1
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Laulumaa S, Kumpula EP, Huiskonen JT, Varjosalo M. Structure and interactions of the endogenous human Commander complex. Nat Struct Mol Biol 2024; 31:925-938. [PMID: 38459129 PMCID: PMC11189303 DOI: 10.1038/s41594-024-01246-1] [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: 05/31/2023] [Accepted: 01/19/2024] [Indexed: 03/10/2024]
Abstract
The Commander complex, a 16-protein assembly, plays multiple roles in cell homeostasis, cell cycle and immune response. It consists of copper-metabolism Murr1 domain proteins (COMMD1-10), coiled-coil domain-containing proteins (CCDC22 and CCDC93), DENND10 and the Retriever subcomplex (VPS26C, VPS29 and VPS35L), all expressed ubiquitously in the body and linked to various diseases. Here, we report the structure and key interactions of the endogenous human Commander complex by cryogenic-electron microscopy and mass spectrometry-based proteomics. The complex consists of a stable core of COMMD1-10 and an effector containing DENND10 and Retriever, scaffolded together by CCDC22 and CCDC93. We establish the composition of Commander and reveal major interaction interfaces. These findings clarify its roles in intracellular transport, and uncover a strong association with cilium assembly, and centrosome and centriole functions.
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Affiliation(s)
- Saara Laulumaa
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
| | - Esa-Pekka Kumpula
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
| | - Juha T Huiskonen
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland.
| | - Markku Varjosalo
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland.
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2
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Huang Y, Gao X, Yang E, Yue K, Cao Y, Zhao B, Zhang H, Dai S, Zhang L, Luo P, Jiang X. Top-down stepwise refinement identifies coding and noncoding RNA-associated epigenetic regulatory maps in malignant glioma. J Cell Mol Med 2022; 26:2230-2250. [PMID: 35194922 PMCID: PMC8995455 DOI: 10.1111/jcmm.17244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/20/2021] [Accepted: 01/21/2022] [Indexed: 11/28/2022] Open
Abstract
With the emergence of the molecular era and retreat of the histology epoch in malignant glioma, it is becoming increasingly necessary to research diagnostic/prognostic/therapeutic biomarkers and their related regulatory mechanisms. While accumulating studies have investigated coding gene‐associated biomarkers in malignant glioma, research on comprehensive coding and noncoding RNA‐associated biomarkers is lacking. Furthermore, few studies have illustrated the cross‐talk signalling pathways among these biomarkers and mechanisms in detail. Here, we identified DEGs and ceRNA networks in malignant glioma and then constructed Cox/Lasso regression models to further identify the most valuable genes through stepwise refinement. Top‐down comprehensive integrated analysis, including functional enrichment, SNV, immune infiltration, transcription factor binding site, and molecular docking analyses, further revealed the regulatory maps among these genes. The results revealed a novel and accurate model (AUC of 0.91 and C‐index of 0.84 in the whole malignant gliomas, AUC of 0.90 and C‐index of 0.86 in LGG, and AUC of 0.75 and C‐index of 0.69 in GBM) that includes twelve ncRNAs, 1 miRNA and 6 coding genes. Stepwise logical reasoning based on top‐down comprehensive integrated analysis and references revealed cross‐talk signalling pathways among these genes that were correlated with the circadian rhythm, tumour immune microenvironment and cellular senescence pathways. In conclusion, our work reveals a novel model where the newly identified biomarkers may contribute to a precise diagnosis/prognosis and subclassification of malignant glioma, and the identified cross‐talk signalling pathways would help to illustrate the noncoding RNA‐associated epigenetic regulatory mechanisms of glioma tumorigenesis and aid in targeted therapy.
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Affiliation(s)
- Yutao Huang
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xiangyu Gao
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China.,State Key Laboratory of Cancer Biology, Fourth Military Medical University, Xi'an, China
| | - Erwan Yang
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Kangyi Yue
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China.,State Key Laboratory of Cancer Biology, Fourth Military Medical University, Xi'an, China
| | - Yuan Cao
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Boyan Zhao
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Haofuzi Zhang
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Shuhui Dai
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Lei Zhang
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Peng Luo
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xiaofan Jiang
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
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3
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Syntaxin 12 and COMMD3 are new factors that function with VPS33B in the biogenesis of platelet α-granules. Blood 2022; 139:922-935. [PMID: 34905616 PMCID: PMC8832482 DOI: 10.1182/blood.2021012056] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 11/30/2021] [Indexed: 11/20/2022] Open
Abstract
Platelet α-granules regulate hemostasis and myriad other physiological processes, but their biogenesis is unclear. Mutations in only 3 proteins are known to cause α-granule defects and bleeding disorders in humans. Two such proteins, VPS16B and VPS33B, form a complex mediating transport of newly synthesized α-granule proteins through megakaryocyte (MK) endosomal compartments. It is unclear how the VPS16B/VPS33B complex accomplishes this function. Here we report VPS16B/VPS33B associates physically with Syntaxin 12 (Stx12), a SNARE protein that mediates vesicle fusion at endosomes. Importantly, Stx12-deficient MKs display reduced α-granule numbers and overall levels of α-granule proteins, thus revealing Stx12 as a new component of the α-granule biogenesis machinery. VPS16B/VPS33B also binds CCDC22, a component of the CCC complex working at endosome exit sites. CCDC22 competes with Stx12 for binding to VPS16B/VPS33B, suggesting a possible hand-off mechanism. Moreover, the major CCC form expressed in MKs contains COMMD3, one of 10 COMMD proteins. Deficiency of COMMD3/CCDC22 causes reduced α-granule numbers and overall levels of α-granule proteins, establishing the COMMD3/CCC complex as a new factor in α-granule biogenesis. Furthermore, P-selectin traffics through the cell surface in a COMMD3-dependent manner and depletion of COMMD3 results in lysosomal degradation of P-selectin and PF4. Stx12 and COMMD3/CCC deficiency cause less severe phenotypes than VPS16B/VPS33B deficiency, suggesting Stx12 and COMMD3/CCC assist but are less important than VPS16B/VPS33B in α-granule biogenesis. Mechanistically, our results suggest VPS16B/VPS33B coordinates the endosomal entry and exit of α-granule proteins by linking the fusogenic machinery with a ubiquitous endosomal retrieval complex that is repurposed in MKs to make α-granules.
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4
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Ma J, Han M, Yang D, Zheng T, Hu R, Wang B, Ye Y, Liu J, Huang G. Vps33B in Dendritic Cells Regulates House Dust Mite-Induced Allergic Lung Inflammation. THE JOURNAL OF IMMUNOLOGY 2021; 207:2649-2659. [PMID: 34732466 DOI: 10.4049/jimmunol.2100502] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 09/27/2021] [Indexed: 12/19/2022]
Abstract
Dendritic cells (DCs) are the most specialized APCs that play a critical role in driving Th2 differentiation, but the mechanism is not fully understood. Here we show that vacuolar protein sorting 33B (Vps33B) plays an important role in this process. Mice with Vps33b-specific deletion in DCs, but not in macrophages or T cells, were more susceptible to Th2-mediated allergic lung inflammation than wild-type mice. Deletion of Vps33B in DCs led to enhanced CD4+ T cell proliferation and Th2 differentiation. Moreover, Vps33B specifically restrained reactive oxygen species production in conventional DC1s to inhibit Th2 responses in vitro, whereas Vps33B in monocyte-derived DCs and conventional DC2s was dispensable for Th2 development in asthma pathogenesis. Taken together, our results identify Vps33B as an important molecule that mediates the cross-talk between DCs and CD4+ T cells to further regulate allergic asthma pathogenesis.
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Affiliation(s)
- Jingyu Ma
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Miaomiao Han
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, China
| | - Di Yang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tingting Zheng
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong, China; and
| | - Ran Hu
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bin Wang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong, China; and
| | - Youqiong Ye
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Junling Liu
- Department of Biochemistry and Molecular Cell Biology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Gonghua Huang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China; .,Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, Guangdong, China; and
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5
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Understanding amphisomes. Biochem J 2021; 478:1959-1976. [PMID: 34047789 DOI: 10.1042/bcj20200917] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/27/2021] [Accepted: 05/06/2021] [Indexed: 12/14/2022]
Abstract
Amphisomes are intermediate/hybrid organelles produced through the fusion of endosomes with autophagosomes within cells. Amphisome formation is an essential step during a sequential maturation process of autophagosomes before their ultimate fusion with lysosomes for cargo degradation. This process is highly regulated with multiple protein machineries, such as SNAREs, Rab GTPases, tethering complexes, and ESCRTs, are involved to facilitate autophagic flux to proceed. In neurons, autophagosomes are robustly generated in axonal terminals and then rapidly fuse with late endosomes to form amphisomes. This fusion event allows newly generated autophagosomes to gain retrograde transport motility and move toward the soma, where proteolytically active lysosomes are predominantly located. Amphisomes are not only the products of autophagosome maturation but also the intersection of the autophagy and endo-lysosomal pathways. Importantly, amphisomes can also participate in non-canonical functions, such as retrograde neurotrophic signaling or autophagy-based unconventional secretion by fusion with the plasma membrane. In this review, we provide an updated overview of the recent discoveries and advancements on the molecular and cellular mechanisms underlying amphisome biogenesis and the emerging roles of amphisomes. We discuss recent developments towards the understanding of amphisome regulation as well as the implications in the context of major neurodegenerative diseases, with a comparative focus on Alzheimer's disease and Parkinson's disease.
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6
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Abstract
SNARE proteins and Sec1/Munc18 (SM) proteins constitute the core molecular engine that drives nearly all intracellular membrane fusion and exocytosis. While SNAREs are known to couple their folding and assembly to membrane fusion, the physiological pathways of SNARE assembly and the mechanistic roles of SM proteins have long been enigmatic. Here, we review recent advances in understanding the SNARE-SM fusion machinery with an emphasis on biochemical and biophysical studies of proteins that mediate synaptic vesicle fusion. We begin by discussing the energetics, pathways, and kinetics of SNARE folding and assembly in vitro. Then, we describe diverse interactions between SM and SNARE proteins and their potential impact on SNARE assembly in vivo. Recent work provides strong support for the idea that SM proteins function as chaperones, their essential role being to enable fast, accurate SNARE assembly. Finally, we review the evidence that SM proteins collaborate with other SNARE chaperones, especially Munc13-1, and briefly discuss some roles of SNARE and SM protein deficiencies in human disease.
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Affiliation(s)
- Yongli Zhang
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06520, USA;
| | - Frederick M Hughson
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA;
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7
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Bowman SL, Bi-Karchin J, Le L, Marks MS. The road to lysosome-related organelles: Insights from Hermansky-Pudlak syndrome and other rare diseases. Traffic 2020; 20:404-435. [PMID: 30945407 DOI: 10.1111/tra.12646] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/02/2019] [Accepted: 04/02/2019] [Indexed: 12/11/2022]
Abstract
Lysosome-related organelles (LROs) comprise a diverse group of cell type-specific, membrane-bound subcellular organelles that derive at least in part from the endolysosomal system but that have unique contents, morphologies and functions to support specific physiological roles. They include: melanosomes that provide pigment to our eyes and skin; alpha and dense granules in platelets, and lytic granules in cytotoxic T cells and natural killer cells, which release effectors to regulate hemostasis and immunity; and distinct classes of lamellar bodies in lung epithelial cells and keratinocytes that support lung plasticity and skin lubrication. The formation, maturation and/or secretion of subsets of LROs are dysfunctional or entirely absent in a number of hereditary syndromic disorders, including in particular the Hermansky-Pudlak syndromes. This review provides a comprehensive overview of LROs in humans and model organisms and presents our current understanding of how the products of genes that are defective in heritable diseases impact their formation, motility and ultimate secretion.
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Affiliation(s)
- Shanna L Bowman
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jing Bi-Karchin
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Linh Le
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Michael S Marks
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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8
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Sparvoli D, Zoltner M, Cheng CY, Field MC, Turkewitz AP. Diversification of CORVET tethers facilitates transport complexity in Tetrahymena thermophila. J Cell Sci 2020; 133:jcs238659. [PMID: 31964712 PMCID: PMC7033735 DOI: 10.1242/jcs.238659] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 01/03/2020] [Indexed: 12/14/2022] Open
Abstract
In endolysosomal networks, two hetero-hexameric tethers called HOPS and CORVET are found widely throughout eukaryotes. The unicellular ciliate Tetrahymena thermophila possesses elaborate endolysosomal structures, but curiously both it and related protozoa lack the HOPS tether and several other trafficking proteins, while retaining the related CORVET complex. Here, we show that Tetrahymena encodes multiple paralogs of most CORVET subunits, which assemble into six distinct complexes. Each complex has a unique subunit composition and, significantly, shows unique localization, indicating participation in distinct pathways. One pair of complexes differ by a single subunit (Vps8), but have late endosomal versus recycling endosome locations. While Vps8 subunits are thus prime determinants for targeting and functional specificity, determinants exist on all subunits except Vps11. This unprecedented expansion and diversification of CORVET provides a potent example of tether flexibility, and illustrates how 'backfilling' following secondary losses of trafficking genes can provide a mechanism for evolution of new pathways.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Daniela Sparvoli
- Department of Molecular Genetics and Cell Biology, 920 E 58th Street, The University of Chicago, Chicago, IL, 60637, USA
| | - Martin Zoltner
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Chao-Yin Cheng
- Department of Molecular Genetics and Cell Biology, 920 E 58th Street, The University of Chicago, Chicago, IL, 60637, USA
| | - Mark C Field
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, 37005 Ceske Budejovice, Czech Republic
| | - Aaron P Turkewitz
- Department of Molecular Genetics and Cell Biology, 920 E 58th Street, The University of Chicago, Chicago, IL, 60637, USA
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9
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Vasilev F, Sukhomyasova A, Otomo T. Mucopolysaccharidosis-Plus Syndrome. Int J Mol Sci 2020; 21:ijms21020421. [PMID: 31936524 PMCID: PMC7013929 DOI: 10.3390/ijms21020421] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 01/07/2020] [Indexed: 12/18/2022] Open
Abstract
Previously, we reported a novel disease of impaired glycosaminoglycans (GAGs) metabolism without deficiency of known lysosomal enzymes—mucopolysaccharidosis-plus syndrome (MPSPS). MPSPS, whose pathophysiology is not elucidated, is an autosomal recessive multisystem disorder caused by a specific mutation p.R498W in the VPS33A gene. VPS33A functions in endocytic and autophagic pathways, but p.R498W mutation did not affect both of these pathways in the patient’s skin fibroblast. Nineteen patients with MPSPS have been identified: seventeen patients were found among the Yakut population (Russia) and two patients from Turkey. Clinical features of MPSPS patients are similar to conventional mucopolysaccharidoses (MPS). In addition to typical symptoms for conventional MPS, MPSPS patients developed other features such as congenital heart defects, renal and hematopoietic disorders. Diagnosis generally requires evidence of clinical picture similar to MPS and molecular genetic testing. Disease is very severe, prognosis is unfavorable and most of patients died at age of 10–20 months. Currently there is no specific therapy for this disease and clinical management is limited to supportive and symptomatic treatment.
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Affiliation(s)
- Filipp Vasilev
- Department of Molecular and Genetic Medicine, Kawasaki Medical School, Kurashiki, Okayama 701-0192, Japan;
- International Research Fellow of Japan Society for the Promotion of Science (Postdoctoral Fellowships for Research in Japan (Standard)), Tokyo 102-0083, Japan
- Laboratory of Genome Medicine, North-Eastern Federal University, 677013 Yakutsk, Sakha Republic, Russia;
| | - Aitalina Sukhomyasova
- Laboratory of Genome Medicine, North-Eastern Federal University, 677013 Yakutsk, Sakha Republic, Russia;
| | - Takanobu Otomo
- Department of Molecular and Genetic Medicine, Kawasaki Medical School, Kurashiki, Okayama 701-0192, Japan;
- Correspondence: ; Tel.: +81-86-462-1111
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10
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van der Beek J, Jonker C, van der Welle R, Liv N, Klumperman J. CORVET, CHEVI and HOPS – multisubunit tethers of the endo-lysosomal system in health and disease. J Cell Sci 2019; 132:132/10/jcs189134. [DOI: 10.1242/jcs.189134] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
ABSTRACT
Multisubunit tethering complexes (MTCs) are multitasking hubs that form a link between membrane fusion, organelle motility and signaling. CORVET, CHEVI and HOPS are MTCs of the endo-lysosomal system. They regulate the major membrane flows required for endocytosis, lysosome biogenesis, autophagy and phagocytosis. In addition, individual subunits control complex-independent transport of specific cargoes and exert functions beyond tethering, such as attachment to microtubules and SNARE activation. Mutations in CHEVI subunits lead to arthrogryposis, renal dysfunction and cholestasis (ARC) syndrome, while defects in CORVET and, particularly, HOPS are associated with neurodegeneration, pigmentation disorders, liver malfunction and various forms of cancer. Diseases and phenotypes, however, vary per affected subunit and a concise overview of MTC protein function and associated human pathologies is currently lacking. Here, we provide an integrated overview on the cellular functions and pathological defects associated with CORVET, CHEVI or HOPS proteins, both with regard to their complexes and as individual subunits. The combination of these data provides novel insights into how mutations in endo-lysosomal proteins lead to human pathologies.
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Affiliation(s)
- Jan van der Beek
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Institute for Biomembranes, Utrecht University, Utrecht 3584 CX, The Netherlands
| | - Caspar Jonker
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Institute for Biomembranes, Utrecht University, Utrecht 3584 CX, The Netherlands
| | - Reini van der Welle
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Institute for Biomembranes, Utrecht University, Utrecht 3584 CX, The Netherlands
| | - Nalan Liv
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Institute for Biomembranes, Utrecht University, Utrecht 3584 CX, The Netherlands
| | - Judith Klumperman
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Institute for Biomembranes, Utrecht University, Utrecht 3584 CX, The Netherlands
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11
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Corona AK, Jackson WT. Finding the Middle Ground for Autophagic Fusion Requirements. Trends Cell Biol 2018; 28:869-881. [PMID: 30115558 PMCID: PMC6197918 DOI: 10.1016/j.tcb.2018.07.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 06/29/2018] [Accepted: 07/06/2018] [Indexed: 12/26/2022]
Abstract
Autophagosome/amphisome-lysosome fusion is a highly regulated process at the protein, lipid, and biochemical level. Each primary component of fusion, such as the core SNAREs, HOPS complex, or physical positioning by microtubule-associated dynein motors, are regulated at multiple points to ensure optimum conditions for autophagic flux to proceed. With the complexity of the membrane fusion system, it is not difficult to imagine how autophagic flux defect-related disorders, such as Huntington's disease, non-familial Alzheimer's disease, and Vici syndrome develop. Each membrane fusion step is regulated at the protein, lipid, and ion level. This review aims to discuss the recent developments toward understanding the regulation of autophagosome, amphisome, and lysosome fusion requirements for successful autophagic flux.
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Affiliation(s)
- Abigail K Corona
- Department of Microbiology and Immunology, University of Maryland School of Medicine, 685 W. Baltimore Avenue, Baltimore, MD 21201, USA
| | - William T Jackson
- Department of Microbiology and Immunology, University of Maryland School of Medicine, 685 W. Baltimore Avenue, Baltimore, MD 21201, USA.
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12
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Gillies CE, Putler R, Menon R, Otto E, Yasutake K, Nair V, Hoover P, Lieb D, Li S, Eddy S, Fermin D, McNulty MT, Hacohen N, Kiryluk K, Kretzler M, Wen X, Sampson MG. An eQTL Landscape of Kidney Tissue in Human Nephrotic Syndrome. Am J Hum Genet 2018; 103:232-244. [PMID: 30057032 PMCID: PMC6081280 DOI: 10.1016/j.ajhg.2018.07.004] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 06/29/2018] [Indexed: 01/14/2023] Open
Abstract
Expression quantitative trait loci (eQTL) studies illuminate the genetics of gene expression and, in disease research, can be particularly illuminating when using the tissues directly impacted by the condition. In nephrology, there is a paucity of eQTL studies of human kidney. Here, we used whole-genome sequencing (WGS) and microdissected glomerular (GLOM) and tubulointerstitial (TI) transcriptomes from 187 individuals with nephrotic syndrome (NS) to describe the eQTL landscape in these functionally distinct kidney structures. Using MatrixEQTL, we performed cis-eQTL analysis on GLOM (n = 136) and TI (n = 166). We used the Bayesian "Deterministic Approximation of Posteriors" (DAP) to fine-map these signals, eQTLBMA to discover GLOM- or TI-specific eQTLs, and single-cell RNA-seq data of control kidney tissue to identify the cell type specificity of significant eQTLs. We integrated eQTL data with an IgA Nephropathy (IgAN) GWAS to perform a transcriptome-wide association study (TWAS). We discovered 894 GLOM eQTLs and 1,767 TI eQTLs at FDR < 0.05. 14% and 19% of GLOM and TI eQTLs, respectively, had >1 independent signal associated with its expression. 12% and 26% of eQTLs were GLOM specific and TI specific, respectively. GLOM eQTLs were most significantly enriched in podocyte transcripts and TI eQTLs in proximal tubules. The IgAN TWAS identified significant GLOM and TI genes, primarily at the HLA region. In this study, we discovered GLOM and TI eQTLs, identified those that were tissue specific, deconvoluted them into cell-specific signals, and used them to characterize known GWAS alleles. These data are available for browsing and download via our eQTL browser, "nephQTL."
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Affiliation(s)
- Christopher E Gillies
- Department of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Rosemary Putler
- Department of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Rajasree Menon
- Department of Computational Medicine and Bioinformatics, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Edgar Otto
- Department of Medicine-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Kalyn Yasutake
- Department of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Viji Nair
- Department of Medicine-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Paul Hoover
- Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA; Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - David Lieb
- Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Shuqiang Li
- Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Sean Eddy
- Department of Medicine-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Damian Fermin
- Department of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Michelle T McNulty
- Department of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Nir Hacohen
- Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA; Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Krzysztof Kiryluk
- Department of Medicine, Division of Nephrology, College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Matthias Kretzler
- Department of Computational Medicine and Bioinformatics, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA; Department of Medicine-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Xiaoquan Wen
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Matthew G Sampson
- Department of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA.
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13
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Proteomic and Biochemical Comparison of the Cellular Interaction Partners of Human VPS33A and VPS33B. J Mol Biol 2018; 430:2153-2163. [PMID: 29778605 PMCID: PMC6005816 DOI: 10.1016/j.jmb.2018.05.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 04/21/2018] [Accepted: 05/11/2018] [Indexed: 01/18/2023]
Abstract
Multi-subunit tethering complexes control membrane fusion events in eukaryotic cells. Class C core vacuole/endosome tethering (CORVET) and homotypic fusion and vacuole protein sorting (HOPS) are two such complexes, both containing the Sec1/Munc18 protein subunit VPS33A. Metazoans additionally possess VPS33B, which has considerable sequence similarity to VPS33A but does not integrate into CORVET or HOPS complexes and instead stably interacts with VIPAR. It has been recently suggested that VPS33B and VIPAR comprise two subunits of a novel multi-subunit tethering complex (named “CHEVI”), perhaps analogous in configuration to CORVET and HOPS. We utilized the BioID proximity biotinylation assay to compare and contrast the interactomes of VPS33A and VPS33B. Overall, few proteins were identified as associating with both VPS33A and VPS33B, suggesting that these proteins have distinct sub-cellular localizations. Consistent with previous reports, we observed that VPS33A was co-localized with many components of class III phosphatidylinositol 3-kinase (PI3KC3) complexes: PIK3C3, PIK3R4, NRBF2, UVRAG and RUBICON. Although VPS33A clearly co-localized with several subunits of CORVET and HOPS in this assay, no proteins with the canonical CORVET/HOPS domain architecture were found to co-localize with VPS33B. Instead, we identified that VPS33B interacts directly with CCDC22, a member of the CCC complex. CCDC22 does not co-fractionate with VPS33B and VIPAR in gel filtration of human cell lysates, suggesting that CCDC22 interacts transiently with VPS33B/VIPAR rather than forming a stable complex with these proteins in cells. We also observed that the protein complex containing VPS33B and VIPAR is considerably smaller than CORVET/HOPS, suggesting that the CHEVI complex comprises just VPS33B and VIPAR. VPS33A and VPS33B co-localize with distinct sets of cellular proteins. VPS33A co-localizes with PI3KC3 complex members. VPS33B interacts directly with CCDC22, a member of the CCC complex. VPS33B and VIPAR do not assemble into a larger stable multi-subunit tethering complex.
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14
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VPS18 recruits VPS41 to the human HOPS complex via a RING-RING interaction. Biochem J 2017; 474:3615-3626. [PMID: 28931724 PMCID: PMC5651818 DOI: 10.1042/bcj20170588] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/13/2017] [Accepted: 09/15/2017] [Indexed: 02/06/2023]
Abstract
Eukaryotic cells use conserved multisubunit membrane tethering complexes, including CORVET (class C core vacuole/endosome tethering) and HOPS (homotypic fusion and vacuole protein sorting), to control the fusion of endomembranes. These complexes have been extensively studied in yeast, but to date there have been far fewer studies of metazoan CORVET and HOPS. Both of these complexes comprise six subunits: a common four-subunit core and two unique subunits. Once assembled, these complexes function to recognise specific endosomal membrane markers and facilitate SNARE-mediated membrane fusion. CORVET promotes the homotypic fusion of early endosomes, while HOPS promotes the fusion of lysosomes to late endosomes and autophagosomes. Many of the subunits of both CORVET and HOPS contain putative C-terminal zinc-finger domains. Here, the contribution of these domains to the assembly of the human CORVET and HOPS complexes has been examined. Using biochemical techniques, we demonstrate that the zinc-containing RING (really interesting new gene) domains of human VPS18 and VPS41 interact directly to form a stable heterodimer. In cells, these RING domains are able to integrate into endogenous HOPS, showing that the VPS18 RING domain is required to recruit VPS41 to the core complex subunits. Importantly, this mechanism is not conserved throughout eukaryotes, as yeast Vps41 does not contain a C-terminal zinc-finger motif. The subunit analogous to VPS41 in human CORVET is VPS8, in which the RING domain has an additional C-terminal segment that is predicted to be disordered. Both the RING and disordered C-terminal domains are required for integration of VPS8 into endogenous CORVET complexes, suggesting that HOPS and CORVET recruit VPS41 and VPS8 via distinct molecular interactions.
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15
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Huang DG, Liu JJ, Guo L, Song YZ. [Clinical features and VPS33B mutations in a family affected by arthrogryposis, renal dysfunction, and cholestasis syndrome]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2017; 19:1077-1082. [PMID: 29046204 PMCID: PMC7389287 DOI: 10.7499/j.issn.1008-8830.2017.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 06/09/2017] [Indexed: 06/07/2023]
Abstract
Arthrogryposis, renal dysfunction, and cholestasis (ARC) syndrome is an autosomal recessive disorder caused by mutations in the VPS33B or VIPAS39 gene. The aim of this study was to investigate the clinical features and VPS33B gene mutations of an infant with ARC syndrome. A 47-day-old female infant was referred to the hospital with the complaint of jaundiced skin and sclera for 45 days and abnormal liver function for 39 days. The patient had been managed in different hospitals, but the therapeutic effects were unsatisfactory due to undetermined diagnosis. Physical examination showed jaundice of the skin and sclera. Systemic skin was dry with desquamation in the limbs and trunk. There were no positive signs on cardiopulmonary examination. The liver was palpable 2.0 cm under the right subcostal margin. The hips and knees were flexed, and the extension was limited, with low muscular tone in the four limbs. Biochemical analysis demonstrated raised serum total bile acids, bilirubin (predominantly conjugated bilirubin) and transaminases, but the γ-glutamyl transpeptidase level was normal. Routine urine test revealed increased glucose as well as red and white blood cells. On genetic analysis, the infant was proved to be homologous for a VPS33B mutation c.1594C>T(p.R532X). She was definitely diagnosed to have ARC syndrome. Symptomatic and supportive therapy was given, but no improvement was observed, and the infant finally died at 3 months and 29 days of life.
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Affiliation(s)
- Da-Gui Huang
- Department of Pediatrics, The First Affiliated Hospital, Jinan University, Guangzhou 510630, China.
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16
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Gruber R, Rogerson C, Windpassinger C, Banushi B, Straatman-Iwanowska A, Hanley J, Forneris F, Strohal R, Ulz P, Crumrine D, Menon GK, Blunder S, Schmuth M, Müller T, Smith H, Mills K, Kroisel P, Janecke AR, Gissen P. Autosomal Recessive Keratoderma-Ichthyosis-Deafness (ARKID) Syndrome Is Caused by VPS33B Mutations Affecting Rab Protein Interaction and Collagen Modification. J Invest Dermatol 2017; 137:845-854. [PMID: 28017832 PMCID: PMC5358661 DOI: 10.1016/j.jid.2016.12.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 11/30/2016] [Accepted: 12/02/2016] [Indexed: 12/21/2022]
Abstract
In this paper, we report three patients with severe palmoplantar keratoderma associated with ichthyosis and sensorineural deafness. Biallelic mutations were found in VPS33B, encoding VPS33B, a Sec1/Munc18 family protein that interacts with Rab11a and Rab25 proteins and is involved in trafficking of the collagen-modifying enzyme LH3. Two patients were homozygous for the missense variant p.Gly131Glu, whereas one patient was compound heterozygous for p.Gly131Glu and the splice site mutation c.240-1G>C, previously reported in patients with arthrogryposis renal dysfunction and cholestasis syndrome. We demonstrated the pathogenicity of variant p.Gly131Glu by assessing the interactions of the mutant VPS33B construct and its ability to traffic LH3. Compared with wild-type VPS33B, the p.Gly131Glu mutant VPS33B had reduced coimmunoprecipitation and colocalization with Rab11a and Rab25 and did not rescue LH3 trafficking. Confirming the cell-based experiments, we found deficient LH3-specific collagen lysine modifications in patients' urine and skin fibroblasts. Additionally, the epidermal ultrastructure of the p.Gly131Glu patients mirrored defects in tamoxifen-inducible VPS33B-deficient Vps33bfl/fl-ERT2 mice. Both patients and murine models revealed an impaired epidermal structure, ascribed to aberrant secretion of lamellar bodies, which are essential for epidermal barrier formation. Our results demonstrate that p.Gly131Glu mutant VPS33B causes an autosomal recessive keratoderma-ichthyosis-deafness syndrome.
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Key Words
- arc, arthrogryposis renal dysfunction and cholestasis
- arkid, autosomal recessive keratoderma-ichthyosis-deafness
- co-ip, co-immunoprecipitation
- corvet, core vacuole/endosome tethering
- hops, homotypic fusion and vacuole protein sorting
- lb, lamellar body
- mimcd3, murine inner medullary collecting duct 3
- ppk, palmoplantar keratoderma
- snp, single nucleotide polymorphism
- vws, vohwinkel syndrome
- wt, wild type
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Affiliation(s)
- Robert Gruber
- Department of Dermatology, Medical University of Innsbruck, Innsbruck, Austria; Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Clare Rogerson
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK; Institute of Child Health, University College London, London, UK
| | | | - Blerida Banushi
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK; Institute of Child Health, University College London, London, UK
| | - Anna Straatman-Iwanowska
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK; Institute of Child Health, University College London, London, UK
| | - Joanna Hanley
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK; Institute of Child Health, University College London, London, UK
| | - Federico Forneris
- The Armenise-Harvard Laboratory of Structural Biology, Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Robert Strohal
- Department of Dermatology, Academic Teaching Hospital Feldkirch, Feldkirch, Austria
| | - Peter Ulz
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Debra Crumrine
- Department of Dermatology, Veterans Affairs Medical Center, University of California, San Francisco, California, USA
| | | | - Stefan Blunder
- Department of Dermatology, Medical University of Innsbruck, Innsbruck, Austria
| | - Matthias Schmuth
- Department of Dermatology, Medical University of Innsbruck, Innsbruck, Austria
| | - Thomas Müller
- Department of Pediatrics I, Medical University of Innsbruck, Innsbruck, Austria
| | - Holly Smith
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Kevin Mills
- Institute of Child Health, University College London, London, UK
| | - Peter Kroisel
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Andreas R Janecke
- Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria; Department of Pediatrics I, Medical University of Innsbruck, Innsbruck, Austria.
| | - Paul Gissen
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK; Institute of Child Health, University College London, London, UK; Inherited Metabolic Diseases Unit, Great Ormond Street Hospital, London, UK.
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17
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Chen CH, Lo RW, Urban D, Pluthero FG, Kahr WHA. α-granule biogenesis: from disease to discovery. Platelets 2017; 28:147-154. [DOI: 10.1080/09537104.2017.1280599] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Chang Hua Chen
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Richard W. Lo
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Denisa Urban
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Fred G. Pluthero
- Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Walter H. A. Kahr
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
- Division of Haematology/Oncology, Department of Paediatrics, University of Toronto and The Hospital for Sick Children, Toronto, ON, Canada
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18
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Gengyo-Ando K, Kage-Nakadai E, Yoshina S, Otori M, Kagawa-Nagamura Y, Nakai J, Mitani S. Distinct roles of the two VPS33 proteins in the endolysosomal system in Caenorhabditis elegans. Traffic 2016; 17:1197-1213. [PMID: 27558849 DOI: 10.1111/tra.12430] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 08/18/2016] [Accepted: 08/18/2016] [Indexed: 02/02/2023]
Abstract
Sec1/Munc-18 (SM) family proteins are essential regulators in intracellular transport in eukaryotic cells. The SM protein Vps33 functions as a core subunit of two tethering complexes, class C core vacuole/endosome tethering (CORVET) and homotypic fusion and vacuole protein sorting (HOPS) in the endocytic pathway in yeast. Metazoan cells possess two Vps33 proteins, VPS33A and VPS33B, but their precise roles remain unknown. Here, we present a comparative analysis of Caenorhabditis elegans null mutants for these proteins. We found that the vps-33.1 (VPS33A) mutants exhibited severe defects in both endocytic function and endolysosomal biogenesis in scavenger cells. Furthermore, vps-33.1 mutations caused endocytosis defects in other tissues, and the loss of maternal and zygotic VPS-33.1 resulted in embryonic lethality. By contrast, vps-33.2 mutants were viable but sterile, with terminally arrested spermatocytes. The spermatogenesis phenotype suggests that VPS33.2 is involved in the formation of a sperm-specific organelle. The endocytosis defect in the vps-33.1 mutant was not restored by the expression of VPS-33.2, which indicates that these proteins have nonredundant functions. Together, our data suggest that VPS-33.1 shares most of the general functions of yeast Vps33 in terms of tethering complexes in the endolysosomal system, whereas VPS-33.2 has tissue/organelle specific functions in C. elegans.
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Affiliation(s)
- Keiko Gengyo-Ando
- Department of Physiology, Tokyo Women's Medical University School of Medicine, Tokyo, Japan. .,Brain and Body System Science Institute, Saitama University, Saitama, Japan. .,Graduate School of Science and Engineering, Saitama University, Saitama, Japan.
| | - Eriko Kage-Nakadai
- Department of Physiology, Tokyo Women's Medical University School of Medicine, Tokyo, Japan.,The OCU Advanced Research Institute for Natural Science and Technology, Osaka City University, Osaka, Japan
| | - Sawako Yoshina
- Department of Physiology, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Muneyoshi Otori
- Department of Physiology, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Yuko Kagawa-Nagamura
- Brain and Body System Science Institute, Saitama University, Saitama, Japan.,Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Junichi Nakai
- Brain and Body System Science Institute, Saitama University, Saitama, Japan.,Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Shohei Mitani
- Department of Physiology, Tokyo Women's Medical University School of Medicine, Tokyo, Japan.
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19
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van der Kant R, Jonker CTH, Wijdeven RH, Bakker J, Janssen L, Klumperman J, Neefjes J. Characterization of the Mammalian CORVET and HOPS Complexes and Their Modular Restructuring for Endosome Specificity. J Biol Chem 2015; 290:30280-90. [PMID: 26463206 DOI: 10.1074/jbc.m115.688440] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Indexed: 01/30/2023] Open
Abstract
Trafficking of cargo through the endosomal system depends on endosomal fusion events mediated by SNARE proteins, Rab-GTPases, and multisubunit tethering complexes. The CORVET and HOPS tethering complexes, respectively, regulate early and late endosomal tethering and have been characterized in detail in yeast where their sequential membrane targeting and assembly is well understood. Mammalian CORVET and HOPS subunits significantly differ from their yeast homologues, and novel proteins with high homology to CORVET/HOPS subunits have evolved. However, an analysis of the molecular interactions between these subunits in mammals is lacking. Here, we provide a detailed analysis of interactions within the mammalian CORVET and HOPS as well as an additional endosomal-targeting complex (VIPAS39-VPS33B) that does not exist in yeast. We show that core interactions within CORVET and HOPS are largely conserved but that the membrane-targeting module in HOPS has significantly changed to accommodate binding to mammalian-specific RAB7 interacting lysosomal protein (RILP). Arthrogryposis-renal dysfunction-cholestasis (ARC) syndrome-associated mutations in VPS33B selectively disrupt recruitment to late endosomes by RILP or binding to its partner VIPAS39. Within the shared core of CORVET/HOPS, we find that VPS11 acts as a molecular switch that binds either CORVET-specific TGFBRAP1 or HOPS-specific VPS39/RILP thereby allowing selective targeting of these tethering complexes to early or late endosomes to time fusion events in the endo/lysosomal pathway.
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Affiliation(s)
- Rik van der Kant
- From the Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, 1066 CX, The Netherlands and
| | - Caspar T H Jonker
- Department of Cell Biology, Center of Molecular Medicine, Utrecht, 3584 CX, The Netherlands
| | - Ruud H Wijdeven
- From the Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, 1066 CX, The Netherlands and
| | - Jeroen Bakker
- From the Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, 1066 CX, The Netherlands and
| | - Lennert Janssen
- From the Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, 1066 CX, The Netherlands and
| | - Judith Klumperman
- Department of Cell Biology, Center of Molecular Medicine, Utrecht, 3584 CX, The Netherlands
| | - Jacques Neefjes
- From the Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, 1066 CX, The Netherlands and
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20
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Xiang B, Zhang G, Ye S, Zhang R, Huang C, Liu J, Tao M, Ruan C, Smyth SS, Whiteheart SW, Li Z. Characterization of a Novel Integrin Binding Protein, VPS33B, Which Is Important for Platelet Activation and In Vivo Thrombosis and Hemostasis. Circulation 2015; 132:2334-44. [PMID: 26399659 DOI: 10.1161/circulationaha.115.018361] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 09/08/2015] [Indexed: 11/16/2022]
Abstract
BACKGROUND Integrins are heterodimeric (α/β) membrane proteins that play fundamental roles in many biological processes, for example, cell adhesion and spreading, which are important for platelet function and hemostasis. The molecular mechanism that regulates integrin activation is not completely understood. METHODS AND RESULTS Here, we show that VPS33B, a member of the Sec1/Munc18 family, binds directly to the integrin β subunit. Overexpression of VPS33B in Chinese hamster ovary cells potentiated αIIbβ3 outside-in signaling but not inside-out signaling. Platelets, from megakaryocyte- and platelet-specific VPS33B conditional knockout mice, had normal morphology, yet their spreading on fibrinogen was impaired and they failed to support clot retraction. Platelet aggregation and ATP secretion in response to low-dose agonists were reduced in the VPS33B knockout mice. αIIbβ3-mediated endocytosis of fibrinogen was also defective. Tail bleeding times and times to occlusion in an FeCl3-induced thrombosis model were prolonged in the VPS33B knockout mice. Furthermore, VPS33B acted upstream of the RhoA-ROCK-MLC and Rac1-dependent pathways that lead to clot retraction and cell spreading, respectively. CONCLUSIONS Our work demonstrates that vesicular trafficking complexes, containing VPS33B, are a novel class of modifiers of integrin function. Our data also provide insights into the molecular mechanism and treatment of arthrogryposis, renal dysfunction, and cholestasis syndrome.
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Affiliation(s)
- Binggang Xiang
- From Division of Cardiovascular Medicine, Saha Cardiovascular Research Center (B.X., G.Z., S.Y., R.Z., S.S.S., Z.L.), Department of Molecular and Cellular Biochemistry (S.Y., S.W.W.), and Markey Cancer Center (C.H.), University of Kentucky, Lexington; Department of Biochemistry and Molecular Biology, Mayo Clinic in Arizona, Scottsdale (J.L.); Department of Oncology (M.T.) and Jiangsu Institute of Hematology, Department of Hematology (C.R.), First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China; and Lexington Veterans Affairs Medical Center, Lexington, KY (S.S.S.)
| | - Guoying Zhang
- From Division of Cardiovascular Medicine, Saha Cardiovascular Research Center (B.X., G.Z., S.Y., R.Z., S.S.S., Z.L.), Department of Molecular and Cellular Biochemistry (S.Y., S.W.W.), and Markey Cancer Center (C.H.), University of Kentucky, Lexington; Department of Biochemistry and Molecular Biology, Mayo Clinic in Arizona, Scottsdale (J.L.); Department of Oncology (M.T.) and Jiangsu Institute of Hematology, Department of Hematology (C.R.), First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China; and Lexington Veterans Affairs Medical Center, Lexington, KY (S.S.S.)
| | - Shaojing Ye
- From Division of Cardiovascular Medicine, Saha Cardiovascular Research Center (B.X., G.Z., S.Y., R.Z., S.S.S., Z.L.), Department of Molecular and Cellular Biochemistry (S.Y., S.W.W.), and Markey Cancer Center (C.H.), University of Kentucky, Lexington; Department of Biochemistry and Molecular Biology, Mayo Clinic in Arizona, Scottsdale (J.L.); Department of Oncology (M.T.) and Jiangsu Institute of Hematology, Department of Hematology (C.R.), First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China; and Lexington Veterans Affairs Medical Center, Lexington, KY (S.S.S.)
| | - Rui Zhang
- From Division of Cardiovascular Medicine, Saha Cardiovascular Research Center (B.X., G.Z., S.Y., R.Z., S.S.S., Z.L.), Department of Molecular and Cellular Biochemistry (S.Y., S.W.W.), and Markey Cancer Center (C.H.), University of Kentucky, Lexington; Department of Biochemistry and Molecular Biology, Mayo Clinic in Arizona, Scottsdale (J.L.); Department of Oncology (M.T.) and Jiangsu Institute of Hematology, Department of Hematology (C.R.), First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China; and Lexington Veterans Affairs Medical Center, Lexington, KY (S.S.S.)
| | - Cai Huang
- From Division of Cardiovascular Medicine, Saha Cardiovascular Research Center (B.X., G.Z., S.Y., R.Z., S.S.S., Z.L.), Department of Molecular and Cellular Biochemistry (S.Y., S.W.W.), and Markey Cancer Center (C.H.), University of Kentucky, Lexington; Department of Biochemistry and Molecular Biology, Mayo Clinic in Arizona, Scottsdale (J.L.); Department of Oncology (M.T.) and Jiangsu Institute of Hematology, Department of Hematology (C.R.), First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China; and Lexington Veterans Affairs Medical Center, Lexington, KY (S.S.S.)
| | - Jun Liu
- From Division of Cardiovascular Medicine, Saha Cardiovascular Research Center (B.X., G.Z., S.Y., R.Z., S.S.S., Z.L.), Department of Molecular and Cellular Biochemistry (S.Y., S.W.W.), and Markey Cancer Center (C.H.), University of Kentucky, Lexington; Department of Biochemistry and Molecular Biology, Mayo Clinic in Arizona, Scottsdale (J.L.); Department of Oncology (M.T.) and Jiangsu Institute of Hematology, Department of Hematology (C.R.), First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China; and Lexington Veterans Affairs Medical Center, Lexington, KY (S.S.S.)
| | - Min Tao
- From Division of Cardiovascular Medicine, Saha Cardiovascular Research Center (B.X., G.Z., S.Y., R.Z., S.S.S., Z.L.), Department of Molecular and Cellular Biochemistry (S.Y., S.W.W.), and Markey Cancer Center (C.H.), University of Kentucky, Lexington; Department of Biochemistry and Molecular Biology, Mayo Clinic in Arizona, Scottsdale (J.L.); Department of Oncology (M.T.) and Jiangsu Institute of Hematology, Department of Hematology (C.R.), First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China; and Lexington Veterans Affairs Medical Center, Lexington, KY (S.S.S.)
| | - Changgeng Ruan
- From Division of Cardiovascular Medicine, Saha Cardiovascular Research Center (B.X., G.Z., S.Y., R.Z., S.S.S., Z.L.), Department of Molecular and Cellular Biochemistry (S.Y., S.W.W.), and Markey Cancer Center (C.H.), University of Kentucky, Lexington; Department of Biochemistry and Molecular Biology, Mayo Clinic in Arizona, Scottsdale (J.L.); Department of Oncology (M.T.) and Jiangsu Institute of Hematology, Department of Hematology (C.R.), First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China; and Lexington Veterans Affairs Medical Center, Lexington, KY (S.S.S.)
| | - Susan S Smyth
- From Division of Cardiovascular Medicine, Saha Cardiovascular Research Center (B.X., G.Z., S.Y., R.Z., S.S.S., Z.L.), Department of Molecular and Cellular Biochemistry (S.Y., S.W.W.), and Markey Cancer Center (C.H.), University of Kentucky, Lexington; Department of Biochemistry and Molecular Biology, Mayo Clinic in Arizona, Scottsdale (J.L.); Department of Oncology (M.T.) and Jiangsu Institute of Hematology, Department of Hematology (C.R.), First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China; and Lexington Veterans Affairs Medical Center, Lexington, KY (S.S.S.)
| | - Sidney W Whiteheart
- From Division of Cardiovascular Medicine, Saha Cardiovascular Research Center (B.X., G.Z., S.Y., R.Z., S.S.S., Z.L.), Department of Molecular and Cellular Biochemistry (S.Y., S.W.W.), and Markey Cancer Center (C.H.), University of Kentucky, Lexington; Department of Biochemistry and Molecular Biology, Mayo Clinic in Arizona, Scottsdale (J.L.); Department of Oncology (M.T.) and Jiangsu Institute of Hematology, Department of Hematology (C.R.), First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China; and Lexington Veterans Affairs Medical Center, Lexington, KY (S.S.S.)
| | - Zhenyu Li
- From Division of Cardiovascular Medicine, Saha Cardiovascular Research Center (B.X., G.Z., S.Y., R.Z., S.S.S., Z.L.), Department of Molecular and Cellular Biochemistry (S.Y., S.W.W.), and Markey Cancer Center (C.H.), University of Kentucky, Lexington; Department of Biochemistry and Molecular Biology, Mayo Clinic in Arizona, Scottsdale (J.L.); Department of Oncology (M.T.) and Jiangsu Institute of Hematology, Department of Hematology (C.R.), First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China; and Lexington Veterans Affairs Medical Center, Lexington, KY (S.S.S.)
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21
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Visanji NP, Kamali Sarvestani I, Creed MC, Shams Shoaei Z, Nobrega JN, Hamani C, Hazrati LN. Deep brain stimulation of the subthalamic nucleus preferentially alters the translational profile of striatopallidal neurons in an animal model of Parkinson's disease. Front Cell Neurosci 2015; 9:221. [PMID: 26106299 PMCID: PMC4460554 DOI: 10.3389/fncel.2015.00221] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/25/2015] [Indexed: 01/17/2023] Open
Abstract
Deep brain stimulation targeting the subthalamic nucleus (STN-DBS) is an effective surgical treatment for the motor symptoms of Parkinson's disease (PD), the precise neuronal mechanisms of which both at molecular and network levels remain a topic of debate. Here we employ two transgenic mouse lines, combining translating ribosomal affinity purification (TRAP) with bacterial artificial chromosome expression (Bac), to selectively identify changes in translational gene expression in either Drd1a-expressing striatonigral or Drd2-expressing striatopallidal medium spiny neurons (MSNs) of the striatum following STN-DBS. 6-hydroxydopamine lesioned mice received either 5 days stimulation via a DBS electrode implanted in the ipsilateral STN or 5 days sham treatment (no stimulation). Striatal polyribosomal RNA was selectively purified from either Drd2 or Drd1a MSNs using the TRAP method and gene expression profiling performed. We identified eight significantly altered genes in Drd2 MSNs (Vps33b, Ppp1r3c, Mapk4, Sorcs2, Neto1, Abca1, Penk1, and Gapdh) and two overlapping genes in Drd1a MSNs (Penk1 and Ppp1r3c) implicated in the molecular mechanisms of STN-DBS. A detailed functional analysis, using a further 728 probes implicated in STN-DBS, suggested an increased ability to receive excitation (mediated by increased dendritic spines, increased calcium influx and enhanced excitatory post synaptic potentials) accompanied by processes that would hamper the initiation of action potentials, transport of neurotransmitters from soma to axon terminals and vesicular release in Drd2-expressing MSNs. Finally, changes in expression of several genes involved in apoptosis as well as cholesterol and fatty acid metabolism were also identified. This increased understanding of the molecular mechanisms induced by STN-DBS may reveal novel targets for future non-surgical therapies for PD.
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Affiliation(s)
- Naomi P Visanji
- Morton and Gloria Shulman Movement Disorders Centre and the Edmund J. Safra Program in Parkinson's disease, Toronto Western Hospital Toronto, ON, Canada
| | - Iman Kamali Sarvestani
- Faculty of Medicine, Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto Toronto, ON, Canada ; Department of Neuroscience, Stockholm Brain Institute, Karolinska Institute Stockholm, Sweden
| | - Meaghan C Creed
- Behavioural Neurobiology Laboratory, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health Toronto, ON, Canada
| | - Zahra Shams Shoaei
- Faculty of Medicine, Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto Toronto, ON, Canada
| | - José N Nobrega
- Behavioural Neurobiology Laboratory, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health Toronto, ON, Canada
| | - Clement Hamani
- Behavioural Neurobiology Laboratory, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health Toronto, ON, Canada ; Division of Neurosurgery, Toronto Western Hospital, University of Toronto Toronto, ON, Canada
| | - Lili-Naz Hazrati
- Faculty of Medicine, Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto Toronto, ON, Canada
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Solinger JA, Spang A. Loss of the Sec1/Munc18-family proteins VPS-33.2 and VPS-33.1 bypasses a block in endosome maturation in Caenorhabditis elegans. Mol Biol Cell 2014; 25:3909-25. [PMID: 25273556 PMCID: PMC4244200 DOI: 10.1091/mbc.e13-12-0710] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Evidence is presented for the existence of HOPS and CORVET tethering complexes in metazoans. A role is shown for the SM protein components of tethers in controlling the flux of material through the endosomal system. The end of the life of a transport vesicle requires a complex series of tethering, docking, and fusion events. Tethering complexes play a crucial role in the recognition of membrane entities and bringing them into close opposition, thereby coordinating and controlling cellular trafficking events. Here we provide a comprehensive RNA interference analysis of the CORVET and HOPS tethering complexes in metazoans. Knockdown of CORVET components promoted RAB-7 recruitment to subapical membranes, whereas in HOPS knockdowns, RAB-5 was found also on membrane structures close to the cell center, indicating the RAB conversion might be impaired in the absence of these tethering complexes. Unlike in yeast, metazoans have two VPS33 homologues, which are Sec1/Munc18 (SM)-family proteins involved in the regulation of membrane fusion. We assume that in wild type, each tethering complex contains a specific SM protein but that they may be able to substitute for each other in case of absence of the other. Of importance, knockdown of both SM proteins allowed bypass of the endosome maturation block in sand-1 mutants. We propose a model in which the SM proteins in tethering complexes are required for coordinated flux of material through the endosomal system.
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Affiliation(s)
- Jachen A Solinger
- Growth and Development, Biozentrum, University of Basel, CH-4056 Basel, Switzerland
| | - Anne Spang
- Growth and Development, Biozentrum, University of Basel, CH-4056 Basel, Switzerland
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Zhou Y, Zhang J. Arthrogryposis-renal dysfunction-cholestasis (ARC) syndrome: from molecular genetics to clinical features. Ital J Pediatr 2014; 40:77. [PMID: 25239142 PMCID: PMC4422138 DOI: 10.1186/s13052-014-0077-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 09/01/2014] [Indexed: 12/22/2022] Open
Abstract
UNLABELLED Arthrogryposis-renal dysfunction-cholestasis (ARC) syndrome is a rare but fatal autosomal recessive multisystem disorder caused by mutations in the VPS33B or VIPAR gene. The classical presentation of ARC includes congenital joint contractures, renal tubular dysfunction, and cholestasis. Additional features include ichthyosis, central nervous system malformation, platelet anomalies, and severe failure to thrive. Diagnosis of ARC syndrome relies on clinical features, organ biopsy, and mutational analysis. However, no specific treatment currently exists for this syndrome. CONCLUSION This is an overview of the latest knowledge regarding the genetic features and clinical manifestations of ARC syndrome. Greater awareness and understanding of this syndrome should allow more timely intervention with potential for improving long-term outcome.
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Affiliation(s)
- Yaoyao Zhou
- Department of Cardiology, No. 3 People's Hospital, Shanghai Jiao Tong University School of Medicine, No. 280, Mohe Road, Baoshan District, 201900, Shanghai, China.
| | - Junfeng Zhang
- Department of Cardiology, No. 3 People's Hospital, Shanghai Jiao Tong University School of Medicine, No. 280, Mohe Road, Baoshan District, 201900, Shanghai, China.
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24
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Abstract
Membrane trafficking depends on transport vesicles and carriers docking and fusing with the target organelle for the delivery of cargo. Membrane tethers and small guanosine triphosphatases (GTPases) mediate the docking of transport vesicles/carriers to enhance the efficiency of the subsequent SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor)-mediated fusion event with the target membrane bilayer. Different classes of membrane tethers and their specific intracellular location throughout the endomembrane system are now well defined. Recent biochemical and structural studies have led to a deeper understanding of the mechanism by which membrane tethers mediate docking of membrane carriers as well as an appreciation of the role of tethers in coordinating the correct SNARE complex and in regulating the organization of membrane compartments. This review will summarize the properties and roles of membrane tethers of both secretory and endocytic systems.
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Affiliation(s)
- Pei Zhi Cheryl Chia
- National Institute of Dental and Craniofacial Research, National Institutes of Health30 Convent Drive, Bethesda, MD 20892-4340USA
| | - Paul A. Gleeson
- The Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute30 Flemington Road, The University of Melbourne, Victoria 3010Australia
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25
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Tornieri K, Zlatic SA, Mullin AP, Werner E, Harrison R, L'hernault SW, Faundez V. Vps33b pathogenic mutations preferentially affect VIPAS39/SPE-39-positive endosomes. Hum Mol Genet 2013; 22:5215-28. [PMID: 23918659 DOI: 10.1093/hmg/ddt378] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mutations in Vps33 isoforms cause pigment dilution in mice (Vps33a, buff) and Drosophila (car) and the neurogenic arthrogryposis, renal dysfunction and cholestasis syndrome in humans (ARC1, VPS33B). The later disease is also caused by mutations in VIPAS39, (Vps33b interacting protein, apical-basolateral polarity regulator, SPE-39 homolog; ARC2), a protein that interacts with the HOmotypic fusion and Protein Sorting (HOPS) complex, a tether necessary for endosome-lysosome traffic. These syndromes offer insight into fundamental endosome traffic processes unique to metazoans. However, the molecular and cellular mechanisms underlying these mutant phenotypes remain poorly understood. Here we investigate interactions of wild-type and disease-causing mutations in VIPAS39/SPE-39 and Vps33b by yeast two hybrid, immunoprecipitation and quantitative fluorescent microscopy. We find that although few mutations prevent interaction between VIPAS39/SPE-39 and Vps33b, some mutants fragment VIPAS39/SPE-39-positive endosomes, but all mutants alter the subcellular localization of Vps33b to VIPAS39/SPE-39-positive endosomes. Our data suggest that the ARC syndrome may result through impaired VIPAS39/SPE-39 and Vps33b-dependent endosomal maturation or fusion.
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Holme A, Hurcombe JA, Straatman-Iwanowska A, Inward CI, Gissen P, Coward RJ. Glomerular involvement in the arthrogryposis, renal dysfunction and cholestasis syndrome. Clin Kidney J 2013; 6:183-8. [PMID: 26019847 PMCID: PMC4432437 DOI: 10.1093/ckj/sfs182] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 12/12/2012] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Arthrogryposis, renal dysfunction and cholestasis (ARC) syndrome is a multisystem autosomal-recessive disorder caused by defects in the VPS33B and VIPAR genes, involved in localization of apical membrane proteins. Affected children usually die by 1 year of age, often secondary to infective complications. The classic renal manifestation previously described in ARC syndrome is proximal-tubular dysfunction. The aim of this study is to gain further insight into the renal manifestations of this syndrome. METHODS Clinical review of three cases of ARC syndrome presenting to a tertiary centre. Together with measurement of VPS33B and VIPAR protein expression in the human glomerulus. RESULTS The cases demonstrated severe failure to thrive and in addition to commonly described features profound proteinuria and albuminuria, together with hypoalbuminaemia, suggesting glomerular involvement of this syndrome. Western blotting of conditionally immortalized human glomerular cells and ex vivo immunofluorescent analysis of the human glomerulus revealed that VPS33B and VIPAR were highly expressed in glomerular endothelium, and podocytes, but not in the mesangium. CONCLUSIONS ARC syndrome affects the glomerulus as well as the proximal tubule in the kidney. Our molecular studies suggest that both cell types that constitute the glomerular filtration barrier are affected in this condition, providing an explanation for the albuminuria that we have observed in our cases.
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Affiliation(s)
- Amelia Holme
- Department of Child and Adolescent Health , University of Bristol , Bristol , UK ; Department of Paediatric Nephrology , Bristol Royal Hospital for Children , Bristol , UK
| | | | | | - Carol I Inward
- Department of Paediatric Nephrology , Bristol Royal Hospital for Children , Bristol , UK
| | - Paul Gissen
- MRC Laboratory for Molecular Cell Biology , University College London , London , UK ; Department of Paediatric Metabolic Medicine , Great Ormond Street Hospital , London , UK
| | - Richard J Coward
- Department of Paediatric Nephrology , Bristol Royal Hospital for Children , Bristol , UK ; Academic Renal Unit , University of Bristol , Bristol , UK
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27
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Solinger JA, Spang A. Tethering complexes in the endocytic pathway: CORVET and HOPS. FEBS J 2013; 280:2743-57. [PMID: 23351085 DOI: 10.1111/febs.12151] [Citation(s) in RCA: 138] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Revised: 01/10/2013] [Accepted: 01/23/2013] [Indexed: 12/21/2022]
Abstract
Endocytosis describes the processes by which proteins, peptides and solutes, and also pathogens, enter the cell. Endocytosed material progresses to endosomes. Genetic studies in yeast, worms, flies and mammals have identified a set of universally conserved proteins that are essential for early-to-late endosome transition and lysosome biogenesis, and for endolysosomal trafficking pathways, including autophagy. The two Vps-C complexes CORVET (class C core vacuole/endosome tethering) and HOPS (homotypic fusion and vacuole protein sorting) perform diverse biochemical functions in endocytosis: they tether membranes, interact with Rab GTPases, activate and proof-read SNARE assembly to drive membrane fusion, and possibly attach endosomes to the cytoskeleton. In addition, several of the CORVET and HOPS subunits have diversified in metazoans, and probably form additional specialized complexes to accomodate the higher complexity of trafficking pathways in these cells. Recent studies offer new insights into the complex relationships between CORVET and HOPS complexes and other factors of the endolysosomal pathway. Interactions with V-ATPase, the ESCRT machinery, phosphoinositides, the cytoskeleton and the Rab switch suggest an intricate cooperative network for endosome maturation. Accumulating evidence supports the view that endosomal tethering complexes implement a regulatory logic that governs endomembrane identity and dynamics.
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28
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van der Kant R, Fish A, Janssen L, Janssen H, Krom S, Ho N, Brummelkamp T, Carette J, Rocha N, Neefjes J. Late endosomal transport and tethering are coupled processes controlled by RILP and the cholesterol sensor ORP1L. J Cell Sci 2013; 126:3462-74. [DOI: 10.1242/jcs.129270] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Late endosomes and lysosomes are dynamic organelles that constantly move and fuse to acquire cargo from early endosomes, phagosomes and autophagosome. Defects in lysosomal dynamics cause severe neurodegenerative and developmental diseases such as Niemann-Pick Type C disease and ARC syndrome, yet little is know about regulation of late endosomal fusion in a mammalian system. Mammalian endosomes destined for fusion need to be transported over very long distances before they tether to initiate contact. Here we describe that lysosomal tethering and transport are combined processes co-regulated by one multi-protein complex; RAB7-RILP-ORP1L. We show that RILP directly and concomitantly binds the tethering HOPS complex and the p150glued subunit of the dynein motor. ORP1L then functions as a cholesterol-sensing switch controlling RILP-HOPS-p150Glued interactions. We show that RILP and ORP1L control Ebola virus infection, a process dependent on late endosomal fusion. By combining recruitment and regulation of both the dynein motor and HOPS complex into a single multiprotein complex, the RAB7-RILP-ORP1L complex efficiently couples and times microtubule minus-end transport and fusion, two major events in endosomal biology.
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29
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Smith H, Galmes R, Gogolina E, Straatman-Iwanowska A, Reay K, Banushi B, Bruce CK, Cullinane AR, Romero R, Chang R, Ackermann O, Baumann C, Cangul H, Cakmak Celik F, Aygun C, Coward R, Dionisi-Vici C, Sibbles B, Inward C, Ae Kim C, Klumperman J, Knisely AS, Watson SP, Gissen P. Associations among genotype, clinical phenotype, and intracellular localization of trafficking proteins in ARC syndrome. Hum Mutat 2012; 33:1656-64. [PMID: 22753090 PMCID: PMC3746110 DOI: 10.1002/humu.22155] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 06/12/2012] [Indexed: 12/31/2022]
Abstract
Arthrogryposis-renal dysfunction-cholestasis (ARC) syndrome is a rare autosomal recessive multisystem disorder caused by mutations in vacuolar protein sorting 33 homologue B (VPS33B) and VPS33B interacting protein, apical-basolateral polarity regulator (VIPAR). Cardinal features of ARC include congenital joint contractures, renal tubular dysfunction, cholestasis, severe failure to thrive, ichthyosis, and a defect in platelet alpha-granule biogenesis. Most patients with ARC do not survive past the first year of life. We report two patients presenting with a mild ARC phenotype, now 5.5 and 3.5 years old. Both patients were compound heterozygotes with the novel VPS33B donor splice-site mutation c.1225+5G>C in common. Immunoblotting and complementary DNA analysis suggest expression of a shorter VPS33B transcript, and cell-based assays show that c.1225+5G>C VPS33B mutant retains some ability to interact with VIPAR (and thus partial wild-type function). This study provides the first evidence of genotype-phenotype correlation in ARC and suggests that VPS33B c.1225+5G>C mutation predicts a mild ARC phenotype. We have established an interactive online database for ARC (https://grenada.lumc.nl/LOVD2/ARC) comprising all known variants in VPS33B and VIPAR. Also included in the database are 15 novel pathogenic variants in VPS33B and five in VIPAR.
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Affiliation(s)
- Holly Smith
- Medical and Molecular Genetics, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of BirminghamBirmingham, United Kingdom
- University College London Institute of Child Health, University College LondonLondon, United Kingdom
| | - Romain Galmes
- Department of Cell Biology, University Medical CenterUtrecht, the Netherlands
| | - Ekaterina Gogolina
- Medical Research Council Laboratory for Molecular Cell Biology, University College LondonLondon, United Kingdom
- University College London Institute of Child Health, University College LondonLondon, United Kingdom
- Medical School, Edinburgh UniversityEdinburgh, United Kingdom
| | - Anna Straatman-Iwanowska
- Medical Research Council Laboratory for Molecular Cell Biology, University College LondonLondon, United Kingdom
- University College London Institute of Child Health, University College LondonLondon, United Kingdom
| | - Kim Reay
- West Midlands Regional Genetics Laboratory, Birmingham Women's HospitalBirmingham, United Kingdom
| | - Blerida Banushi
- Medical and Molecular Genetics, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of BirminghamBirmingham, United Kingdom
- University College London Institute of Child Health, University College LondonLondon, United Kingdom
| | - Christopher K Bruce
- Medical and Molecular Genetics, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of BirminghamBirmingham, United Kingdom
| | - Andrew R Cullinane
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of HealthBethesda, Maryland
| | - Rene Romero
- Emory Children's Center Division of Gastroenterology, Hepatology, and NutritionAtlanta, Georgia
| | - Richard Chang
- Division of Metabolic Disorders, Children's Hospital of Orange CountyOrange, California
| | | | | | - Hakan Cangul
- Medical and Molecular Genetics, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of BirminghamBirmingham, United Kingdom
| | | | - Canan Aygun
- Neonatology Unit, Mayis UniversitySamsun, Turkey
| | - Richard Coward
- Bristol Royal Hospital for Sick ChildrenBristol, United Kingdom
| | - Carlo Dionisi-Vici
- Division of Metabolism, Bambino Gesú Children's Hospital IRCCSRome, Italy
| | - Barbara Sibbles
- Erasmus University Medical Center, Sophia Children's HospitalRotterdam, the Netherlands
| | - Carol Inward
- Bristol Royal Hospital for Sick ChildrenBristol, United Kingdom
| | - Chong Ae Kim
- Department of Pediatrics, Instituto da Criança, University of Sao PauloSao Paulo, Brazil
| | - Judith Klumperman
- Department of Cell Biology, University Medical CenterUtrecht, the Netherlands
| | - A S Knisely
- Institute of Liver Studies/Histopathology, King's College HospitalLondon, United Kingdom
| | - Steven P Watson
- The Platelet Group, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of BirminghamBirmingham, United Kingdom
| | - Paul Gissen
- Medical Research Council Laboratory for Molecular Cell Biology, University College LondonLondon, United Kingdom
- University College London Institute of Child Health, University College LondonLondon, United Kingdom
- Inherited Metabolic Diseases, Great Ormond Street HospitalLondon, United Kingdom
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30
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An integrated approach to uncover drivers of cancer. Cell 2010; 143:1005-17. [PMID: 21129771 DOI: 10.1016/j.cell.2010.11.013] [Citation(s) in RCA: 354] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Revised: 08/31/2010] [Accepted: 10/22/2010] [Indexed: 11/23/2022]
Abstract
Systematic characterization of cancer genomes has revealed a staggering number of diverse aberrations that differ among individuals, such that the functional importance and physiological impact of most tumor genetic alterations remain poorly defined. We developed a computational framework that integrates chromosomal copy number and gene expression data for detecting aberrations that promote cancer progression. We demonstrate the utility of this framework using a melanoma data set. Our analysis correctly identified known drivers of melanoma and predicted multiple tumor dependencies. Two dependencies, TBC1D16 and RAB27A, confirmed empirically, suggest that abnormal regulation of protein trafficking contributes to proliferation in melanoma. Together, these results demonstrate the ability of integrative Bayesian approaches to identify candidate drivers with biological, and possibly therapeutic, importance in cancer.
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31
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Cullinane AR, Straatman-Iwanowska A, Zaucker A, Wakabayashi Y, Bruce CK, Luo G, Rahman F, Gürakan F, Utine E, Ozkan TB, Denecke J, Vukovic J, Di Rocco M, Mandel H, Cangul H, Matthews RP, Thomas SG, Rappoport JZ, Arias IM, Wolburg H, Knisely AS, Kelly DA, Müller F, Maher ER, Gissen P. Mutations in VIPAR cause an arthrogryposis, renal dysfunction and cholestasis syndrome phenotype with defects in epithelial polarization. Nat Genet 2010; 42:303-12. [PMID: 20190753 PMCID: PMC5308204 DOI: 10.1038/ng.538] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2009] [Accepted: 01/25/2010] [Indexed: 02/06/2023]
Abstract
Arthrogryposis, renal dysfunction and cholestasis syndrome (ARC) is a multisystem disorder associated with abnormalities in polarized liver and kidney cells. Mutations in VPS33B account for most cases of ARC. We identified mutations in VIPAR (also called C14ORF133) in individuals with ARC without VPS33B defects. We show that VIPAR forms a functional complex with VPS33B that interacts with RAB11A. Knockdown of vipar in zebrafish resulted in biliary excretion and E-cadherin defects similar to those in individuals with ARC. Vipar- and Vps33b-deficient mouse inner medullary collecting duct (mIMDC-3) cells expressed membrane proteins abnormally and had structural and functional tight junction defects. Abnormal Ceacam5 expression was due to mis-sorting toward lysosomal degradation, but reduced E-cadherin levels were associated with transcriptional downregulation. The VPS33B-VIPAR complex thus has diverse functions in the pathways regulating apical-basolateral polarity in the liver and kidney.
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Affiliation(s)
- Andrew R Cullinane
- Medical and Molecular Genetics, School of Clinical and Experimental Medicine, University of Birmingham, Birmingham, UK
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32
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Cullinane AR, Straatman-Iwanowska A, Seo JK, Ko JS, Song KS, Gizewska M, Gruszfeld D, Gliwicz D, Tuysuz B, Erdemir G, Sougrat R, Wakabayashi Y, Hinds R, Barnicoat A, Mandel H, Chitayat D, Fischler B, Garcia-Cazorla A, Knisely AS, Kelly DA, Maher ER, Gissen P. Molecular investigations to improve diagnostic accuracy in patients with ARC syndrome. Hum Mutat 2009; 30:E330-7. [PMID: 18853461 DOI: 10.1002/humu.20900] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Arthrogryposis, Renal dysfunction and Cholestasis (ARC) syndrome is a multi-system autosomal recessive disorder caused by germline mutations in VPS33B. The detection of germline VPS33B mutations removes the need for diagnostic organ biopsies (these carry a>50% risk of life-threatening haemorrhage due to platelet dysfunction); however, VPS33B mutations are not detectable in approximately 25% of patients. In order further to define the molecular basis of ARC we performed mutation analysis and mRNA and protein studies in patients with a clinical diagnosis of ARC. Here we report novel mutations in VPS33B in patients from Eastern Europe and South East Asia. One of the mutations was present in 7 unrelated Korean patients. Reduced expression of VPS33B and cellular phenotype was detected in fibroblasts from patients clinically diagnosed with ARC with and without known VPS33B mutations. One mutation-negative patient was found to have normal mRNA and protein levels. This patient's clinical condition improved and he is alive at the age of 2.5 years. Thus we show that all patients with a classical clinical course of ARC had decreased expression of VPS33B whereas normal VPS33B expression was associated with good prognosis despite initial diagnosis of ARC.
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Affiliation(s)
- Andrew R Cullinane
- Department of Medical and Molecular Genetics, University of Birmingham, Birmingham, UK
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Pryor PR, Luzio JP. Delivery of endocytosed membrane proteins to the lysosome. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2009; 1793:615-24. [DOI: 10.1016/j.bbamcr.2008.12.022] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2008] [Revised: 12/01/2008] [Accepted: 12/12/2008] [Indexed: 01/21/2023]
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34
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Navarro RE, Ramos-Balderas JL, Guerrero I, Pelcastre V, Maldonado E. Pigment dilution mutants from fish models with connection to lysosome-related organelles and vesicular traffic genes. Zebrafish 2009; 5:309-18. [PMID: 19133829 DOI: 10.1089/zeb.2008.0549] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
An interesting question in developmental biology is why mutations in genes with functions essential for the majority of cells produce diseases affecting only specific tissues. For example, pigment dilution disorders are often the consequence of mutations in conserved vesicular traffic genes. In Hermansky-Pudlak, Griscelli, and Chediak-Higashi pigment dilution syndromes, vesicular traffic mutations affect several organs with one characteristic in common: to carry out their functions they depend to a great extent on lysosome-related organelles (LROs), such as the melanosomes in melanocytes. Conserved multimeric complexes, present in most cell types, target proteins to lysosomes or selected LROs using transport vesicles. By studying these diseases or the model organisms that are defective in these processes, we have learned that every cell type possesses a unique way to regulate its vesicular traffic machinery and to assemble its multimeric complexes. This is accomplished by subunits from these multimeric complexes acting in a cell-specific manner. Here, we review several fish pigment dilution mutants that represent models for human vesicular traffic diseases.
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Affiliation(s)
- Rosa E Navarro
- Departamento de Biología Celular, Instituto de Fisiología Celular , Universidad Nacional Autónoma de México, UNAM, México City, México
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35
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Abstract
OBJECTIVES ARC (arthrogryposis, renal dysfunction, and cholestasis) syndrome is a rare, fatal cause of neonatal intrahepatic cholestasis without known treatment modalities and has recently been ascribed to a mutation in the VPS33B gene. We assessed the clinical characteristics and investigated the VPS33B mutations in Korean patients with ARC syndrome. PATIENTS AND METHODS We reviewed the medical records of 6 patients with ARC syndrome among 90 patients with neonatal cholestasis from 2000 to 2005 and assessed the relative incidence rate ratio, clinical symptoms, laboratory findings, and pathological findings. DNA samples from 5 patients, 4 parents, and 2 fetuses were analyzed for VPS33B mutations. RESULTS The relative incidence rate ratio was 1/7 that of biliary atresia (95% CI 0.33-0.06). All 6 patients presented with ichthyosis and recurrent infection, and failed to thrive with the 3 main symptoms. All of the patients died within the age of 12 months. They had various severities of cholestasis, metabolic acidosis, nephrogenic diabetes insipidus, chronic diarrhea, platelet abnormalities, and central nervous system anomalies. We identified 1 novel c.403+2T>A splice-site mutation, 2 frame-shift mutations (c.1509_1510insG, c.790_791del), 1 nonsense mutation (c.661C>A), and 1 known nonsense mutation (c.1518C>T) in the VPS33B gene. Prenatal diagnosis was performed in 2 different families. CONCLUSIONS This study indicates that the incidence of ARC syndrome is not as rare as has been thought. We found 4 novel and 1 known mutations in ARC syndrome patients and performed prenatal diagnosis in 2 families, which will facilitate genetic diagnosis and counseling for affected families.
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Akbar MA, Ray S, Krämer H. The SM protein Car/Vps33A regulates SNARE-mediated trafficking to lysosomes and lysosome-related organelles. Mol Biol Cell 2009; 20:1705-14. [PMID: 19158398 PMCID: PMC2655250 DOI: 10.1091/mbc.e08-03-0282] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2008] [Revised: 11/25/2008] [Accepted: 01/09/2009] [Indexed: 01/18/2023] Open
Abstract
The SM proteins Vps33A and Vps33B are believed to act in membrane fusions in endosomal pathways, but their specific roles are controversial. In Drosophila, Vps33A is the product of the carnation (car) gene. We generated a null allele of car to test its requirement for trafficking to different organelles. Complete loss of car function is lethal during larval development. Eye-specific loss of Car causes late, light-independent degeneration of photoreceptor cells. Earlier in these cells, two distinct phenotypes were detected. In young adults, autophagosomes amassed indicating that their fusion with lysosomes requires Car. In eye discs, endocytosed receptors and ligands accumulate in Rab7-positive prelysosomal compartments. The requirement of Car for late endosome-to-lysosome fusion in imaginal discs is specific as early endosomes are unaffected. Furthermore, lysosomal delivery is not restored by expression of dVps33B. This specificity reflects the distinct pattern of binding to different Syntaxins in vitro: dVps33B predominantly binds the early endosomal Avl and Car to dSyntaxin16. Consistent with a role in Car-mediated fusion, dSyntaxin16 is not restricted to Golgi membranes but also present on lysosomes.
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Affiliation(s)
| | - Sanchali Ray
- Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9111
| | - Helmut Krämer
- Departments of *Neuroscience and
- Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9111
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Zhu GD, Salazar G, Zlatic SA, Fiza B, Doucette MM, Heilman CJ, Levey AI, Faundez V, L'Hernault SW. SPE-39 family proteins interact with the HOPS complex and function in lysosomal delivery. Mol Biol Cell 2009; 20:1223-40. [PMID: 19109425 PMCID: PMC2642739 DOI: 10.1091/mbc.e08-07-0728] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2008] [Revised: 12/02/2008] [Accepted: 12/05/2008] [Indexed: 01/19/2023] Open
Abstract
Yeast and animal homotypic fusion and vacuole protein sorting (HOPS) complexes contain conserved subunits, but HOPS-mediated traffic in animals might require additional proteins. Here, we demonstrate that SPE-39 homologues, which are found only in animals, are present in RAB5-, RAB7-, and RAB11-positive endosomes where they play a conserved role in lysosomal delivery and probably function via their interaction with the core HOPS complex. Although Caenorhabditis elegans spe-39 mutants were initially identified as having abnormal vesicular biogenesis during spermatogenesis, we show that these mutants also have disrupted processing of endocytosed proteins in oocytes and coelomocytes. C. elegans SPE-39 interacts in vitro with both VPS33A and VPS33B, whereas RNA interference of VPS33B causes spe-39-like spermatogenesis defects. The human SPE-39 orthologue C14orf133 also interacts with VPS33 homologues and both coimmunoprecipitates and cosediments with other HOPS subunits. SPE-39 knockdown in cultured human cells altered the morphology of syntaxin 7-, syntaxin 8-, and syntaxin 13-positive endosomes. These effects occurred concomitantly with delayed mannose 6-phosphate receptor-mediated cathepsin D delivery and degradation of internalized epidermal growth factor receptors. Our findings establish that SPE-39 proteins are a previously unrecognized regulator of lysosomal delivery and that C. elegans spermatogenesis is an experimental system useful for identifying conserved regulators of metazoan lysosomal biogenesis.
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Affiliation(s)
| | | | - Stephanie A. Zlatic
- Graduate Program in Biochemistry, Cell, and Developmental Biology
- Cell Biology, and
| | | | | | - Craig J. Heilman
- Department of Neurology
- Center for Neurodegenerative Disease, Emory University, Atlanta, GA 30322
| | - Allan I. Levey
- Department of Neurology
- Center for Neurodegenerative Disease, Emory University, Atlanta, GA 30322
| | - Victor Faundez
- Graduate Program in Biochemistry, Cell, and Developmental Biology
- Cell Biology, and
- Center for Neurodegenerative Disease, Emory University, Atlanta, GA 30322
| | - Steven W. L'Hernault
- Graduate Program in Biochemistry, Cell, and Developmental Biology
- Departments of *Biology and
- Center for Neurodegenerative Disease, Emory University, Atlanta, GA 30322
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Dilmeç F, Varışlı L, Özgönül A, Cen O. Analysis Of STK11/LKB1 Gene Using Bioinformatics Tools. ELECTRONIC JOURNAL OF GENERAL MEDICINE 2007. [DOI: 10.29333/ejgm/82526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Parmley JL, Hurst LD. How common are intragene windows with KA > KS owing to purifying selection on synonymous mutations? J Mol Evol 2007; 64:646-55. [PMID: 17557167 DOI: 10.1007/s00239-006-0207-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2006] [Accepted: 03/07/2007] [Indexed: 12/14/2022]
Abstract
One method for diagnosing the mode of sequence evolution considers the ratio of nonsynonymous substitutions per nonsynonymous site (K (A)) to the corresponding figure for synonymous substitutions (K (S)). A ratio (K (A)/K (S)) greater than unity is taken as evidence for positive selection. This, however, need not necessarily be the case. Notably, there is one instance of a high intragenic K (A)/K (S) peak, revealed by sliding window analysis and observed in two pairwise comparisons, better accounted for by localised purifying selection on synonymous mutations that affect splicing. Is this example exceptional? To address this we isolate intragenic domains with K (A)/K (S) > 1 from more than 1000 long mouse-rat orthologues. Approximately one K (A)/K (S) > 1 peak is found per 12-15 kb of coding sequence. Surprisingly, low synonymous substitution rates underpin more incidences than do high nonsynonymous rates. Several reasons, however, prevent us from supposing that the low synonymous rates reflect purifying selection on synonymous mutations. First, for many peaks, the null that the peak is no higher than expected given the underlying rates of evolution, cannot be rejected. Second, of 18 statistically significant incidences with unusually low K (S) values, only 3 are repeatable across independent comparisons. At least two of these are within alternatively spliced exons. We conclude that repeatable statistically significant intragenic domains of low intragenic K (S) are rare. As so few K (A)/K (S) peaks reflect increased rates of protein evolution and so few hold statistical support, we additionally conclude that sliding window analysis to infer domains of positive selection is highly error-prone.
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Affiliation(s)
- Joanna L Parmley
- Department of Biology and Biochemistry, University of Bath, Bath, UK
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40
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Gissen P, Maher ER. Cargos and genes: insights into vesicular transport from inherited human disease. J Med Genet 2007; 44:545-55. [PMID: 17526798 PMCID: PMC2597945 DOI: 10.1136/jmg.2007.050294] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Many cellular functions depend on the correct delivery of proteins to specific intracellular destinations. Mutations that alter protein structure and disrupt trafficking of the protein (the "cargo") occur in many genetic disorders. In addition, an increasing number of disorders have been linked to mutations in the genes encoding components of the vesicular transport machinery responsible for normal protein trafficking. We review the clinical phenotypes and molecular pathology of such inherited "protein-trafficking disorders", which provide seminal insights into the molecular mechanisms of protein trafficking. Further characterisation of this expanding group of disorders will provide a basis for developing new diagnostic techniques and treatment strategies and offer insights into the molecular pathology of common multifactorial diseases that have been linked to disordered trafficking mechanisms.
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Affiliation(s)
- Paul Gissen
- Department of Medical and Molecular Genetics, University of Birmingham School of Medicine, Institute of Biomedical Research West, Edgbaston, Birmingham, B15 2TT, UK.
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41
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Olkkonen VM, Ikonen E. When intracellular logistics fails--genetic defects in membrane trafficking. J Cell Sci 2007; 119:5031-45. [PMID: 17158910 DOI: 10.1242/jcs.03303] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The number of human genetic disorders shown to be due to defects in membrane trafficking has greatly increased during the past five years. Defects have been identified in components involved in sorting of cargo into transport carriers, vesicle budding and scission, movement of vesicles along cytoskeletal tracks, as well as in vesicle tethering, docking and fusion at the target membrane. The nervous system is extremely sensitive to such disturbances of the membrane trafficking machinery, and the majority of these disorders display neurological defects--particularly diseases affecting the motility of transport carriers along cytoskeletal tracks. In several disorders, defects in a component that represents a fundamental part of the trafficking machinery fail to cause global transport defects but result in symptoms limited to specific cell types and transport events; this apparently reflects the redundancy of the transport apparatus. In groups of closely related diseases such as Hermansky-Pudlak and Griscelli syndromes, identification of the underlying gene defects has revealed groups of genes in which mutations lead to similar phenotypic consequences. New functionally linked trafficking components and regulatory mechanisms have thus been discovered. Studies of the gene defects in trafficking disorders therefore not only open avenues for new therapeutic approaches but also significantly contribute to our knowledge of the fundamental mechanisms of intracellular membrane transport.
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Affiliation(s)
- Vesa M Olkkonen
- Department of Molecular Medicine, National Public Health Institute (KTL), Biomedicum, POBox 104, FI-00251 Helsinki, Finland.
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Gissen P, Tee L, Johnson CA, Genin E, Caliebe A, Chitayat D, Clericuzio C, Denecke J, Di Rocco M, Fischler B, FitzPatrick D, García-Cazorla A, Guyot D, Jacquemont S, Koletzko S, Leheup B, Mandel H, Sanseverino MTV, Houwen RHJ, McKiernan PJ, Kelly DA, Maher ER. Clinical and molecular genetic features of ARC syndrome. Hum Genet 2006; 120:396-409. [PMID: 16896922 DOI: 10.1007/s00439-006-0232-z] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2006] [Accepted: 07/04/2006] [Indexed: 12/21/2022]
Abstract
Arthrogryposis, renal dysfunction and cholestasis (ARC) syndrome (MIM 208085) is an autosomal recessive multisystem disorder that may be associated with germline VPS33B mutations. VPS33B is involved in regulation of vesicular membrane fusion by interacting with SNARE proteins, and evidence of abnormal polarised membrane protein trafficking has been reported in ARC patients. We characterised clinical and molecular features of ARC syndrome in order to identify potential genotype-phenotype correlations. The clinical phenotype of 62 ARC syndrome patients was analysed. In addition to classical features described previously, all patients had severe failure to thrive, which was not adequately explained by the degree of liver disease and 10% had structural cardiac defects. Almost half of the patients who underwent diagnostic organ biopsy (7/16) developed life-threatening haemorrhage. We found that most patients (9/11) who suffered severe haemorrhage (7 post biopsy and 4 spontaneous) had normal platelet count and morphology. Germline VPS33B mutations were detected in 28/35 families (48/62 individuals) with ARC syndrome. Several mutations were restricted to specific ethnic groups. Thus p.Arg438X mutation was common in the UK Pakistani families and haplotyping was consistent with a founder mutation with the most recent common ancestor 900-1,000 years ago. Heterozygosity was found in the VPS33B locus in some cases of ARC providing the first evidence of a possible second ARC syndrome gene. In conclusion we state that molecular diagnosis is possible for most children in whom ARC syndrome is suspected and VPS33B mutation analysis should replace organ biopsy as a first line diagnostic test for ARC syndrome.
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Affiliation(s)
- Paul Gissen
- Section of Medical and Molecular Genetics, Norton Court, Birmingham Women's Hospital, University of Birmingham, B15 2TG, Edgbaston, Birmingham, UK.
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Slater R, Bishop NE. Genetic structure and evolution of the Vps25 family, a yeast ESCRT-II component. BMC Evol Biol 2006; 6:59. [PMID: 16889659 PMCID: PMC1579232 DOI: 10.1186/1471-2148-6-59] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2006] [Accepted: 08/04/2006] [Indexed: 11/10/2022] Open
Abstract
Background Vps25p is the product of yeast gene VPS25 and is found in an endosomal sorting complex required for transport (ESCRT)-II, along with Vps22p and Vps36p. This complex is essential for sorting of ubiquitinated biosynthetic and endosomal cargoes into endosomes. Results We found that VPS25 is a highly conserved and widely expressed eukaryotic gene, with single orthologs in chromalveolate, excavate, amoebozoan, plant, fungal and metazoan species. Two paralogs were found in Trichomonas vaginalis. An ortholog was strikingly absent from the Encephalitozoon cuniculi genome. Intron positions were analyzed in VPS25 from 36 species. We found evidence for five ancestral VPS25 introns, intron loss, and single instances of intron gain (a Paramecium species) and intron slippage (Theileria species). Processed pseudogenes were identified in four mammalian genomes, with a notable absence in the mouse genome. Two retropseudogenes were found in the chimpanzee genome, one more recently inserted, and one evolving from a common primate ancestor. The amino acid sequences of 119 Vps25 orthologs are aligned, compared with the known secondary structure of yeast Vps25p, and used to carry out phylogenetic analysis. Residues in two amino-terminal PPXY motifs (motif I and II), involved in dimerization of Vps25p and interaction with Vps22p and Vps36p, were closely, but not absolutely conserved. Specifically, motif I was absent in Vps25 homologs of chromalveolates, euglenozoa, and diplomonads. A highly conserved carboxy-terminal lysine was identified, which suggests Vps25 is ubiquitinated. Arginine-83 of yeast Vps25p involved in Vps22p interaction was highly, but not absolutely, conserved. Human tissue expression analysis showed universal expression. Conclusion We have identified 119 orthologs of yeast Vps25p. Expression of mammalian VPS25 in a wide range of tissues, and the presence in a broad range of eukaryotic species, indicates a basic role in eukaryotic cell function. Intron splice site positions were highly conserved across all major eukaryotic species, suggesting an ancestral origin. Amino acid sequence analysis showed the consensus for the amino-terminal proline-rich motifs is P- [WP]-X-[YF] for motif I (when present) and P-P-[FYL]-[FY] for motif II, and that Vps25 may be ubiquitinated.
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Affiliation(s)
- Ruth Slater
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Greater Manchester M13 9PT, UK
| | - Naomi E Bishop
- Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Greater Manchester M13 9PT, UK
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44
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Kempermann G, Chesler EJ, Lu L, Williams RW, Gage FH. Natural variation and genetic covariance in adult hippocampal neurogenesis. Proc Natl Acad Sci U S A 2006; 103:780-5. [PMID: 16407118 PMCID: PMC1325968 DOI: 10.1073/pnas.0510291103] [Citation(s) in RCA: 153] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Adult hippocampal neurogenesis is highly variable and heritable among laboratory strains of mice. Adult neurogenesis is also remarkably plastic and can be modulated by environment and activity. Here, we provide a systematic quantitative analysis of adult hippocampal neurogenesis in two large genetic reference panels of recombinant inbred strains (BXD and AXB/BXA, n = 52 strains). We combined data on variation in neurogenesis with a new transcriptome database to extract a set of 190 genes with expression patterns that are also highly variable and that covary with rates of (i) cell proliferation, (ii) cell survival, or the numbers of surviving (iii) new neurons, and (iv) astrocytes. Expression of a subset of these neurogenesis-associated transcripts was controlled in cis across the BXD set. These self-modulating genes are particularly interesting candidates to control neurogenesis. Among these were musashi (Msi1h) and prominin1/CD133 (Prom1), both of which are linked to stem-cell maintenance and division. Twelve neurogenesis-associated transcripts had significant cis-acting quantitative trait loci, and, of these, six had plausible biological association with adult neurogenesis (Prom1, Ssbp2, Kcnq2, Ndufs2, Camk4, and Kcnj9). Only one cis-acting candidate was linked to both neurogenesis and gliogenesis, Rapgef6, a downstream target of ras signaling. The use of genetic reference panels coupled with phenotyping and global transcriptome profiling thus allowed insight into the complexity of the genetic control of adult neurogenesis.
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Affiliation(s)
- Gerd Kempermann
- Max Delbröck Center for Molecular Medicine, Berlin-Buch, 13125 Berlin, Germany.
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45
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Matthews RP, Plumb-Rudewiez N, Lorent K, Gissen P, Johnson CA, Lemaigre F, Pack M. Zebrafish vps33b, an ortholog of the gene responsible for human arthrogryposis-renal dysfunction-cholestasis syndrome, regulates biliary development downstream of the onecut transcription factor hnf6. Development 2005; 132:5295-306. [PMID: 16284120 DOI: 10.1242/dev.02140] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Arthrogryposis-renal dysfunction-cholestasis syndrome (ARC) is a rare cause of cholestasis in infants. Causative mutations in VPS33B, a gene that encodes a Class C vacuolar sorting protein, have recently been reported in individuals with ARC. We have identified a zebrafish vps33b-ortholog that is expressed in developing liver and intestine. Knockdown of vps33b causes bile duct paucity and impairs intestinal lipid absorption, thus phenocopying digestive defects characteristic of ARC. By contrast, neither motor axon nor kidney epithelial defects typically seen in ARC could be identified in vps33b-deficient larvae. Biliary defects in vps33b-deficient zebrafish larvae closely resemble the bile duct paucity associated with knockdown of the onecut transcription factor hnf6. Consistent with this, reduced vps33b expression was evident in hnf6-deficient larvae and in larvae with mutation of vhnf1, a downstream target of hnf6. Zebrafish vhnf1, but not hnf6, increases vps33b expression in zebrafish embryos and in mammalian liver cells. Electrophoretic mobility shift assays suggest that this regulation occurs through direct binding of vHnf1 to the vps33b promoter. These findings identify vps33b as a novel downstream target gene of the hnf6/vhnf1 pathway that regulates bile duct development in zebrafish. Furthermore, they show that tissue-specific roles for genes that regulate trafficking of intracellular proteins have been modified during vertebrate evolution.
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Affiliation(s)
- Randolph P Matthews
- Division of Gastroenterology and Nutrition, The Children's Hospital of Philadelphia and Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
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Falcón-Pérez JM, Nazarian R, Sabatti C, Dell'Angelica EC. Distribution and dynamics of Lamp1-containing endocytic organelles in fibroblasts deficient in BLOC-3. J Cell Sci 2005; 118:5243-55. [PMID: 16249233 DOI: 10.1242/jcs.02633] [Citation(s) in RCA: 156] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Late endosomes and lysosomes of mammalian cells in interphase tend to concentrate in the perinuclear region that harbors the microtubule-organizing center. We have previously reported abnormal distribution of these organelles - as judged by reduced percentages of cells displaying pronounced perinuclear accumulation - in mutant fibroblasts lacking BLOC-3 (for ;biogenesis of lysosome-related organelles complex 3'). BLOC-3 is a protein complex that contains the products of the genes mutated in Hermansky-Pudlak syndrome types 1 and 4. Here, we developed a method based on image analysis to estimate the extent of organelle clustering in the perinuclear region of cultured cells. Using this method, we corroborated that the perinuclear clustering of late endocytic organelles containing Lamp1 (for ;lysosome-associated membrane protein 1') is reduced in BLOC-3-deficient murine fibroblasts, and found that it is apparently normal in fibroblasts deficient in BLOC-1 or BLOC-2, which are another two protein complexes associated with Hermansky-Pudlak syndrome. Wild-type and mutant fibroblasts were transfected to express human LAMP1 fused at its cytoplasmic tail to green fluorescence protein (GFP). At low expression levels, LAMP1-GFP was targeted correctly to late endocytic organelles in both wild-type and mutant cells. High levels of LAMP1-GFP overexpression elicited aberrant aggregation of late endocytic organelles, a phenomenon that probably involved formation of anti-parallel dimers of LAMP1-GFP as it was not observed in cells expressing comparable levels of a non-dimerizing mutant variant, LAMP1-mGFP. To test whether BLOC-3 plays a role in the movement of late endocytic organelles, time-lapse fluorescence microscopy experiments were performed using live cells expressing low levels of LAMP1-GFP or LAMP1-mGFP. Although active movement of late endocytic organelles was observed in both wild-type and mutant fibroblasts, quantitative analyses revealed a relatively lower frequency of microtubule-dependent movement events, either towards or away from the perinuclear region, within BLOC-3-deficient cells. By contrast, neither the duration nor the speed of these microtubule-dependent events seemed to be affected by the lack of BLOC-3 function. These results suggest that BLOC-3 function is required, directly or indirectly, for optimal attachment of late endocytic organelles to microtubule-dependent motors.
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Affiliation(s)
- Juan M Falcón-Pérez
- Department of Human Genetics, University of California, Los Angeles, CA 90095, USA
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47
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Staleva L, Orlow SJ. Ocular albinism 1 protein: trafficking and function when expressed in Saccharomyces cerevisiae. Exp Eye Res 2005; 82:311-8. [PMID: 16154128 DOI: 10.1016/j.exer.2005.07.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2005] [Revised: 05/30/2005] [Accepted: 07/05/2005] [Indexed: 12/29/2022]
Abstract
The ocular albinism 1 (Oa1) protein is believed to be involved in the biogenesis of melanosomes, but its cellular localization is controversial and its function is unknown. Based upon sequence homology, it has been predicted that Oa1 belongs to the G protein coupled receptor (GPCR) superfamily. We used the yeast Saccharomyces cerevisiae as a genetically amenable system to study the localization and function of Oa1. Sucrose gradient and immunofluorescence studies revealed that when expressed in yeast, Oa1 localizes to the prevacuolar compartment, the functional equivalent of the mammalian late endosome. Oa1 behaved as G protein coupled receptor in a yeast-based GPCR signalling assay. Extracts of cultured melanocytes, and, in particular, a particulate fraction from cultured melanocytes, stimulated Oa1-mediated GPCR signalling.
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Affiliation(s)
- Liliana Staleva
- Department of Dermatology, New York University School of Medicine, 560 First Avenue, New York, NY 10016, USA
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