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Moran AL, Louzao-Martinez L, Norris DP, Peters DJM, Blacque OE. Transport and barrier mechanisms that regulate ciliary compartmentalization and ciliopathies. Nat Rev Nephrol 2024; 20:83-100. [PMID: 37872350 DOI: 10.1038/s41581-023-00773-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2023] [Indexed: 10/25/2023]
Abstract
Primary cilia act as cell surface antennae, coordinating cellular responses to sensory inputs and signalling molecules that regulate developmental and homeostatic pathways. Cilia are therefore critical to physiological processes, and defects in ciliary components are associated with a large group of inherited pleiotropic disorders - known collectively as ciliopathies - that have a broad spectrum of phenotypes and affect many or most tissues, including the kidney. A central feature of the cilium is its compartmentalized structure, which imparts its unique molecular composition and signalling environment despite its membrane and cytosol being contiguous with those of the cell. Such compartmentalization is achieved via active transport pathways that bring protein cargoes to and from the cilium, as well as gating pathways at the ciliary base that establish diffusion barriers to protein exchange into and out of the organelle. Many ciliopathy-linked proteins, including those involved in kidney development and homeostasis, are components of the compartmentalizing machinery. New insights into the major compartmentalizing pathways at the cilium, namely, ciliary gating, intraflagellar transport, lipidated protein flagellar transport and ciliary extracellular vesicle release pathways, have improved our understanding of the mechanisms that underpin ciliary disease and associated renal disorders.
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Affiliation(s)
- Ailis L Moran
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Laura Louzao-Martinez
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Dorien J M Peters
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
| | - Oliver E Blacque
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland.
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2
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Bhat S, Dietz A, Senf K, Nietzsche S, Hirabayashi Y, Westermann M, Neuhaus EM. GPRC5C regulates the composition of cilia in the olfactory system. BMC Biol 2023; 21:292. [PMID: 38110903 PMCID: PMC10729543 DOI: 10.1186/s12915-023-01790-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/30/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Olfactory sensory neurons detect odourants via multiple long cilia that protrude from their dendritic endings. The G protein-coupled receptor GPRC5C was identified as part of the olfactory ciliary membrane proteome, but its function and localization is unknown. RESULTS High-resolution confocal and electron microscopy revealed that GPRC5C is located at the base of sensory cilia in olfactory neurons, but not in primary cilia of immature neurons or stem cells. Additionally, GPRC5C localization in sensory cilia parallels cilia formation and follows the formation of the basal body. In closer examination, GPRC5C was found in the ciliary transition zone. GPRC5C deficiency altered the structure of sensory cilia and increased ciliary layer thickness. However, primary cilia were unaffected. Olfactory sensory neurons from Gprc5c-deficient mice exhibited altered localization of olfactory signalling cascade proteins, and of ciliary phosphatidylinositol-4,5-bisphosphat. Sensory neurons also exhibited increased neuronal activity as well as altered mitochondrial morphology, and knockout mice had an improved ability to detect food pellets based on smell. CONCLUSIONS Our study shows that GPRC5C regulates olfactory cilia composition and length, thereby controlling odour perception.
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Affiliation(s)
- Sneha Bhat
- Pharmacology and Toxicology, Jena University Hospital, Friedrich Schiller University Jena, Drackendorfer Str. 1, 07747, Jena, Germany
| | - André Dietz
- Pharmacology and Toxicology, Jena University Hospital, Friedrich Schiller University Jena, Drackendorfer Str. 1, 07747, Jena, Germany
| | - Katja Senf
- Pharmacology and Toxicology, Jena University Hospital, Friedrich Schiller University Jena, Drackendorfer Str. 1, 07747, Jena, Germany
| | - Sandor Nietzsche
- Centre for Electron Microscopy, Jena University Hospital, Friedrich Schiller University Jena, Ziegelmühlenweg 1, 07743, Jena, Germany
| | - Yoshio Hirabayashi
- Institute for Environmental and Gender-Specific Medicine, Juntendo University Graduate School of Medicine, Chiba, 279-0021, Japan
- RIKEN Cluster for Pioneering Research, RIKEN, Wako, Saitama, 351-0198, Japan
| | - Martin Westermann
- Centre for Electron Microscopy, Jena University Hospital, Friedrich Schiller University Jena, Ziegelmühlenweg 1, 07743, Jena, Germany
| | - Eva Maria Neuhaus
- Pharmacology and Toxicology, Jena University Hospital, Friedrich Schiller University Jena, Drackendorfer Str. 1, 07747, Jena, Germany.
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3
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Park K, Leroux MR. Composition, organization and mechanisms of the transition zone, a gate for the cilium. EMBO Rep 2022; 23:e55420. [PMID: 36408840 PMCID: PMC9724682 DOI: 10.15252/embr.202255420] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/08/2022] [Accepted: 10/31/2022] [Indexed: 11/22/2022] Open
Abstract
The cilium evolved to provide the ancestral eukaryote with the ability to move and sense its environment. Acquiring these functions required the compartmentalization of a dynein-based motility apparatus and signaling proteins within a discrete subcellular organelle contiguous with the cytosol. Here, we explore the potential molecular mechanisms for how the proximal-most region of the cilium, termed transition zone (TZ), acts as a diffusion barrier for both membrane and soluble proteins and helps to ensure ciliary autonomy and homeostasis. These include a unique complement and spatial organization of proteins that span from the microtubule-based axoneme to the ciliary membrane; a protein picket fence; a specialized lipid microdomain; differential membrane curvature and thickness; and lastly, a size-selective molecular sieve. In addition, the TZ must be permissive for, and functionally integrates with, ciliary trafficking systems (including intraflagellar transport) that cross the barrier and make the ciliary compartment dynamic. The quest to understand the TZ continues and promises to not only illuminate essential aspects of human cell signaling, physiology, and development, but also to unravel how TZ dysfunction contributes to ciliopathies that affect multiple organ systems, including eyes, kidney, and brain.
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Affiliation(s)
- Kwangjin Park
- Department of Molecular Biology and BiochemistrySimon Fraser UniversityBurnabyBCCanada
- Centre for Cell Biology, Development, and DiseaseSimon Fraser UniversityBurnabyBCCanada
- Present address:
Terry Fox LaboratoryBC CancerVancouverBCCanada
- Present address:
Department of Medical GeneticsUniversity of British ColumbiaVancouverBCCanada
| | - Michel R Leroux
- Department of Molecular Biology and BiochemistrySimon Fraser UniversityBurnabyBCCanada
- Centre for Cell Biology, Development, and DiseaseSimon Fraser UniversityBurnabyBCCanada
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4
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Ciliary Proteins Repurposed by the Synaptic Ribbon: Trafficking Myristoylated Proteins at Rod Photoreceptor Synapses. Int J Mol Sci 2022; 23:ijms23137135. [PMID: 35806143 PMCID: PMC9266639 DOI: 10.3390/ijms23137135] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 12/25/2022] Open
Abstract
The Unc119 protein mediates transport of myristoylated proteins to the photoreceptor outer segment, a specialized primary cilium. This transport activity is regulated by the GTPase Arl3 as well as by Arl13b and Rp2 that control Arl3 activation/inactivation. Interestingly, Unc119 is also enriched in photoreceptor synapses and can bind to RIBEYE, the main component of synaptic ribbons. In the present study, we analyzed whether the known regulatory proteins, that control the Unc119-dependent myristoylated protein transport at the primary cilium, are also present at the photoreceptor synaptic ribbon complex by using high-resolution immunofluorescence and immunogold electron microscopy. We found Arl3 and Arl13b to be enriched at the synaptic ribbon whereas Rp2 was predominantly found on vesicles distributed within the entire terminal. These findings indicate that the synaptic ribbon could be involved in the discharge of Unc119-bound lipid-modified proteins. In agreement with this hypothesis, we found Nphp3 (Nephrocystin-3), a myristoylated, Unc119-dependent cargo protein enriched at the basal portion of the ribbon in close vicinity to the active zone. Mutations in Nphp3 are known to be associated with Senior–Løken Syndrome 3 (SLS3). Visual impairment and blindness in SLS3 might thus not only result from ciliary dysfunctions but also from malfunctions of the photoreceptor synapse.
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Turn RE, Hu Y, Dewees SI, Devi N, East MP, Hardin KR, Khatib T, Linnert J, Wolfrum U, Lim MJ, Casanova JE, Caspary T, Kahn RA. The ARF GAPs ELMOD1 and ELMOD3 act at the Golgi and cilia to regulate ciliogenesis and ciliary protein traffic. Mol Biol Cell 2022; 33:ar13. [PMID: 34818063 PMCID: PMC9236152 DOI: 10.1091/mbc.e21-09-0443] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 11/11/2022] Open
Abstract
ELMODs are a family of three mammalian paralogues that display GTPase-activating protein (GAP) activity toward a uniquely broad array of ADP-ribosylation factor (ARF) family GTPases that includes ARF-like (ARL) proteins. ELMODs are ubiquitously expressed in mammalian tissues, highly conserved across eukaryotes, and ancient in origin, being present in the last eukaryotic common ancestor. We described functions of ELMOD2 in immortalized mouse embryonic fibroblasts (MEFs) in the regulation of cell division, microtubules, ciliogenesis, and mitochondrial fusion. Here, using similar strategies with the paralogues ELMOD1 and ELMOD3, we identify novel functions and locations of these cell regulators and compare them to those of ELMOD2, allowing the determination of functional redundancy among the family members. We found strong similarities in phenotypes resulting from deletion of either Elmod1 or Elmod3 and marked differences from those arising in Elmod2 deletion lines. Deletion of either Elmod1 or Elmod3 results in the decreased ability of cells to form primary cilia, loss of a subset of proteins from cilia, and accumulation of some ciliary proteins at the Golgi, predicted to result from compromised traffic from the Golgi to cilia. These phenotypes are reversed upon activating mutant expression of either ARL3 or ARL16, linking their roles to ELMOD1/3 actions.
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Affiliation(s)
- Rachel E. Turn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Biochemistry, Cell & Developmental Biology Graduate Program, Emory University, Atlanta, GA 30322
- Department of Microbiology and Immunology, Stanford University, Palo Alto, CA 94305
| | - Yihan Hu
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, 410008 Hunan, China
| | - Skylar I. Dewees
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Biochemistry, Cell & Developmental Biology Graduate Program, Emory University, Atlanta, GA 30322
| | - Narra Devi
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
| | - Michael P. East
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Katherine R. Hardin
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322
- Biochemistry, Cell & Developmental Biology Graduate Program, Emory University, Atlanta, GA 30322
| | - Tala Khatib
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322
- Biochemistry, Cell & Developmental Biology Graduate Program, Emory University, Atlanta, GA 30322
| | - Joshua Linnert
- Institute of Molecular Physiology, Johannes Gutenberg University, Mainz 55128, Germany
| | - Uwe Wolfrum
- Institute of Molecular Physiology, Johannes Gutenberg University, Mainz 55128, Germany
| | - Michael J. Lim
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908
| | - James E. Casanova
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908
| | - Tamara Caspary
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Richard A. Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
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6
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Fujisawa S, Qiu H, Nozaki S, Chiba S, Katoh Y, Nakayama K. ARL3 and ARL13B GTPases participate in distinct steps of INPP5E targeting to the ciliary membrane. Biol Open 2021; 10:bio058843. [PMID: 34447983 PMCID: PMC8496693 DOI: 10.1242/bio.058843] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 08/19/2021] [Indexed: 01/02/2023] Open
Abstract
INPP5E, a phosphoinositide 5-phosphatase, localizes on the ciliary membrane via its C-terminal prenyl moiety, and maintains the distinct ciliary phosphoinositide composition. The ARL3 GTPase contributes to the ciliary membrane localization of INPP5E by stimulating the release of PDE6D bound to prenylated INPP5E. Another GTPase, ARL13B, which is localized on the ciliary membrane, contributes to the ciliary membrane retention of INPP5E by directly binding to its ciliary targeting sequence. However, as ARL13B was shown to act as a guanine nucleotide exchange factor (GEF) for ARL3, it is also possible that ARL13B indirectly mediates the ciliary INPP5E localization via activating ARL3. We here show that INPP5E is delocalized from cilia in both ARL3-knockout (KO) and ARL13B-KO cells. However, some of the abnormal phenotypes were different between these KO cells, while others were found to be common, indicating the parallel roles of ARL3 and ARL13B, at least concerning some cellular functions. For several variants of ARL13B, their ability to interact with INPP5E, rather than their ability as an ARL3-GEF, was associated with whether they could rescue the ciliary localization of INPP5E in ARL13B-KO cells. These observations together indicate that ARL13B determines the ciliary localization of INPP5E, mainly by its direct binding to INPP5E.
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Affiliation(s)
- Sayaka Fujisawa
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hantian Qiu
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shohei Nozaki
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shuhei Chiba
- Department of Genetic Disease Research, Graduate School of Medicine, Osaka City University, Abeno-ku, Osaka 545-8585, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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7
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Booth WT, Clodfelter JE, Leone-Kabler S, Hughes EK, Eldeeb K, Howlett AC, Lowther WT. Cannabinoid receptor interacting protein 1a interacts with myristoylated Gα i N terminus via a unique gapped β-barrel structure. J Biol Chem 2021; 297:101099. [PMID: 34418434 PMCID: PMC8446797 DOI: 10.1016/j.jbc.2021.101099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/11/2021] [Accepted: 08/17/2021] [Indexed: 11/15/2022] Open
Abstract
Cannabinoid receptor interacting protein 1a (CRIP1a) modulates CB1 cannabinoid receptor G-protein coupling in part by altering the selectivity for Gαi subtype activation, but the molecular basis for this function of CRIP1a is not known. We report herein the first structure of CRIP1a at a resolution of 1.55 Å. CRIP1a exhibits a 10-stranded and antiparallel β-barrel with an interior comprised of conserved hydrophobic residues and loops at the bottom and a short helical cap at the top to exclude solvent. The β-barrel has a gap between strands β8 and β10, which deviates from β-sandwich fatty acid–binding proteins that carry endocannabinoid compounds and the Rho-guanine nucleotide dissociation inhibitor predicted by computational threading algorithms. The structural homology search program DALI identified CRIP1a as homologous to a family of lipidated-protein carriers that includes phosphodiesterase 6 delta subunit and Unc119. Comparison with these proteins suggests that CRIP1a may carry two possible types of cargo: either (i) like phosphodiesterase 6 delta subunit, cargo with a farnesyl moiety that enters from the top of the β-barrel to occupy the hydrophobic interior or (ii) like Unc119, cargo with a palmitoyl or a myristoyl moiety that enters from the side where the missing β-strand creates an opening to the hydrophobic pocket. Fluorescence polarization analysis demonstrated CRIP1a binding of an N-terminally myristoylated 9-mer peptide mimicking the Gαi N terminus. However, CRIP1a could not bind the nonmyristolyated Gαi peptide or cargo of homologs. Thus, binding of CRIP1a to Gαi proteins represents a novel mechanism to regulate cell signaling initiated by the CB1 receptor.
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Affiliation(s)
- William T Booth
- Department of Biochemistry and Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Jill E Clodfelter
- Department of Biochemistry and Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Sandra Leone-Kabler
- Department of Physiology and Pharmacology and Center for Research on Substance Use and Addiction, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Erin K Hughes
- Department of Biochemistry and Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA; Department of Physiology and Pharmacology and Center for Research on Substance Use and Addiction, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Khalil Eldeeb
- Department of Physiology and Pharmacology and Center for Research on Substance Use and Addiction, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Allyn C Howlett
- Department of Physiology and Pharmacology and Center for Research on Substance Use and Addiction, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA; Center for Molecular Signaling, Wake Forest University, Winston-Salem, North Carolina, USA.
| | - W Todd Lowther
- Department of Biochemistry and Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA; Center for Molecular Signaling, Wake Forest University, Winston-Salem, North Carolina, USA.
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8
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Vargová R, Wideman JG, Derelle R, Klimeš V, Kahn RA, Dacks JB, Eliáš M. A Eukaryote-Wide Perspective on the Diversity and Evolution of the ARF GTPase Protein Family. Genome Biol Evol 2021; 13:6319025. [PMID: 34247240 PMCID: PMC8358228 DOI: 10.1093/gbe/evab157] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2021] [Indexed: 12/21/2022] Open
Abstract
The evolution of eukaryotic cellular complexity is interwoven with the extensive diversification of many protein families. One key family is the ARF GTPases that act in eukaryote-specific processes, including membrane traffic, tubulin assembly, actin dynamics, and cilia-related functions. Unfortunately, our understanding of the evolution of this family is limited. Sampling an extensive set of available genome and transcriptome sequences, we have assembled a data set of over 2,000 manually curated ARF family genes from 114 eukaryotic species, including many deeply diverged protist lineages, and carried out comprehensive molecular phylogenetic analyses. These reconstructed as many as 16 ARF family members present in the last eukaryotic common ancestor, nearly doubling the previously inferred ancient system complexity. Evidence for the wide occurrence and ancestral origin of Arf6, Arl13, and Arl16 is presented for the first time. Moreover, Arl17, Arl18, and SarB, newly described here, are absent from well-studied model organisms and as a result their function(s) remain unknown. Analyses of our data set revealed a previously unsuspected diversity of membrane association modes and domain architectures within the ARF family. We detail the step-wise expansion of the ARF family in the metazoan lineage, including discovery of several new animal-specific family members. Delving back to its earliest evolution in eukaryotes, the resolved relationship observed between the ARF family paralogs sets boundaries for scenarios of vesicle coat origins during eukaryogenesis. Altogether, our work fundamentally broadens the understanding of the diversity and evolution of a protein family underpinning the structural and functional complexity of the eukaryote cells.
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Affiliation(s)
- Romana Vargová
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Czech Republic
| | - Jeremy G Wideman
- Biodesign Center for Mechanisms of Evolution, School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Romain Derelle
- Station d'Ecologie Théorique et Expérimentale, UMR CNRS 5321, Moulis, France
| | - Vladimír Klimeš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Czech Republic
| | - Richard A Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Joel B Dacks
- Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada.,Centre for Life's Origin and Evolution, Department of Genetics, Evolution and Environment, University College of London, United Kingdom
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Czech Republic
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9
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May EA, Kalocsay M, D'Auriac IG, Schuster PS, Gygi SP, Nachury MV, Mick DU. Time-resolved proteomics profiling of the ciliary Hedgehog response. J Cell Biol 2021; 220:211991. [PMID: 33856408 PMCID: PMC8054476 DOI: 10.1083/jcb.202007207] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 02/01/2021] [Accepted: 03/03/2021] [Indexed: 12/12/2022] Open
Abstract
The primary cilium is a signaling compartment that interprets Hedgehog signals through changes of its protein, lipid, and second messenger compositions. Here, we combine proximity labeling of cilia with quantitative mass spectrometry to unbiasedly profile the time-dependent alterations of the ciliary proteome in response to Hedgehog. This approach correctly identifies the three factors known to undergo Hedgehog-regulated ciliary redistribution and reveals two such additional proteins. First, we find that a regulatory subunit of the cAMP-dependent protein kinase (PKA) rapidly exits cilia together with the G protein-coupled receptor GPR161 in response to Hedgehog, and we propose that the GPR161/PKA module senses and amplifies cAMP signals to modulate ciliary PKA activity. Second, we identify the phosphatase Paladin as a cell type-specific regulator of Hedgehog signaling that enters primary cilia upon pathway activation. The broad applicability of quantitative ciliary proteome profiling promises a rapid characterization of ciliopathies and their underlying signaling malfunctions.
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Affiliation(s)
- Elena A May
- Center of Human and Molecular Biology, Saarland University School of Medicine, Homburg, Germany
| | - Marian Kalocsay
- Department of Systems Biology, Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA.,Department of Cell Biology, Harvard Medical School, Boston, MA
| | - Inès Galtier D'Auriac
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA
| | - Patrick S Schuster
- Center of Human and Molecular Biology, Saarland University School of Medicine, Homburg, Germany
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA
| | - Maxence V Nachury
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA
| | - David U Mick
- Center of Human and Molecular Biology, Saarland University School of Medicine, Homburg, Germany.,Center for Molecular Signaling, Department of Medical Biochemistry and Molecular Biology, Saarland University School of Medicine, Homburg, Germany
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10
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Qiu H, Fujisawa S, Nozaki S, Katoh Y, Nakayama K. Interaction of INPP5E with ARL13B is essential for its ciliary membrane retention but dispensable for its ciliary entry. Biol Open 2021; 10:bio057653. [PMID: 33372066 PMCID: PMC7860134 DOI: 10.1242/bio.057653] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 12/09/2020] [Indexed: 12/11/2022] Open
Abstract
Compositions of proteins and lipids within cilia and on the ciliary membrane are maintained to be distinct from those of the cytoplasm and plasma membrane, respectively, by the presence of the ciliary gate. INPP5E is a phosphoinositide 5-phosphatase that is localized on the ciliary membrane by anchorage via its C-terminal prenyl moiety. In addition, the ciliary membrane localization of INPP5E is determined by the small GTPase ARL13B. However, it remained unclear as to how ARL13B participates in the localization of INPP5E. We here show that wild-type INPP5E, INPP5E(WT), in ARL13B-knockout cells and an INPP5E mutant defective in ARL13B binding, INPP5E(ΔCTS), in control cells were unable to show steady-state localization on the ciliary membrane. However, not only INPP5E(WT) but also INPP5E(ΔCTS) was able to rescue the abnormal localization of ciliary proteins in INPP5E-knockout cells. Analysis using the chemically induced dimerization system demonstrated that INPP5E(WT) in ARL13B-knockout cells and INPP5E(ΔCTS) in control cells were able to enter cilia, but neither was retained on the ciliary membrane due to the lack of the INPP5E-ARL13B interaction. Thus, our data demonstrate that binding of INPP5E to ARL13B is essential for its steady-state localization on the ciliary membrane but is dispensable for its entry into cilia.
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Affiliation(s)
- Hantian Qiu
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Sayaka Fujisawa
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shohei Nozaki
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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11
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Pandey M, Huang Y, Lim TK, Lin Q, He CY. Flagellar targeting of an arginine kinase requires a conserved lipidated protein intraflagellar transport (LIFT) pathway in Trypanosoma brucei. J Biol Chem 2020; 295:11326-11336. [PMID: 32587088 DOI: 10.1074/jbc.ra120.014287] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/18/2020] [Indexed: 12/31/2022] Open
Abstract
Both intraflagellar transport (IFT) and lipidated protein intraflagellar transport (LIFT) pathways are essential for cilia/flagella biogenesis, motility, and sensory functions. In the LIFT pathway, lipidated cargoes are transported into the cilia through the coordinated actions of cargo carrier proteins such as Unc119 or PDE6δ, as well as small GTPases Arl13b and Arl3 in the cilium. Our previous studies have revealed a single Arl13b ortholog in the evolutionarily divergent Trypanosoma brucei, the causative agent of African sleeping sickness. TbArl13 catalyzes two TbArl3 homologs, TbArl3A and TbArl3C, suggesting the presence of a conserved LIFT pathway in these protozoan parasites. Only a single homolog to the cargo carrier protein Unc119 has been identified in T. brucei genome, but its function in lipidated protein transport has not been characterized. In this study, we exploited the proximity-based biotinylation approach to identify binding partners of TbUnc119. We showed that TbUnc119 binds to a flagellar arginine kinase TbAK3 in a myristoylation-dependent manner and is responsible for its targeting to and enrichment in the flagellum. Interestingly, only TbArl3A, but not TbArl3C interacted with TbUnc119 in a GTP-dependent manner, suggesting functional specialization of Arl3-GTPases in T. brucei These results establish the function of TbUnc119 as a myristoylated cargo carrier and support the presence of a conserved LIFT pathway in T. brucei.
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Affiliation(s)
- Maneesha Pandey
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Yameng Huang
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Teck Kwang Lim
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Qingsong Lin
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Cynthia Y He
- Department of Biological Sciences, National University of Singapore, Singapore
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12
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Garcia E, Ismail S. Spatiotemporal Regulation of Signaling: Focus on T Cell Activation and the Immunological Synapse. Int J Mol Sci 2020; 21:E3283. [PMID: 32384769 PMCID: PMC7247333 DOI: 10.3390/ijms21093283] [Citation(s) in RCA: 20] [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: 03/31/2020] [Revised: 05/01/2020] [Accepted: 05/03/2020] [Indexed: 01/22/2023] Open
Abstract
In a signaling network, not only the functions of molecules are important but when (temporal) and where (spatial) those functions are exerted and orchestrated is what defines the signaling output. To temporally and spatially modulate signaling events, cells generate specialized functional domains with variable lifetime and size that concentrate signaling molecules, enhancing their transduction potential. The plasma membrane is a key in this regulation, as it constitutes a primary signaling hub that integrates signals within and across the membrane. Here, we examine some of the mechanisms that cells exhibit to spatiotemporally regulate signal transduction, focusing on the early events of T cell activation from triggering of T cell receptor to formation and maturation of the immunological synapse.
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Affiliation(s)
- Esther Garcia
- CR-UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Shehab Ismail
- CR-UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
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13
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Establishing and regulating the composition of cilia for signal transduction. Nat Rev Mol Cell Biol 2020; 20:389-405. [PMID: 30948801 DOI: 10.1038/s41580-019-0116-4] [Citation(s) in RCA: 246] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The primary cilium is a hair-like surface-exposed organelle of the eukaryotic cell that decodes a variety of signals - such as odorants, light and Hedgehog morphogens - by altering the local concentrations and activities of signalling proteins. Signalling within the cilium is conveyed through a diverse array of second messengers, including conventional signalling molecules (such as cAMP) and some unusual intermediates (such as sterols). Diffusion barriers at the ciliary base establish the unique composition of this signalling compartment, and cilia adapt their proteome to signalling demands through regulated protein trafficking. Much progress has been made on the molecular understanding of regulated ciliary trafficking, which encompasses not only exchanges between the cilium and the rest of the cell but also the shedding of signalling factors into extracellular vesicles.
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14
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Powell L, Samarakoon YH, Ismail S, Sayer JA. ARL3, a small GTPase with a functionally conserved role in primary cilia and immune synapses. Small GTPases 2019; 12:167-176. [PMID: 31826708 DOI: 10.1080/21541248.2019.1703466] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
The primary cilium and the immunological synapse are both specialized functional plasma membrane domains that share several similarities. Signalling output of membrane domains is regulated, spatially and temporally, by segregating and focusing lipids and proteins. ARL3, a small GTPase, plays a major role in concentrating lipid-modified proteins in both the immunological synapse and the primary cilia. Here in this review we will introduce the role of ARL3 in health and disease and its role in polarizing signalling at the primary cilia and immunological synapses.
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Affiliation(s)
- Laura Powell
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Newcastle upon Tyne, UK
| | - Youhani H Samarakoon
- Spatial segregation of signalling Lab, Beatson Institute for Cancer Research, Glasgow, UK.,Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Shehab Ismail
- Spatial segregation of signalling Lab, Beatson Institute for Cancer Research, Glasgow, UK.,Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - John A Sayer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Newcastle upon Tyne, UK.,Renal Services, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.,NIHR Newcastle Biomedical Research Centre, Newcastle upon Tyne, UK
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15
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Carter SP, Blacque OE. Membrane retrieval, recycling and release pathways that organise and sculpt the ciliary membrane. Curr Opin Cell Biol 2019; 59:133-139. [PMID: 31146146 DOI: 10.1016/j.ceb.2019.04.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/15/2019] [Accepted: 04/17/2019] [Indexed: 12/16/2022]
Abstract
The microtubule-based cilium that extends from the surface of most eukaryotic cell types serves motility, sensory reception and cell-cell signaling functions, and is disrupted in wide-ranging ciliopathy disorders. The cilium is heavily reliant on dynamic and tuneable intracellular trafficking systems such as intraflagellar transport and Golgi-derived secretory pathways, which control the organelle's structure, function and molecular composition. More recently, endosomal retrieval and recycling, as well as extracellular vesicle (EV) release, pathways have been associated with ciliary membrane control. Here, we discuss the emerging role of these pathways in the control of ciliary membrane homeostasis. The new findings provide a deeper and more integrated understanding of how the ciliary membrane is organised.
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Affiliation(s)
- Stephen P Carter
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Oliver E Blacque
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland.
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16
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Mégarbané A, Hmaimess G, Bizzari S, El-Bazzal L, Al-Ali MT, Stora S, Delague V, El-Hayek S. A novel PDE6D mutation in a patient with Joubert syndrome type 22 (JBTS22). Eur J Med Genet 2018; 62:103576. [PMID: 30423442 DOI: 10.1016/j.ejmg.2018.11.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 10/02/2018] [Accepted: 11/09/2018] [Indexed: 10/27/2022]
Abstract
Joubert syndrome (JS) is an autosomal or X-linked recessive syndrome principally characterized by hypotonia, ataxia, cognitive impairment, and a specific finding on brain imaging called a "molar tooth sign" (MTS), which can be isolated or in conjunction with variable organ involvement. The genetic basis of JS is heterogeneous, with over 35 ciliary genes being implicated in its pathogenesis. However, some of these genes (such as PDE6D) have been associated to JS only in single families, seeking confirmation. Here we report a boy, born to first cousin parents, presenting with developmental delay, hypotonia, microcephaly, post axial polydactyly, oculomotor apraxia, and MTS. Whole exome sequencing revealed the presence of a novel homozygous truncating variant in the PDE6D gene: NM_002601.3:c.367_368insG [p.(Leu123Cysfs*13)]. The variant was confirmed by Sanger sequencing and found at the heterozygous state in both parents. A review of the literature pertaining to the role of PDE6D in JS is discussed.
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Affiliation(s)
| | | | - Sami Bizzari
- Centre for Arab Genomic Studies, Dubai, United Arab Emirates
| | - Lara El-Bazzal
- Aix Marseille Univ, Inserm, MMG, U 1251, Marseille, France
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17
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Structural basis of Gip1 for cytosolic sequestration of G protein in wide-range chemotaxis. Nat Commun 2018; 9:4635. [PMID: 30401901 PMCID: PMC6219514 DOI: 10.1038/s41467-018-07035-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 10/10/2018] [Indexed: 12/15/2022] Open
Abstract
G protein interacting protein 1 (Gip1) binds and sequesters heterotrimeric G proteins in the cytosolic pool, thus regulating G protein-coupled receptor (GPCR) signalling for eukaryotic chemotaxis. Here, we report the underlying structural basis of Gip1 function. The crystal structure reveals that the region of Gip1 that binds to the G protein has a cylinder-like fold with a central hydrophobic cavity composed of six α-helices. Mutagenesis and biochemical analyses indicate that the hydrophobic cavity and the hydrogen bond network at the entrance of the cavity are essential for complex formation with the geranylgeranyl modification on the Gγ subunit. Mutations of the cavity impair G protein sequestration and translocation to the membrane from the cytosol upon receptor stimulation, leading to defects in chemotaxis at higher chemoattractant concentrations. These results demonstrate that the Gip1-dependent regulation of G protein shuttling ensures wide-range gradient sensing in eukaryotic chemotaxis. Gip1 sequesters heterotrimeric G proteins in the cytosolic pool which regulates G protein-coupled receptor signalling for eukaryotic chemotaxis. Here the authors provide the crystal structure of Gip1's G protein-binding region and show that mutations in this region lead to G protein sequestration and ultimately chemotaxis defects.
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18
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ARL3 subcellular localization and its suspected role in autophagy. Biochimie 2018; 154:187-193. [DOI: 10.1016/j.biochi.2018.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 09/13/2018] [Indexed: 11/23/2022]
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19
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Morthorst SK, Christensen ST, Pedersen LB. Regulation of ciliary membrane protein trafficking and signalling by kinesin motor proteins. FEBS J 2018; 285:4535-4564. [PMID: 29894023 DOI: 10.1111/febs.14583] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/09/2018] [Accepted: 06/11/2018] [Indexed: 12/14/2022]
Abstract
Primary cilia are antenna-like sensory organelles that regulate a substantial number of cellular signalling pathways in vertebrates, both during embryonic development as well as in adulthood, and mutations in genes coding for ciliary proteins are causative of an expanding group of pleiotropic diseases known as ciliopathies. Cilia consist of a microtubule-based axoneme core, which is subtended by a basal body and covered by a bilayer lipid membrane of unique protein and lipid composition. Cilia are dynamic organelles, and the ability of cells to regulate ciliary protein and lipid content in response to specific cellular and environmental cues is crucial for balancing ciliary signalling output. Here we discuss mechanisms involved in regulation of ciliary membrane protein trafficking and signalling, with main focus on kinesin-2 and kinesin-3 family members.
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20
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Stephen LA, Elmaghloob Y, Ismail S. Maintaining protein composition in cilia. Biol Chem 2017; 399:1-11. [PMID: 28850540 DOI: 10.1515/hsz-2017-0168] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 08/18/2017] [Indexed: 01/10/2023]
Abstract
The primary cilium is a sensory organelle that is vital in regulating several signalling pathways. Unlike most organelles cilia are open to the rest of the cell, not enclosed by membranes. The distinct protein composition is crucial to the function of cilia and many signalling proteins and receptors are specifically concentrated within distinct compartments. To maintain this composition, a mechanism is required to deliver proteins to the cilium whilst another must counter the entropic tendency of proteins to distribute throughout the cell. The combination of the two mechanisms should result in the concentration of ciliary proteins to the cilium. In this review we will look at different cellular mechanisms that play a role in maintaining the distinct composition of cilia, including regulation of ciliary access and trafficking of ciliary proteins to, from and within the cilium.
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Affiliation(s)
- Louise A Stephen
- CR-UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Yasmin Elmaghloob
- CR-UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Shehab Ismail
- CR-UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
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21
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Jensen VL, Leroux MR. Gates for soluble and membrane proteins, and two trafficking systems (IFT and LIFT), establish a dynamic ciliary signaling compartment. Curr Opin Cell Biol 2017; 47:83-91. [PMID: 28432921 DOI: 10.1016/j.ceb.2017.03.012] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 02/18/2017] [Accepted: 03/21/2017] [Indexed: 12/28/2022]
Abstract
Primary cilia are microtubule-based organelles found on most mammalian cell surfaces. They possess a soluble matrix and membrane contiguous with the cell body cytosol and plasma membrane, and yet, have distinct compositions that can be modulated to enable dynamic signal transduction. Here, we discuss how specialized ciliary compartments are established using a coordinated network of gating, trafficking and targeting activities. Cilium homeostasis is maintained by a size-selective molecular mesh that limits soluble protein entry, and by a membrane diffusion barrier localized at the transition zone. Bidirectional protein shuttling between the cell body and cilium uses IntraFlagellar Transport (IFT), and prenylated ciliary protein delivery is achieved through Lipidated protein IntraFlagellar Targeting (LIFT). Elucidating how these gates and transport systems function will help reveal the roles that cilia play in ciliary signaling and the growing spectrum of disorders termed ciliopathies.
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Affiliation(s)
- Victor L Jensen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada; Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, Canada
| | - Michel R Leroux
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada; Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, Canada.
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