for many Dot/Icm effectors is still unknown. Here, we present a structural and functional study of L. pneumophila effector RavA (Lpg0008). Structural analysis revealed that the RavA consists of four ~85 residue long α-helical domains with similar folds, which show only a low level of structural similarity to other protein domains. The ~90 residues long C-terminal segment is predicted to be natively unfolded. We show that during L. pneumophila infection of human cells, RavA localizes to the Golgi apparatus and to the plasma membrane. The same localization is observed when RavA is expressed in human cells. The localization signal resides within the C-terminal sequence C409 WTSFCGLF417 . Yeast-two-hybrid screen using RavA as bait identified RAB11A as a potential binding partner. RavA is present in L. pneumophila strains but only distant homologs are found in other Legionella species, where the number of repeats varies.
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Affiliation(s)
- Ivy Y W Chung
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Lei Li
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Oleg Tyurin
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,Symvivo Corporation, Burnaby, British Columbia, Canada
| | - Alla Gagarinova
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Raissa Wibawa
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, and Department of Molecular and Translational Science, Monash University, Clayton, Australia
| | - Pengfei Li
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, and Department of Molecular and Translational Science, Monash University, Clayton, Australia
| | - Elizabeth L Hartland
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, and Department of Molecular and Translational Science, Monash University, Clayton, Australia
| | - Miroslaw Cygler
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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17
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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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18
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Dobbs JM, Jenkins ML, Burke JE. Escherichia coli and Sf9 Contaminant Databases to Increase Efficiency of Tandem Mass Spectrometry Peptide Identification in Structural Mass Spectrometry Experiments. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2202-2209. [PMID: 32869988 DOI: 10.1021/jasms.0c00283] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Filtering of nonspecifically binding contaminant proteins from affinity purification mass spectrometry (AP-MS) data is a well-established strategy to improve statistical confidence in identified proteins. The CRAPome (contaminant repository for affinity purification) describes the contaminating background content present in many purification strategies. However, full contaminant lists for nickel-nitrilotriacetic acid (NiNTA) and glutathione S-transferase (GST) affinity matrices are lacking. Similarly, no Spodoptera frugiperda (Sf9) contaminants are available, and only the FLAG-purified contaminants are described for Escherichia coli. For MS experiments that use recombinant protein, such as structural mass spectrometry experiments (hydrogen-deuterium exchange mass spectrometry (HDX-MS), chemical cross-linking, and radical foot-printing), failing to include these contaminants in the search database during the initial tandem MS (MS/MS) identification stage can result in complications in peptide identification. We have created contaminant FASTA databases for Sf9 and E. coli NiNTA or GST purification strategies and show that the use of these databases can effectively improve HDX-MS protein coverage, fragment count, and confidence in peptide identification. This approach provides a robust strategy toward the design of contaminant databases for any purification approach that will expand the complexity of systems able to be interrogated by HDX-MS.
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Affiliation(s)
- Joseph M Dobbs
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
| | - Meredith L Jenkins
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
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19
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Génier S, Létourneau D, Gauthier E, Picard S, Boisvert M, Parent JL, Lavigne P. In-depth NMR characterization of Rab4a structure, nucleotide exchange and hydrolysis kinetics reveals an atypical GTPase profile. J Struct Biol 2020; 212:107582. [PMID: 32707235 DOI: 10.1016/j.jsb.2020.107582] [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: 05/27/2020] [Revised: 07/15/2020] [Accepted: 07/17/2020] [Indexed: 10/23/2022]
Abstract
Rab4a is a small GTPase associated with endocytic compartments and a key regulator of early endosomes recycling. Gathering evidence indicates that its expression and activation are required for the development of metastases. Rab4a-intrinsic GTPase properties that control its activity, i.e. nucleotide exchange and hydrolysis rates, have not yet been thoroughly studied. The determination of these properties is of the utmost importance to understand its functions and contributions to tumorigenesis. Here, we used the constitutively active (Rab4aQ67L) and dominant negative (Rab4aS22N) mutants to characterize the thermodynamical and structural determinants of the interaction between Rab4a and GTP (GTPγS) as well as GDP. We report the first 1H, 13C, 15N backbone NMR assignments of a Rab GTPase family member with Rab4a in complex with GDP and GTPγS. We also provide a qualitative description of the extent of structural and dynamical changes caused by the Q67L and S22N mutations. Using a real-time NMR approach and the two aforementioned mutants as controls, we evaluated Rab4a intrinsic nucleotide exchange and hydrolysis rates. Compared to most small GTPases such as Ras, a rapid GTP exchange rate along with slow hydrolysis rate were observed. This suggests that, in a cellular context, Rab4a can self-activate and persist in an activated state in absence of regulatory mechanisms. This peculiar profile is uncommon among the Ras superfamily members, making Rab4a an atypical fast-cycling GTPase and may explain, at least in part, how it contributes to metastases.
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Affiliation(s)
- Samuel Génier
- Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada; Institut de Pharmacologie de Sherbrooke, Sherbrooke, Québec, Canada
| | - Danny Létourneau
- Département de Biochimie et Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada; Institut de Pharmacologie de Sherbrooke, Sherbrooke, Québec, Canada
| | - Esther Gauthier
- Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada; Institut de Pharmacologie de Sherbrooke, Sherbrooke, Québec, Canada
| | - Samuel Picard
- Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada; Institut de Pharmacologie de Sherbrooke, Sherbrooke, Québec, Canada
| | - Marilou Boisvert
- Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada; Institut de Pharmacologie de Sherbrooke, Sherbrooke, Québec, Canada
| | - Jean-Luc Parent
- Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada; Institut de Pharmacologie de Sherbrooke, Sherbrooke, Québec, Canada.
| | - Pierre Lavigne
- Département de Biochimie et Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada; Institut de Pharmacologie de Sherbrooke, Sherbrooke, Québec, Canada.
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20
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Garcia VJ, Xu SL, Ravikumar R, Wang W, Elliott L, Gonzalez E, Fesenko M, Altmann M, Brunschweiger B, Falter-Braun P, Moore I, Burlingame A, Assaad FF, Wang ZY. TRIPP Is a Plant-Specific Component of the Arabidopsis TRAPPII Membrane Trafficking Complex with Important Roles in Plant Development. THE PLANT CELL 2020; 32:2424-2443. [PMID: 32371545 PMCID: PMC7346556 DOI: 10.1105/tpc.20.00044] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/25/2020] [Accepted: 04/23/2020] [Indexed: 05/23/2023]
Abstract
How the membrane trafficking system spatially organizes intracellular activities and intercellular signaling networks in plants is not well understood. Transport Protein Particle (TRAPP) complexes play key roles in the selective delivery of membrane vesicles to various subcellular compartments in yeast and animals but remain to be fully characterized in plants. Here, we investigated TRAPP complexes in Arabidopsis (Arabidopsis thaliana) using immunoprecipitation followed by quantitative mass spectrometry analysis of AtTRS33, a conserved core component of all TRAPP complexes. We identified 14 AtTRS33-interacting proteins, including homologs of all 13 TRAPP components in mammals and a protein that has homologs only in multicellular photosynthetic organisms and is thus named TRAPP-Interacting Plant Protein (TRIPP). TRIPP specifically associates with the TRAPPII complex through binary interactions with two TRAPPII-specific subunits. TRIPP colocalized with a subset of TRS33 compartments and trans-Golgi network markers in a TRS33-dependent manner. Loss-of-function tripp mutants exhibited dwarfism, sterility, partial photomorphogenesis in the dark, reduced polarity of the auxin transporter PIN2, incomplete cross wall formation, and altered localization of a TRAPPII-specific component. Therefore, TRIPP is a plant-specific component of the TRAPPII complex with important functions in trafficking, plant growth, and development.
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Affiliation(s)
- Veder J Garcia
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Shou-Ling Xu
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Raksha Ravikumar
- Plant Science Department, Botany, Technische Universität München, 85354 Freising, Germany
| | - Wenfei Wang
- Basic Forestry and Proteomics Research Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liam Elliott
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, United Kingdom
| | - Efren Gonzalez
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Mary Fesenko
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, United Kingdom
| | - Melina Altmann
- Institute of Network Biology, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt, 85764 Neuherberg, Germany
| | - Barbara Brunschweiger
- Plant Science Department, Botany, Technische Universität München, 85354 Freising, Germany
| | - Pascal Falter-Braun
- Institute of Network Biology, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt, 85764 Neuherberg, Germany
- Faculty of Biology, Microbe-Host-Interactions, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Ian Moore
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, United Kingdom
| | - Alma Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158
| | - Farhah F Assaad
- Plant Science Department, Botany, Technische Universität München, 85354 Freising, Germany
| | - Zhi-Yong Wang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
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21
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Seacrist CD, Kuenze G, Hoffmann RM, Moeller BE, Burke JE, Meiler J, Blind RD. Integrated Structural Modeling of Full-Length LRH-1 Reveals Inter-domain Interactions Contribute to Receptor Structure and Function. Structure 2020; 28:830-846.e9. [PMID: 32433991 DOI: 10.1016/j.str.2020.04.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/03/2020] [Accepted: 04/27/2020] [Indexed: 01/06/2023]
Abstract
Liver receptor homolog-1 (LRH-1; NR5A2) is a nuclear receptor that regulates a diverse array of biological processes. In contrast to dimeric nuclear receptors, LRH-1 is an obligate monomer and contains a subtype-specific helix at the C terminus of the DNA-binding domain (DBD), termed FTZ-F1. Although detailed structural information is available for individual domains of LRH-1, it is unknown how these domains exist in the intact nuclear receptor. Here, we developed an integrated structural model of human full-length LRH-1 using a combination of HDX-MS, XL-MS, Rosetta computational docking, and SAXS. The model predicts the DBD FTZ-F1 helix directly interacts with ligand binding domain helix 2. We confirmed several other predicted inter-domain interactions via structural and functional analyses. Comparison between the LRH-1/Dax-1 co-crystal structure and the integrated model predicted and confirmed Dax-1 co-repressor to modulate LRH-1 inter-domain dynamics. Together, these data support individual LRH-1 domains interacting to influence receptor structure and function.
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Affiliation(s)
- Corey D Seacrist
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Georg Kuenze
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Reece M Hoffmann
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Brandon E Moeller
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Jens Meiler
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA; Department of Chemistry, Vanderbilt University, Nashville, TN, USA; Institute for Drug Discovery, Leipzig University, Leipzig, Germany; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA.
| | - Raymond D Blind
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA; Department of Medicine, Division of Diabetes Endocrinology and Metabolism, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA.
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22
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Structural Insights into the Regulation Mechanism of Small GTPases by GEFs. Molecules 2019; 24:molecules24183308. [PMID: 31514408 PMCID: PMC6767298 DOI: 10.3390/molecules24183308] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 12/12/2022] Open
Abstract
Small GTPases are key regulators of cellular events, and their dysfunction causes many types of cancer. They serve as molecular switches by cycling between inactive guanosine diphosphate (GDP)-bound and active guanosine triphosphate (GTP)-bound states. GTPases are deactivated by GTPase-activating proteins (GAPs) and are activated by guanine-nucleotide exchange factors (GEFs). The intrinsic GTP hydrolysis activity of small GTPases is generally low and is accelerated by GAPs. GEFs promote GDP dissociation from small GTPases to allow for GTP binding, which results in a conformational change of two highly flexible segments, called switch I and switch II, that enables binding of the gamma phosphate and allows small GTPases to interact with downstream effectors. For several decades, crystal structures of many GEFs and GAPs have been reported and have shown tremendous structural diversity. In this review, we focus on the latest structural studies of GEFs. Detailed pictures of the variety of GEF mechanisms at atomic resolution can provide insights into new approaches for drug discovery.
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23
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Lipatova Z, Segev N. Ypt/Rab GTPases and their TRAPP GEFs at the Golgi. FEBS Lett 2019; 593:2488-2500. [PMID: 31400292 PMCID: PMC6989042 DOI: 10.1002/1873-3468.13574] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/07/2019] [Accepted: 08/08/2019] [Indexed: 11/06/2022]
Abstract
The conserved Ypt/Rab GTPases regulate the different steps of all intracellular trafficking pathways. Ypt/Rabs are activated by their specific nucleotide exchangers termed GEFs, and when GTP bound, they recruit their downstream effectors, which mediate vesicular transport substeps. In the yeast exocytic pathway, Ypt1 and Ypt31/32 regulate traffic through the Golgi and the conserved modular TRAPP complex acts a GEF for both Ypt1 and Ypt31/32. However, the precise localization and function of these Ypts have been under debate, as is the identity of their corresponding GEFs. We have established that Ypt1 and Ypt31 reside on the two sides of the Golgi, early and late, respectively, and regulate Golgi cisternal progression. We and others have shown that whereas a single TRAPP complex, TRAPP II, activates Ypt31, three TRAPP complexes can activate Ypt1: TRAPPs I, III, and IV. We propose that TRAPP I and II activate Ypt1 and Ypt31, respectively, at the Golgi, whereas TRAPP III and IV activate Ypt1 in autophagy. Resolving these issues is important because both Rabs and TRAPPs are implicated in multiple human diseases, ranging from cancer to neurodegenerative diseases.
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Affiliation(s)
- Zhanna Lipatova
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, IL, USA
| | - Nava Segev
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, IL, USA
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24
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Lamber EP, Siedenburg AC, Barr FA. Rab regulation by GEFs and GAPs during membrane traffic. Curr Opin Cell Biol 2019; 59:34-39. [PMID: 30981180 DOI: 10.1016/j.ceb.2019.03.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 03/06/2019] [Indexed: 01/05/2023]
Abstract
Rab GTPases and their regulatory proteins play a crucial role in vesicle-mediated membrane trafficking. During vesicle membrane tethering Rab GTPases are activated by GEFs (guanine nucleotide exchange factors) and then inactivated by GAPs (GTPase activating proteins). Recent evidence shows that in addition to activating and inactivating Rab GTPases, both Rab GEFs and GAPs directly contribute to membrane tethering events during vesicle traffic. Other studies have extended the range of processes, in which Rabs function, and revealed roles for Rabs and their GAPs in the regulation of autophagy. Here, we will discuss these advances and the emerging relationship between the domain architectures of Rab GEFs and vesicle coat protein complexes linked with GTPases of the Sar, ARF and Arl families in animal cells.
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Affiliation(s)
- Ekaterina P Lamber
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | | | - Francis A Barr
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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25
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Gulluni F, De Santis MC, Margaria JP, Martini M, Hirsch E. Class II PI3K Functions in Cell Biology and Disease. Trends Cell Biol 2019; 29:339-359. [DOI: 10.1016/j.tcb.2019.01.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 12/21/2018] [Accepted: 01/02/2019] [Indexed: 12/12/2022]
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26
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Goto-Ito S, Morooka N, Yamagata A, Sato Y, Sato K, Fukai S. Structural basis of guanine nucleotide exchange for Rab11 by SH3BP5. Life Sci Alliance 2019; 2:2/2/e201900297. [PMID: 30872413 PMCID: PMC6419104 DOI: 10.26508/lsa.201900297] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 01/30/2023] Open
Abstract
The Rab GTPase family is a major regulator of membrane traffic in eukaryotic cells. The Rab11 subfamily plays important roles in specific trafficking events such as exocytosis, endosomal recycling, and cytokinesis. SH3BP5 and SH3BP5-like (SH3BP5L) proteins have recently been found to serve as guanine nucleotide exchange factors (GEF) for Rab11. Here, we report the crystal structures of the SH3BP5 GEF domain alone and its complex with Rab11a. SH3BP5 exhibits a V-shaped structure comprising two coiled coils. The coiled coil composed of α1, and α4 is solely responsible for the Rab11a binding and GEF activity. SH3BP5 pulls out and deforms switch I of Rab11a so as to facilitate the GDP release from Rab11a. SH3BP5 interacts with the N-terminal region, switch I, interswitch, and switch II of Rab11a. SH3BP5 and SH3BP5L localize to Rab11-positive recycling endosomes and show GEF activity for all of the Rab11 family but not for Rab14. Fluorescence-based GEF assays combined with site-directed mutagenesis reveal the essential interactions between SH3BP5 and Rab11 family proteins for the GEF reaction on recycling endosomes.
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Affiliation(s)
- Sakurako Goto-Ito
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, Japan
| | - Nobukatsu Morooka
- Laboratory of Molecular Traffic, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan
| | - Atsushi Yamagata
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Yusuke Sato
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Ken Sato
- Laboratory of Molecular Traffic, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan
| | - Shuya Fukai
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan .,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
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27
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Abstract
Since I started doing scientific research, I've been fascinated by the interplay of protein structure and dynamics and how they together mediate protein function. A particular area of interest has been in understanding the mechanistic basis of how lipid-signaling enzymes function on membrane surfaces. In this award lecture article, I will describe my laboratory's studies on the structure and dynamics of lipid-signaling enzymes on membrane surfaces. This is important, as many lipid-signaling enzymes are regulated through dynamic regulatory mechanisms that control their enzymatic activity. This article will discuss my continued enthusiasm in using a synergistic application of hydrogen-deuterium exchange MS (HDX-MS) with other structural biology techniques to probe the mechanistic basis for how membrane-localized signaling enzymes are regulated and how these approaches can be used to understand how they are misregulated in disease. I will discuss specific examples of how we have used HDX-MS to study phosphoinositide kinases and the protein kinase Akt. An important focus will be on a description of how HDX-MS can be used as a powerful tool to optimize the design of constructs for X-ray crystallography and EM. The use of a diverse toolbox of biophysical methods has revealed novel insight into the complex and varied regulatory networks that control the function of lipid-signaling enzymes and enabled unique insight into the mechanics of membrane recruitment.
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Affiliation(s)
- John E Burke
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
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