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KIF13B establishes a CAV1-enriched microdomain at the ciliary transition zone to promote Sonic hedgehog signalling. Nat Commun 2017; 8:14177. [PMID: 28134340 PMCID: PMC5290278 DOI: 10.1038/ncomms14177] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 12/06/2016] [Indexed: 12/20/2022] Open
Abstract
Ciliary membrane composition is controlled by transition zone (TZ) proteins such as RPGRIP1, RPGRIPL and NPHP4, which are vital for balanced coordination of diverse signalling systems like the Sonic hedgehog (Shh) pathway. Activation of this pathway involves Shh-induced ciliary accumulation of Smoothened (SMO), which is disrupted by disease-causing mutations in TZ components. Here we identify kinesin-3 motor protein KIF13B as a novel member of the RPGRIP1N-C2 domain-containing protein family and show that KIF13B regulates TZ membrane composition and ciliary SMO accumulation. KIF13B is upregulated during ciliogenesis and is recruited to the ciliary base by NPHP4, which binds to two distinct sites in the KIF13B tail region, including an RPGRIP1N-C2 domain. KIF13B and NPHP4 are both essential for establishment of a CAV1 membrane microdomain at the TZ, which in turn is required for Shh-induced ciliary SMO accumulation. Thus KIF13B is a novel regulator of ciliary TZ configuration, membrane composition and Shh signalling.
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52
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Abstract
The axoneme is the main extracellular part of cilia and flagella in eukaryotes. It consists of a microtubule cytoskeleton, which normally comprises nine doublets. In motile cilia, dynein ATPase motor proteins generate sliding motions between adjacent microtubules, which are integrated into a well-orchestrated beating or rotational motion. In primary cilia, there are a number of sensory proteins functioning on membranes surrounding the axoneme. In both cases, as the study of proteomics has elucidated, hundreds of proteins exist in this compartmentalized biomolecular system. In this article, we review the recent progress of structural studies of the axoneme and its components using electron microscopy and X-ray crystallography, mainly focusing on motile cilia. Structural biology presents snapshots (but not live imaging) of dynamic structural change and gives insights into the force generation mechanism of dynein, ciliary bending mechanism, ciliogenesis, and evolution of the axoneme.
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Affiliation(s)
- Takashi Ishikawa
- Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland.,Department of Biology, ETH Zurich, 5232 Villigen PSI, Switzerland
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53
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Dutcher SK, O'Toole ET. The basal bodies of Chlamydomonas reinhardtii. Cilia 2016; 5:18. [PMID: 27252853 PMCID: PMC4888484 DOI: 10.1186/s13630-016-0039-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 03/09/2016] [Indexed: 12/13/2022] Open
Abstract
The unicellular green alga, Chlamydomonas reinhardtii, is a biflagellated cell that can swim or glide. C. reinhardtii cells are amenable to genetic, biochemical, proteomic, and microscopic analysis of its basal bodies. The basal bodies contain triplet microtubules and a well-ordered transition zone. Both the mother and daughter basal bodies assemble flagella. Many of the proteins found in other basal body-containing organisms are present in the Chlamydomonas genome, and mutants in these genes affect the assembly of basal bodies. Electron microscopic analysis shows that basal body duplication is site-specific and this may be important for the proper duplication and spatial organization of these organelles. Chlamydomonas is an excellent model for the study of basal bodies as well as the transition zone.
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54
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Reck J, Schauer AM, VanderWaal Mills K, Bower R, Tritschler D, Perrone CA, Porter ME. The role of the dynein light intermediate chain in retrograde IFT and flagellar function in Chlamydomonas. Mol Biol Cell 2016; 27:2404-22. [PMID: 27251063 PMCID: PMC4966982 DOI: 10.1091/mbc.e16-03-0191] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 05/26/2016] [Indexed: 12/28/2022] Open
Abstract
The assembly of cilia and flagella depends on the activity of two microtubule motor complexes, kinesin-2 and dynein-2/1b, but the specific functions of the different subunits are poorly defined. Here we analyze Chlamydomonas strains expressing different amounts of the dynein 1b light intermediate chain (D1bLIC). Disruption of D1bLIC alters the stability of the dynein 1b complex and reduces both the frequency and velocity of retrograde intraflagellar transport (IFT), but it does not eliminate retrograde IFT. Flagellar assembly, motility, gliding, and mating are altered in a dose-dependent manner. iTRAQ-based proteomics identifies a small subset of proteins that are significantly reduced or elevated in d1blic flagella. Transformation with D1bLIC-GFP rescues the mutant phenotypes, and D1bLIC-GFP assembles into the dynein 1b complex at wild-type levels. D1bLIC-GFP is transported with anterograde IFT particles to the flagellar tip, dissociates into smaller particles, and begins processive retrograde IFT in <2 s. These studies demonstrate the role of D1bLIC in facilitating the recycling of IFT subunits and other proteins, identify new components potentially involved in the regulation of IFT, flagellar assembly, and flagellar signaling, and provide insight into the role of D1bLIC and retrograde IFT in other organisms.
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Affiliation(s)
- Jaimee Reck
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455 R&D Systems, Minneapolis, MN 55413
| | - Alexandria M Schauer
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455 College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108
| | - Kristyn VanderWaal Mills
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455 Anoka Technical College, Anoka, MN 55303
| | - Raqual Bower
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455
| | - Douglas Tritschler
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455
| | - Catherine A Perrone
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455 Medtronic, Minneapolis, MN 55432
| | - Mary E Porter
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455
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55
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Verhey KJ, Yang W. Permeability barriers for generating a unique ciliary protein and lipid composition. Curr Opin Cell Biol 2016; 41:109-16. [PMID: 27232950 DOI: 10.1016/j.ceb.2016.05.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 05/04/2016] [Accepted: 05/10/2016] [Indexed: 01/08/2023]
Abstract
Cilia (and flagella) are microtubule-based protrusions that are found in single or multiple copies on the surface of most eukaryotic cells. Defects in cilia formation and/or function have now been correlated with an expanding spectrum of human genetic diseases termed ciliopathies. Recent work indicates that cilia are indeed a bona fide organelle with a unique protein and lipid content that enables specific cellular functions. Despite the physiological and clinical relevance of cilia, our understanding of how a unique protein and lipid composition is generated for this organelle remains poor. Here we review recent work on the mechanisms that determine the protein and lipid content, and thus the functional outputs, of this unique organelle.
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Affiliation(s)
- Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
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56
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Lee J, Chung YD. Ciliary subcompartments: how are they established and what are their functions? BMB Rep 2016; 48:380-7. [PMID: 25936781 PMCID: PMC4577287 DOI: 10.5483/bmbrep.2015.48.7.084] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Indexed: 12/15/2022] Open
Abstract
Cilia are conserved subcellular organelles with diverse sensory and developmental roles. Recently, they have emerged as crucial organelles whose dysfunction causes a wide spectrum of disorders called ciliopathies. Recent studies on the pathological mechanisms underlying ciliopathies showed that the ciliary compartment is further divided into subdomains with specific roles in the biogenesis, maintenance and function of cilia. Several conserved sets of molecules that play specific roles in each subcompartment have been discovered. Here we review recent progress on our understanding of ciliary subcompartments, especially focusing on the molecules required for their structure and/or function. [BMB Reports 2015; 48(7): 380-387]
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Affiliation(s)
- Jeongmi Lee
- Department of Life Science, University of Seoul, Seoul 130-743, Korea
| | - Yun Doo Chung
- Department of Life Science, University of Seoul, Seoul 130-743, Korea
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57
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Abstract
Primary ciliary dyskinesia (PCD) is a genetic disease of motile cilia, which belongs to a group of disorders resulting from dysfunction of cilia, collectively known as ciliopathies. Insights into the genetics and phenotypes of PCD have grown over the last decade, in part propagated by the discovery of a number of novel cilia-related genes. These genes encode proteins that segregate into structural axonemal, regulatory, as well as cytoplasmic assembly proteins. Our understanding of primary (sensory) cilia has also expanded, and an ever-growing list of diverse conditions has been linked to defective function and signaling of the sensory cilium. Recent multicenter clinical and genetic studies have uncovered the heterogeneity of motile and sensory ciliopathies, and in some cases, the overlap between these conditions. Here, we will describe the genetics and pathophysiology of ciliopathies in children, focusing on PCD, review emerging genotype-phenotype relationships, and diagnostic tools available for the clinician.
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Affiliation(s)
- Amjad Horani
- a Department of Pediatrics , Washington University School of Medicine , St. Louis , MO , USA
| | - Thomas W Ferkol
- a Department of Pediatrics , Washington University School of Medicine , St. Louis , MO , USA.,b Department of Cell Biology and Physiology , Washington University School of Medicine , St. Louis , MO , USA
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58
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Li C, Jensen VL, Park K, Kennedy J, Garcia-Gonzalo FR, Romani M, De Mori R, Bruel AL, Gaillard D, Doray B, Lopez E, Rivière JB, Faivre L, Thauvin-Robinet C, Reiter JF, Blacque OE, Valente EM, Leroux MR. MKS5 and CEP290 Dependent Assembly Pathway of the Ciliary Transition Zone. PLoS Biol 2016; 14:e1002416. [PMID: 26982032 PMCID: PMC4794247 DOI: 10.1371/journal.pbio.1002416] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 02/24/2016] [Indexed: 11/19/2022] Open
Abstract
Cilia have a unique diffusion barrier (“gate”) within their proximal region, termed transition zone (TZ), that compartmentalises signalling proteins within the organelle. The TZ is known to harbour two functional modules/complexes (Meckel syndrome [MKS] and Nephronophthisis [NPHP]) defined by genetic interaction, interdependent protein localisation (hierarchy), and proteomic studies. However, the composition and molecular organisation of these modules and their links to human ciliary disease are not completely understood. Here, we reveal Caenorhabditis elegans CEP-290 (mammalian Cep290/Mks4/Nphp6 orthologue) as a central assembly factor that is specific for established MKS module components and depends on the coiled coil region of MKS-5 (Rpgrip1L/Rpgrip1) for TZ localisation. Consistent with a critical role in ciliary gate function, CEP-290 prevents inappropriate entry of membrane-associated proteins into cilia and keeps ARL-13 (Arl13b) from leaking out of cilia via the TZ. We identify a novel MKS module component, TMEM-218 (Tmem218), that requires CEP-290 and other MKS module components for TZ localisation and functions together with the NPHP module to facilitate ciliogenesis. We show that TZ localisation of TMEM-138 (Tmem138) and CDKL-1 (Cdkl1/Cdkl2/Cdkl3/Cdlk4 related), not previously linked to a specific TZ module, similarly depends on CEP-290; surprisingly, neither TMEM-138 or CDKL-1 exhibit interdependent localisation or genetic interactions with core MKS or NPHP module components, suggesting they are part of a distinct, CEP-290-associated module. Lastly, we show that families presenting with Oral-Facial-Digital syndrome type 6 (OFD6) have likely pathogenic mutations in CEP-290-dependent TZ proteins, namely Tmem17, Tmem138, and Tmem231. Notably, patient fibroblasts harbouring mutated Tmem17, a protein not yet ciliopathy-associated, display ciliogenesis defects. Together, our findings expand the repertoire of MKS module-associated proteins—including the previously uncharacterised mammalian Tmem80—and suggest an MKS-5 and CEP-290-dependent assembly pathway for building a functional TZ. The transition zone is a barrier structure required to maintain the dynamic composition and functional integrity of the cilium. This study describes the pathway by which the transition zone is assembled during cilium formation. The primary cilium is a structure found in most animal cell types. Much like an antenna, it is responsible for sensing extracellular signals, including light and small molecules, and conveying this information to the receiving cell and respective tissue or organ. At the base of the cilium is the transition zone (TZ), which acts as a “gate” to regulate the entry and exit of ciliary proteins required for signal transduction. Here, we use the nematode Caenorhabditis elegans as a model system to dissect how different proteins within the TZ assemble to form a functional barrier. We find that the TZ protein MKS-5 (Rpgrip1/Rpgrip1L orthologue) forms the foundation for two different assembly pathways involving two distinct modules: Nephronophthisis (NPHP) and Meckel syndrome (MKS). We show that at the base of the MKS module is CEP-290, another TZ protein that assembles MKS module proteins, including a novel TZ protein we identify as TMEM-218. CEP-290 also helps assemble a potentially separate submodule containing TMEM-138 and CDKL-1. Notably, we provide evidence that the MKS module protein TMEM-17 facilitates cilium formation and is disrupted in the human disorder (ciliopathy) Oral-Facial-Digital Syndrome type 6 (OFD6). Together, our findings provide essential insights into the assembly pathway of the ciliary TZ and suggest further connections between the transition zone and human health.
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Affiliation(s)
- Chunmei Li
- Department of Molecular Biology and Biochemistry and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Victor L. Jensen
- Department of Molecular Biology and Biochemistry and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Kwangjin Park
- Department of Molecular Biology and Biochemistry and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Julie Kennedy
- School of Biomolecular & Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Francesc R. Garcia-Gonzalo
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, United States of America
| | - Marta Romani
- Neurogenetics Unit, Mendel Laboratory, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Roberta De Mori
- Neurogenetics Unit, Mendel Laboratory, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Ange-Line Bruel
- EA4271 GAD Génétique des Anomalies du Développement, FHU-TRANSLAD, Université Fédérale Bourgogne Franche-Comté, Dijon, France
| | | | - Bérénice Doray
- Service de Génétique clinique, CHRU Strasbourg, Strasbourg, France
| | - Estelle Lopez
- EA4271 GAD Génétique des Anomalies du Développement, FHU-TRANSLAD, Université Fédérale Bourgogne Franche-Comté, Dijon, France
| | - Jean-Baptiste Rivière
- EA4271 GAD Génétique des Anomalies du Développement, FHU-TRANSLAD, Université Fédérale Bourgogne Franche-Comté, Dijon, France
- Laboratoire de Génétique moléculaire, Plateau Technique de Biologie, CHU Dijon, Dijon, France
| | - Laurence Faivre
- EA4271 GAD Génétique des Anomalies du Développement, FHU-TRANSLAD, Université Fédérale Bourgogne Franche-Comté, Dijon, France
- Centre de Génétique, FHU-TRANSLAD, Hôpital d’Enfants, CHU Dijon, Dijon, France
| | - Christel Thauvin-Robinet
- EA4271 GAD Génétique des Anomalies du Développement, FHU-TRANSLAD, Université Fédérale Bourgogne Franche-Comté, Dijon, France
- Centre de Génétique, FHU-TRANSLAD, Hôpital d’Enfants, CHU Dijon, Dijon, France
| | - Jeremy F. Reiter
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, United States of America
| | - Oliver E. Blacque
- School of Biomolecular & Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Enza Maria Valente
- Neurogenetics Unit, Mendel Laboratory, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
- Department of Medicine and Surgery, University of Salerno, Salerno, Italy
| | - Michel R. Leroux
- Department of Molecular Biology and Biochemistry and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, British Columbia, Canada
- * E-mail:
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59
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Takao D, Verhey KJ. Gated entry into the ciliary compartment. Cell Mol Life Sci 2016; 73:119-27. [PMID: 26472341 PMCID: PMC4959937 DOI: 10.1007/s00018-015-2058-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 09/28/2015] [Accepted: 09/29/2015] [Indexed: 11/26/2022]
Abstract
Cilia and flagella play important roles in cell motility and cell signaling. These functions require that the cilium establishes and maintains a unique lipid and protein composition. Recent work indicates that a specialized region at the base of the cilium, the transition zone, serves as both a barrier to entry and a gate for passage of select components. For at least some cytosolic proteins, the barrier and gate functions are provided by a ciliary pore complex (CPC) that shares molecular and mechanistic properties with nuclear gating. Specifically, nucleoporins of the CPC limit the diffusional entry of cytosolic proteins in a size-dependent manner and enable the active transport of large molecules and complexes via targeting signals, importins, and the small G protein Ran. For membrane proteins, the septin protein SEPT2 is part of the barrier to entry whereas the gating function is carried out and/or regulated by proteins associated with ciliary diseases (ciliopathies) such as nephronophthisis, Meckel–Gruber syndrome and Joubert syndrome. Here, we discuss the evidence behind these models of ciliary gating as well as the similarities to and differences from nuclear gating.
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Affiliation(s)
- Daisuke Takao
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Pl, Ann Arbor, MI 48109 USA
| | - Kristen J. Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Pl, Ann Arbor, MI 48109 USA
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60
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Hunter EL, Sale WS, Alford LM. Analysis of Axonemal Assembly During Ciliary Regeneration in Chlamydomonas. Methods Mol Biol 2016; 1454:237-43. [PMID: 27514926 DOI: 10.1007/978-1-4939-3789-9_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Chlamydomonas reinhardtii is an outstanding model genetic organism for study of assembly of cilia. Here, methods are described for synchronization of ciliary regeneration in Chlamydomonas to analyze the sequence in which ciliary proteins assemble. In addition, the methods described allow analysis of the mechanisms involved in regulation of ciliary length, the proteins required for ciliary assembly, and the temporal expression of genes encoding ciliary proteins. Ultimately, these methods can contribute to discovery of conserved genes that when defective lead to abnormal ciliary assembly and human disease.
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Affiliation(s)
- Emily L Hunter
- Department of Cell Biology, Emory University, 465 Whitehead Biomedical Research Building, 615 Michael Street, Atlanta, GA, 30322, USA
| | - Winfield S Sale
- Department of Cell Biology, Emory University, 465 Whitehead Biomedical Research Building, 615 Michael Street, Atlanta, GA, 30322, USA.
| | - Lea M Alford
- Department of Cell Biology, Emory University, 465 Whitehead Biomedical Research Building, 615 Michael Street, Atlanta, GA, 30322, USA
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61
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Abstract
Cilia and flagella are microtubule-based organelles that play important roles in human health by contributing to cellular motility as well as sensing and responding to environmental cues. Defects in cilia formation and function cause a broad class of human genetic diseases called ciliopathies. To carry out their specialized functions, cilia contain a unique complement of proteins that must be imported into the ciliary compartment. In this chapter, we describe methods to measure the permeability barrier of the ciliary gate by microinjection of fluorescent proteins and dextrans of different sizes into ciliated cells. We also describe a fluorescence recovery after photobleaching (FRAP) assay to measure the entry of ciliary proteins into the ciliary compartment. These assays can be used to determine the molecular mechanisms that regulate the formation and function of cilia in mammalian cells.
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Affiliation(s)
- Daisuke Takao
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI, 48109, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI, 48109, USA.
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62
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Yee LE, Garcia-Gonzalo FR, Bowie RV, Li C, Kennedy JK, Ashrafi K, Blacque OE, Leroux MR, Reiter JF. Conserved Genetic Interactions between Ciliopathy Complexes Cooperatively Support Ciliogenesis and Ciliary Signaling. PLoS Genet 2015; 11:e1005627. [PMID: 26540106 PMCID: PMC4635004 DOI: 10.1371/journal.pgen.1005627] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/05/2015] [Indexed: 11/18/2022] Open
Abstract
Mutations in genes encoding cilia proteins cause human ciliopathies, diverse disorders affecting many tissues. Individual genes can be linked to ciliopathies with dramatically different phenotypes, suggesting that genetic modifiers may participate in their pathogenesis. The ciliary transition zone contains two protein complexes affected in the ciliopathies Meckel syndrome (MKS) and nephronophthisis (NPHP). The BBSome is a third protein complex, affected in the ciliopathy Bardet-Biedl syndrome (BBS). We tested whether mutations in MKS, NPHP and BBS complex genes modify the phenotypic consequences of one another in both C. elegans and mice. To this end, we identified TCTN-1, the C. elegans ortholog of vertebrate MKS complex components called Tectonics, as an evolutionarily conserved transition zone protein. Neither disruption of TCTN-1 alone or together with MKS complex components abrogated ciliary structure in C. elegans. In contrast, disruption of TCTN-1 together with either of two NPHP complex components, NPHP-1 or NPHP-4, compromised ciliary structure. Similarly, disruption of an NPHP complex component and the BBS complex component BBS-5 individually did not compromise ciliary structure, but together did. As in nematodes, disrupting two components of the mouse MKS complex did not cause additive phenotypes compared to single mutants. However, disrupting both Tctn1 and either Nphp1 or Nphp4 exacerbated defects in ciliogenesis and cilia-associated developmental signaling, as did disrupting both Tctn1 and the BBSome component Bbs1. Thus, we demonstrate that ciliary complexes act in parallel to support ciliary function and suggest that human ciliopathy phenotypes are altered by genetic interactions between different ciliary biochemical complexes. Ciliopathies, diseases arising from defects in the functions of primary cilia, have many different manifestations and vary dramatically in severity. How genetics influence ciliopathy phenotypes is poorly understood. Building off of our increasing knowledge of how different biochemical complexes contribute to ciliary function, we investigated how ciliopathy-associated genes interact to support ciliogenesis. Using a combination of nematode and mouse genetics, we found that genes encoding components of different biochemical complexes interact, whereas genes encoding different components within a single complex do not. These results revealed overlapping ciliary functions of biochemically distinct proteins complexes such as the BBSome, the transition zone MKS complex and the transition zone NPHP complex. This work indicates the genetic interactions that may alter the phenotypic consequences of human ciliopathy mutations.
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Affiliation(s)
- Laura E. Yee
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, United States of America
| | - Francesc R. Garcia-Gonzalo
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, United States of America
| | - Rachel V. Bowie
- School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Chunmei Li
- Department of Molecular Biology and Biochemistry and Centre for Cell Biology, Development, and Disease, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Julie K. Kennedy
- School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Kaveh Ashrafi
- Department of Physiology, University of California, San Francisco, San Francisco, California, United States of America
| | - Oliver E. Blacque
- School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Michel R. Leroux
- Department of Molecular Biology and Biochemistry and Centre for Cell Biology, Development, and Disease, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jeremy F. Reiter
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail:
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63
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Jensen VL, Li C, Bowie RV, Clarke L, Mohan S, Blacque OE, Leroux MR. Formation of the transition zone by Mks5/Rpgrip1L establishes a ciliary zone of exclusion (CIZE) that compartmentalises ciliary signalling proteins and controls PIP2 ciliary abundance. EMBO J 2015; 34:2537-56. [PMID: 26392567 PMCID: PMC4609185 DOI: 10.15252/embj.201488044] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 08/22/2015] [Accepted: 08/26/2015] [Indexed: 01/09/2023] Open
Abstract
Cilia are thought to harbour a membrane diffusion barrier within their transition zone (TZ) that compartmentalises signalling proteins. How this "ciliary gate" assembles and functions remains largely unknown. Contrary to current models, we present evidence that Caenorhabditis elegans MKS-5 (orthologue of mammalian Mks5/Rpgrip1L/Nphp8 and Rpgrip1) may not be a simple structural scaffold for anchoring > 10 different proteins at the TZ, but instead, functions as an assembly factor. This activity is needed to form TZ ultrastructure, which comprises Y-shaped axoneme-to-membrane connectors. Coiled-coil and C2 domains within MKS-5 enable TZ localisation and functional interactions with two TZ modules, consisting of Meckel syndrome (MKS) and nephronophthisis (NPHP) proteins. Discrete roles for these modules at basal body-associated transition fibres and TZ explain their redundant functions in making essential membrane connections and thus sealing the ciliary compartment. Furthermore, MKS-5 establishes a ciliary zone of exclusion (CIZE) at the TZ that confines signalling proteins, including GPCRs and NPHP-2/inversin, to distal ciliary subdomains. The TZ/CIZE, potentially acting as a lipid gate, limits the abundance of the phosphoinositide PIP2 within cilia and is required for cell signalling. Together, our findings suggest a new model for Mks5/Rpgrip1L in TZ assembly and function that is essential for establishing the ciliary signalling compartment.
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Affiliation(s)
- Victor L Jensen
- Department of Molecular Biology and Biochemistry and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC, Canada
| | - Chunmei Li
- Department of Molecular Biology and Biochemistry and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC, Canada
| | - Rachel V Bowie
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Lara Clarke
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Swetha Mohan
- Department of Molecular Biology and Biochemistry and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC, Canada
| | - Oliver E Blacque
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Michel R Leroux
- Department of Molecular Biology and Biochemistry and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC, Canada
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64
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Awata J, Song K, Lin J, King SM, Sanderson MJ, Nicastro D, Witman GB. DRC3 connects the N-DRC to dynein g to regulate flagellar waveform. Mol Biol Cell 2015; 26:2788-800. [PMID: 26063732 PMCID: PMC4571338 DOI: 10.1091/mbc.e15-01-0018] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 05/26/2015] [Accepted: 06/03/2015] [Indexed: 01/30/2023] Open
Abstract
The nexin-dynein regulatory complex (N-DRC), which is a major hub for the control of flagellar motility, contains at least 11 different subunits. A major challenge is to determine the location and function of each of these subunits within the N-DRC. We characterized a Chlamydomonas mutant defective in the N-DRC subunit DRC3. Of the known N-DRC subunits, the drc3 mutant is missing only DRC3. Like other N-DRC mutants, the drc3 mutant has a defect in flagellar motility. However, in contrast to other mutations affecting the N-DRC, drc3 does not suppress flagellar paralysis caused by loss of radial spokes. Cryo-electron tomography revealed that the drc3 mutant lacks a portion of the N-DRC linker domain, including the L1 protrusion, part of the distal lobe, and the connection between these two structures, thus localizing DRC3 to this part of the N-DRC. This and additional considerations enable us to assign DRC3 to the L1 protrusion. Because the L1 protrusion is the only non-dynein structure in contact with the dynein g motor domain in wild-type axonemes and this is the only N-DRC-dynein connection missing in the drc3 mutant, we conclude that DRC3 interacts with dynein g to regulate flagellar waveform.
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Affiliation(s)
- Junya Awata
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655
| | - Kangkang Song
- Biology Department and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454
| | - Jianfeng Lin
- Biology Department and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454
| | - Stephen M King
- Department of Molecular Biology and Biophysics and Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT 06030
| | - Michael J Sanderson
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655
| | - Daniela Nicastro
- Biology Department and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454
| | - George B Witman
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655
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65
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Brown JM, Cochran DA, Craige B, Kubo T, Witman GB. Assembly of IFT trains at the ciliary base depends on IFT74. Curr Biol 2015; 25:1583-93. [PMID: 26051893 PMCID: PMC4482480 DOI: 10.1016/j.cub.2015.04.060] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 04/07/2015] [Accepted: 04/29/2015] [Indexed: 12/20/2022]
Abstract
Intraflagellar transport (IFT) moves IFT trains carrying cargoes from the cell body into the flagellum and from the flagellum back to the cell body. IFT trains are composed of complexes IFT-A and IFT-B and cargo adaptors such as the BBSome. The IFT-B core proteins IFT74 and IFT81 interact directly through central and C-terminal coiled-coil domains, and recently it was shown that the N termini of these proteins form a tubulin-binding module important for ciliogenesis. To investigate the function of IFT74 and its domains in vivo, we have utilized Chlamydomonas reinhardtii ift74 mutants. In a null mutant, lack of IFT74 destabilized IFT-B, leading to flagella assembly failure. In this null background, expression of IFT74 lacking 130 amino acids (aa) of the charged N terminus stabilized IFT-B and promoted slow assembly of nearly full-length flagella. A further truncation (lacking aa 1-196, including part of coiled-coil 1) also stabilized IFT-B, but failure in IFT-A/IFT-B interaction within the pool at the base of the flagellum prevented entry of IFT-A into the flagellum and led to severely decreased IFT injection frequency and flagellar-assembly defects. Decreased IFT-A in these short flagella resulted in aggregates of stalled IFT-B in the flagella. We conclude that IFT74 is required to stabilize IFT-B; aa 197-641 are sufficient for this function in vivo. The N terminus of IFT74 may be involved in, but is not required for, tubulin entry into flagella. It is required for association of IFT-A and IFT-B at the base of the flagellum and flagellar import of IFT-A.
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Affiliation(s)
- Jason M Brown
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA; Biology Department, Salem State University, 352 Lafayette Street, Salem, MA 01970, USA
| | - Deborah A Cochran
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Branch Craige
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Tomohiro Kubo
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - George B Witman
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA.
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66
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Rao KN, Li L, Anand M, Khanna H. Ablation of retinal ciliopathy protein RPGR results in altered photoreceptor ciliary composition. Sci Rep 2015; 5:11137. [PMID: 26068394 PMCID: PMC4463945 DOI: 10.1038/srep11137] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 05/14/2015] [Indexed: 11/09/2022] Open
Abstract
Cilia regulate several developmental and homeostatic pathways that are critical to survival. Sensory cilia of photoreceptors regulate phototransduction cascade for visual processing. Mutations in the ciliary protein RPGR (retinitis pigmentosa GTPase regulator) are a prominent cause of severe blindness disorders due to degeneration of mature photoreceptors. However, precise function of RPGR is still unclear. Here we studied the involvement of RPGR in ciliary trafficking by analyzing the composition of photoreceptor sensory cilia (PSC) in Rpgrko retina. Using tandem mass spectrometry analysis followed by immunoblotting, we detected few alterations in levels of proteins involved in proteasomal function and vesicular trafficking in Rpgrko PSC, prior to onset of degeneration. We also found alterations in the levels of high molecular weight soluble proteins in Rpgrko PSC. Our data indicate RPGR regulates entry or retention of soluble proteins in photoreceptor cilia but spares the trafficking of key structural and phototransduction-associated proteins. Given a frequent occurrence of RPGR mutations in severe photoreceptor degeneration due to ciliary disorders, our results provide insights into pathways resulting in altered mature cilia function in ciliopathies.
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Affiliation(s)
- Kollu N Rao
- Department of Ophthalmology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Linjing Li
- Department of Ophthalmology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Manisha Anand
- Department of Ophthalmology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Hemant Khanna
- Department of Ophthalmology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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67
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TCTEX1D2 mutations underlie Jeune asphyxiating thoracic dystrophy with impaired retrograde intraflagellar transport. Nat Commun 2015; 6:7074. [PMID: 26044572 PMCID: PMC4468853 DOI: 10.1038/ncomms8074] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 03/31/2015] [Indexed: 02/06/2023] Open
Abstract
The analysis of individuals with ciliary chondrodysplasias can shed light on sensitive mechanisms controlling ciliogenesis and cell signalling that are essential to embryonic development and survival. Here we identify TCTEX1D2 mutations causing Jeune asphyxiating thoracic dystrophy with partially penetrant inheritance. Loss of TCTEX1D2 impairs retrograde intraflagellar transport (IFT) in humans and the protist Chlamydomonas, accompanied by destabilization of the retrograde IFT dynein motor. We thus define TCTEX1D2 as an integral component of the evolutionarily conserved retrograde IFT machinery. In complex with several IFT dynein light chains, it is required for correct vertebrate skeletal formation but may be functionally redundant under certain conditions. Severe congenital development defects such as Jeune syndrome can result from the malfunction of primary cilia and dynein. Here Schmidts et al. report unique biallelic null mutations in a gene encoding a dynein light chain, helping to explain the nature of ciliopathies in human patients.
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68
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Song K, Awata J, Tritschler D, Bower R, Witman GB, Porter ME, Nicastro D. In situ localization of N and C termini of subunits of the flagellar nexin-dynein regulatory complex (N-DRC) using SNAP tag and cryo-electron tomography. J Biol Chem 2015; 290:5341-53. [PMID: 25564608 DOI: 10.1074/jbc.m114.626556] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cryo-electron tomography (cryo-ET) has reached nanoscale resolution for in situ three-dimensional imaging of macromolecular complexes and organelles. Yet its current resolution is not sufficient to precisely localize or identify most proteins in situ; for example, the location and arrangement of components of the nexin-dynein regulatory complex (N-DRC), a key regulator of ciliary/flagellar motility that is conserved from algae to humans, have remained elusive despite many cryo-ET studies of cilia and flagella. Here, we developed an in situ localization method that combines cryo-ET/subtomogram averaging with the clonable SNAP tag, a widely used cell biological probe to visualize fusion proteins by fluorescence microscopy. Using this hybrid approach, we precisely determined the locations of the N and C termini of DRC3 and the C terminus of DRC4 within the three-dimensional structure of the N-DRC in Chlamydomonas flagella. Our data demonstrate that fusion of SNAP with target proteins allowed for protein localization with high efficiency and fidelity using SNAP-linked gold nanoparticles, without disrupting the native assembly, structure, or function of the flagella. After cryo-ET and subtomogram averaging, we localized DRC3 to the L1 projection of the nexin linker, which interacts directly with a dynein motor, whereas DRC4 was observed to stretch along the N-DRC base plate to the nexin linker. Application of the technique developed here to the N-DRC revealed new insights into the organization and regulatory mechanism of this complex, and provides a valuable tool for the structural dissection of macromolecular complexes in situ.
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Affiliation(s)
- Kangkang Song
- From the Biology Department, Brandeis University, Waltham, Massachusetts 02454
| | - Junya Awata
- the Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, and
| | - Douglas Tritschler
- the Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455
| | - Raqual Bower
- the Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455
| | - George B Witman
- the Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, and
| | - Mary E Porter
- the Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455
| | - Daniela Nicastro
- From the Biology Department, Brandeis University, Waltham, Massachusetts 02454,
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69
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Barbelanne M, Hossain D, Chan DP, Peränen J, Tsang WY. Nephrocystin proteins NPHP5 and Cep290 regulate BBSome integrity, ciliary trafficking and cargo delivery. Hum Mol Genet 2014; 24:2185-200. [PMID: 25552655 DOI: 10.1093/hmg/ddu738] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Proper functioning of cilia, hair-like structures responsible for sensation and locomotion, requires nephrocystin-5 (NPHP5) and a multi-subunit complex called the Bardet-Biedl syndrome (BBS)ome, but their precise relationship is not understood. The BBSome is involved in the trafficking of membrane cargos to cilia. While it is known that a loss of any single subunit prevents ciliary trafficking of the BBSome and its cargos, the mechanisms underlying ciliary entry of this complex are not well characterized. Here, we report that a transition zone protein NPHP5 contains two separate BBS-binding sites and interacts with the BBSome to mediate its integrity. Depletion of NPHP5, or expression of NPHP5 mutant missing one binding site, specifically leads to dissociation of BBS2 and BBS5 from the BBSome and loss of ciliary BBS2 and BBS5 without compromising the ability of the other subunits to traffic into cilia. Depletion of Cep290, another transition zone protein that directly binds to NPHP5, causes additional dissociation of BBS8 and loss of ciliary BBS8. Furthermore, delivery of BBSome cargos, smoothened, VPAC2 and Rab8a, to the ciliary compartment is completely disabled in the absence of single BBS subunits, but is selectively impaired in the absence of NPHP5 or Cep290. These findings define a new role of NPHP5 and Cep290 in controlling integrity and ciliary trafficking of the BBSome, which in turn impinge on the delivery of ciliary cargo.
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Affiliation(s)
- Marine Barbelanne
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada, Faculté de Médecine, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Delowar Hossain
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada, Division of Experimental Medicine, McGill University, Montréal, QC H3A 1A3, Canada and
| | - David Puth Chan
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Johan Peränen
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - William Y Tsang
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada, Faculté de Médecine, Université de Montréal, Montréal, QC H3C 3J7, Canada, Division of Experimental Medicine, McGill University, Montréal, QC H3A 1A3, Canada and
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