1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Tran MV, Khuntsariya D, Fetter RD, Ferguson JW, Wang JT, Long AF, Cote LE, Wellard SR, Vázquez-Martínez N, Sallee MD, Genova M, Magiera MM, Eskinazi S, Lee JD, Peel N, Janke C, Stearns T, Shen K, Lansky Z, Magescas J, Feldman JL. MAP9/MAPH-9 supports axonemal microtubule doublets and modulates motor movement. Dev Cell 2024; 59:199-210.e11. [PMID: 38159567 DOI: 10.1016/j.devcel.2023.12.001] [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: 01/09/2023] [Revised: 08/15/2023] [Accepted: 12/04/2023] [Indexed: 01/03/2024]
Abstract
Microtubule doublets (MTDs) comprise an incomplete microtubule (B-tubule) attached to the side of a complete cylindrical microtubule. These compound microtubules are conserved in cilia across the tree of life; however, the mechanisms by which MTDs form and are maintained in vivo remain poorly understood. Here, we identify microtubule-associated protein 9 (MAP9) as an MTD-associated protein. We demonstrate that C. elegans MAPH-9, a MAP9 homolog, is present during MTD assembly and localizes exclusively to MTDs, a preference that is in part mediated by tubulin polyglutamylation. We find that loss of MAPH-9 causes ultrastructural MTD defects, including shortened and/or squashed B-tubules with reduced numbers of protofilaments, dysregulated axonemal motor velocity, and perturbed cilia function. Because we find that the mammalian ortholog MAP9 localizes to axonemes in cultured mammalian cells and mouse tissues, we propose that MAP9/MAPH-9 plays a conserved role in regulating ciliary motors and supporting the structure of axonemal MTDs.
Collapse
Affiliation(s)
- Michael V Tran
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Daria Khuntsariya
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, 25250 Vestec, Prague West, Czech Republic
| | - Richard D Fetter
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - James W Ferguson
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Jennifer T Wang
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Alexandra F Long
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Lauren E Cote
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | | | | | - Maria D Sallee
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Mariya Genova
- Institut Curie, Université PSL, CNRS UMR3348, Orsay, France; Université Paris-Saclay, CNRS UMR3348, Orsay, France
| | - Maria M Magiera
- Institut Curie, Université PSL, CNRS UMR3348, Orsay, France; Université Paris-Saclay, CNRS UMR3348, Orsay, France
| | - Sani Eskinazi
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Nina Peel
- The College of New Jersey, Ewing, NJ 08628, USA
| | - Carsten Janke
- Institut Curie, Université PSL, CNRS UMR3348, Orsay, France; Université Paris-Saclay, CNRS UMR3348, Orsay, France
| | - Tim Stearns
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kang Shen
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Zdenek Lansky
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, 25250 Vestec, Prague West, Czech Republic
| | - Jérémy Magescas
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
| | - Jessica L Feldman
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
3
|
Serres MP, Shaughnessy R, Escot S, Hammich H, Cuvelier F, Salles A, Rocancourt M, Verdon Q, Gaffuri AL, Sourigues Y, Malherbe G, Velikovsky L, Chardon F, Sassoon N, Tinevez JY, Callebaut I, Formstecher E, Houdusse A, David NB, Pylypenko O, Echard A. MiniBAR/GARRE1 is a dual Rac and Rab effector required for ciliogenesis. Dev Cell 2023; 58:2477-2494.e8. [PMID: 37875118 DOI: 10.1016/j.devcel.2023.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 07/07/2023] [Accepted: 09/29/2023] [Indexed: 10/26/2023]
Abstract
Cilia protrude from the cell surface and play critical roles in intracellular signaling, environmental sensing, and development. Reduced actin-dependent contractility and intracellular trafficking are both required for ciliogenesis, but little is known about how these processes are coordinated. Here, we identified a Rac1- and Rab35-binding protein with a truncated BAR (Bin/amphiphysin/Rvs) domain that we named MiniBAR (also known as KIAA0355/GARRE1), which plays a key role in ciliogenesis. MiniBAR colocalizes with Rac1 and Rab35 at the plasma membrane and on intracellular vesicles trafficking to the ciliary base and exhibits fast pulses at the ciliary membrane. MiniBAR depletion leads to short cilia, resulting from abnormal Rac-GTP/Rho-GTP levels and increased acto-myosin-II-dependent contractility together with defective trafficking of IFT88 and ARL13B into cilia. MiniBAR-depleted zebrafish embryos display dysfunctional short cilia and hallmarks of ciliopathies, including left-right asymmetry defects. Thus, MiniBAR is a dual Rac and Rab effector that controls both actin cytoskeleton and membrane trafficking for ciliogenesis.
Collapse
Affiliation(s)
- Murielle P Serres
- Institut Pasteur, Université de Paris, CNRS UMR3691, Membrane Traffic and Cell Division Laboratory, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Ronan Shaughnessy
- Institut Pasteur, Université de Paris, CNRS UMR3691, Membrane Traffic and Cell Division Laboratory, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Sophie Escot
- Laboratoire d'Optique et Biosciences (LOB), CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Hussein Hammich
- Institut Curie, PSL Research University, CNRS UMR144, Structural Motility, 26 rue d'Ulm, 75005 Paris, France
| | - Frédérique Cuvelier
- Institut Pasteur, Université de Paris, CNRS UMR3691, Membrane Traffic and Cell Division Laboratory, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Audrey Salles
- Institut Pasteur, Université de Paris, UTechS Photonic BioImaging (UTechS PBI), Centre de Recherche et de Ressources Technologiques C2RT, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Murielle Rocancourt
- Institut Pasteur, Université de Paris, CNRS UMR3691, Membrane Traffic and Cell Division Laboratory, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Quentin Verdon
- Institut Pasteur, Université de Paris, CNRS UMR3691, Membrane Traffic and Cell Division Laboratory, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Anne-Lise Gaffuri
- Institut Pasteur, Université de Paris, CNRS UMR3691, Membrane Traffic and Cell Division Laboratory, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Yannick Sourigues
- Institut Curie, PSL Research University, CNRS UMR144, Structural Motility, 26 rue d'Ulm, 75005 Paris, France
| | - Gilles Malherbe
- Institut Curie, PSL Research University, CNRS UMR144, Structural Motility, 26 rue d'Ulm, 75005 Paris, France
| | - Leonid Velikovsky
- Institut Curie, PSL Research University, CNRS UMR144, Structural Motility, 26 rue d'Ulm, 75005 Paris, France
| | - Florian Chardon
- Institut Curie, PSL Research University, CNRS UMR144, Structural Motility, 26 rue d'Ulm, 75005 Paris, France
| | - Nathalie Sassoon
- Institut Pasteur, Université de Paris, CNRS UMR3691, Membrane Traffic and Cell Division Laboratory, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Jean-Yves Tinevez
- Institut Pasteur, Université de Paris, Image Analysis Hub, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Etienne Formstecher
- Hybrigenics Services SAS, 1 rue Pierre Fontaine 91000 Evry, Courcouronnes, France
| | - Anne Houdusse
- Institut Curie, PSL Research University, CNRS UMR144, Structural Motility, 26 rue d'Ulm, 75005 Paris, France
| | - Nicolas B David
- Laboratoire d'Optique et Biosciences (LOB), CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Olena Pylypenko
- Institut Curie, PSL Research University, CNRS UMR144, Structural Motility, 26 rue d'Ulm, 75005 Paris, France
| | - Arnaud Echard
- Institut Pasteur, Université de Paris, CNRS UMR3691, Membrane Traffic and Cell Division Laboratory, 25-28 rue du Dr Roux, 75015 Paris, France.
| |
Collapse
|
4
|
Yin G, Huang J, Petela J, Jiang H, Zhang Y, Gong S, Wu J, Liu B, Shi J, Gao Y. Targeting small GTPases: emerging grasps on previously untamable targets, pioneered by KRAS. Signal Transduct Target Ther 2023; 8:212. [PMID: 37221195 DOI: 10.1038/s41392-023-01441-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/28/2023] [Accepted: 04/14/2023] [Indexed: 05/25/2023] Open
Abstract
Small GTPases including Ras, Rho, Rab, Arf, and Ran are omnipresent molecular switches in regulating key cellular functions. Their dysregulation is a therapeutic target for tumors, neurodegeneration, cardiomyopathies, and infection. However, small GTPases have been historically recognized as "undruggable". Targeting KRAS, one of the most frequently mutated oncogenes, has only come into reality in the last decade due to the development of breakthrough strategies such as fragment-based screening, covalent ligands, macromolecule inhibitors, and PROTACs. Two KRASG12C covalent inhibitors have obtained accelerated approval for treating KRASG12C mutant lung cancer, and allele-specific hotspot mutations on G12D/S/R have been demonstrated as viable targets. New methods of targeting KRAS are quickly evolving, including transcription, immunogenic neoepitopes, and combinatory targeting with immunotherapy. Nevertheless, the vast majority of small GTPases and hotspot mutations remain elusive, and clinical resistance to G12C inhibitors poses new challenges. In this article, we summarize diversified biological functions, shared structural properties, and complex regulatory mechanisms of small GTPases and their relationships with human diseases. Furthermore, we review the status of drug discovery for targeting small GTPases and the most recent strategic progress focused on targeting KRAS. The discovery of new regulatory mechanisms and development of targeting approaches will together promote drug discovery for small GTPases.
Collapse
Affiliation(s)
- Guowei Yin
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China.
| | - Jing Huang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Johnny Petela
- Wake Forest University School of Medicine, Winston-Salem, NC, 27101, USA
| | - Hongmei Jiang
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
| | - Yuetong Zhang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Siqi Gong
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
- School of Medicine, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Jiaxin Wu
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Bei Liu
- National Biomedical Imaging Center, School of Future Technology, Peking University, Beijing, 100871, China
| | - Jianyou Shi
- Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology, Chengdu, 610072, China.
| | - Yijun Gao
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
| |
Collapse
|
5
|
Lin T, Sun Y. Arl13b promotes the proliferation, migration, osteogenesis, and mechanosensation of osteoblasts. Tissue Cell 2023; 82:102088. [PMID: 37058812 DOI: 10.1016/j.tice.2023.102088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/27/2023] [Accepted: 04/10/2023] [Indexed: 04/16/2023]
Abstract
Primary cilia are microtubule-based organelles presenting on the surface of most postmitotic mammalian cells. As being signaling hubs and sensory organelles, primary cilia can respond to mechanical and chemical stimuli from the extracellular environment. Arl13b (ADP-ribosylation factor-like 13B), an atypical Arf/Arl family GTPase, was identified in genetic screening as a protein essential for maintaining the integrity of cilia and neural tubes. Previous studies on Arl13b have mostly focused on its role in the development of neural tubes, polycystic kidneys, and tumors, but no role in bone patterns was described. This study reported the essential roles of Arl13b in bone formation and osteogenic differentiation. Arl13b was highly expressed in bone tissues and osteoblasts, positively correlated with osteogenic activity during bone development. Furthermore, Arl13b was essential for primary cilium maintenance and Hedgehog signaling activation in osteoblasts. Arl13b knockdown in osteoblasts decreased the length of primary cilia and the upregulated levels of Gli1, Smo, and Ptch1 upon Smo agonist treatment. Additionally, Arl13b knockdown inhibited cell proliferation and migration. Moreover, Arl13b mediated osteogenesis and cell mechanosensation. Cyclic tension strain upregulated the Arl13b expression. Arl13b knockdown suppressed osteogenesis and mitigated cyclic tension strain-induced osteogenesis. These results suggest that Arl13b have important roles in bone formation and mechanosensation.
Collapse
Affiliation(s)
- Tingting Lin
- Department of Implantology, Stomatological Hospital and Dental School of Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai 200072, China
| | - Yao Sun
- Department of Implantology, Stomatological Hospital and Dental School of Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai 200072, China.
| |
Collapse
|
6
|
Mahajan D, Madugula V, Lu L. Rab8 and TNPO1 are ciliary transport adaptors for GTPase Arl13b by interacting with its RVEP motif-containing ciliary targeting sequence. J Biol Chem 2023; 299:104604. [PMID: 36907439 PMCID: PMC10124946 DOI: 10.1016/j.jbc.2023.104604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 03/04/2023] [Accepted: 03/06/2023] [Indexed: 03/12/2023] Open
Abstract
Arl13b, an ARF/Arl-family GTPase, is highly enriched in the cilium. Recent studies have established Arl13b as one of the most crucial regulators for ciliary organization, trafficking, and signaling. The ciliary localization of Arl13b is known to require the RVEP motif. However, its cognitive ciliary transport adaptor has been elusive. Here, by imaging the ciliary localization of truncation and point mutations, we defined the ciliary targeting sequence (CTS) of Arl13b as a C-terminal stretch of 17 amino acids containing the RVEP motif. We found Rab8-GDP, but not Rab8-GTP, and TNPO1 simultaneously and directly bind to the CTS of Arl13b in pull-down assays using cell lysates or purified recombinant proteins. Furthermore, Rab8-GDP substantially enhances the interaction between TNPO1 and CTS. Additionally, we determined that the RVEP motif is an essential element as its mutation abolishes the interaction of the CTS with Rab8-GDP and TNPO1 in pull-down and TurboID-based proximity ligation assays. Finally, knockdown of endogenous Rab8 or TNPO1 decreases the ciliary localization of endogenous Arl13b. Therefore, our results suggest Rab8 and TNPO1 might function together as a ciliary transport adaptor for Arl13b by interacting with its RVEP-containing CTS.
Collapse
Affiliation(s)
- Divyanshu Mahajan
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Viswanadh Madugula
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Lei Lu
- School of Biological Sciences, Nanyang Technological University, Singapore.
| |
Collapse
|
7
|
Palicharla VR, Hwang SH, Somatilaka BN, Legué E, Shimada IS, Familiari NE, Tran VM, Woodruff JB, Liem KF, Mukhopadhyay S. Interactions between TULP3 tubby domain and ARL13B amphipathic helix promote lipidated protein transport to cilia. Mol Biol Cell 2023; 34:ar18. [PMID: 36652335 PMCID: PMC10011728 DOI: 10.1091/mbc.e22-10-0473] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The primary cilium is a nexus for cell signaling and relies on specific protein trafficking for function. The tubby family protein TULP3 transports integral membrane proteins into cilia through interactions with the intraflagellar transport complex-A (IFT-A) and phosphoinositides. It was previously shown that short motifs called ciliary localization sequences (CLSs) are necessary and sufficient for TULP3-dependent ciliary trafficking of transmembrane cargoes. However, the mechanisms by which TULP3 regulates ciliary compartmentalization of nonintegral, membrane-associated proteins and whether such trafficking requires TULP3-dependent CLSs is unknown. Here we show that TULP3 is required for ciliary transport of the Joubert syndrome-linked palmitoylated GTPase ARL13B through a CLS. An N-terminal amphipathic helix, preceding the GTPase domain of ARL13B, couples with the TULP3 tubby domain for ciliary trafficking, irrespective of palmitoylation. ARL13B transport requires TULP3 binding to IFT-A but not to phosphoinositides, indicating strong membrane-proximate interactions, unlike transmembrane cargo transport requiring both properties of TULP3. TULP3-mediated trafficking of ARL13B also regulates ciliary enrichment of farnesylated and myristoylated downstream effectors of ARL13B. The lipidated cargoes show distinctive depletion kinetics from kidney epithelial cilia with relation to Tulp3 deletion-induced renal cystogenesis. Overall, these findings indicate an expanded role of the tubby domain in capturing analogous helical secondary structural motifs from diverse cargoes.
Collapse
Affiliation(s)
- Vivek Reddy Palicharla
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Sun-Hee Hwang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | | | - Emilie Legué
- Vertebrate Developmental Biology Program, Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06520
| | - Issei S Shimada
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Nicole E Familiari
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Vanna M Tran
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Jeffrey B Woodruff
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Karel F Liem
- Vertebrate Developmental Biology Program, Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06520
| | - Saikat Mukhopadhyay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| |
Collapse
|
8
|
Habif JC, Xie C, de Celis C, Ukhanov K, Green WW, Moretta JC, Zhang L, Campbell RJ, Martens JR. The role of a ciliary GTPase in the regulation of neuronal maturation of olfactory sensory neurons. Development 2023; 150:286702. [PMID: 36661357 PMCID: PMC10110495 DOI: 10.1242/dev.201116] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 12/19/2022] [Indexed: 01/20/2023]
Abstract
Olfactory sensory neurons (OSNs) form embryonically and mature perinatally, innervating glomeruli and extending dendrites with multiple cilia. This process and its timing are crucial for odor detection and perception and continues throughout life. In the olfactory epithelium (OE), differentiated OSNs proceed from an immature (iOSN) to a mature (mOSN) state through well-defined sequential morphological and molecular transitions, but the precise mechanisms controlling OSN maturation remain largely unknown. We have identified that a GTPase, ARL13B, has a transient and maturation state-dependent expression in OSNs marking the emergence of a primary cilium. Utilizing an iOSN-specific Arl13b-null murine model, we examined the role of ARL13B in the maturation of OSNs. The loss of Arl13b in iOSNs caused a profound dysregulation of the cellular homeostasis and development of the OE. Importantly, Arl13b null OSNs demonstrated a delay in the timing of their maturation. Finally, the loss of Arl13b resulted in severe deformation in the structure and innervation of glomeruli. Our findings demonstrate a previously unknown role of ARL13B in the maturation of OSNs and development of the OE.
Collapse
Affiliation(s)
- Julien C Habif
- Department of Pharmacology and Therapeutics, University of Florida, College of Medicine, Gainesville, FL 32610, USA
- University of Florida Center for Smell and Taste, Gainesville, FL 32610, USA
| | - Chao Xie
- Department of Pharmacology and Therapeutics, University of Florida, College of Medicine, Gainesville, FL 32610, USA
- University of Florida Center for Smell and Taste, Gainesville, FL 32610, USA
| | - Carlos de Celis
- Department of Pharmacology and Therapeutics, University of Florida, College of Medicine, Gainesville, FL 32610, USA
- University of Florida Center for Smell and Taste, Gainesville, FL 32610, USA
| | - Kirill Ukhanov
- Department of Pharmacology and Therapeutics, University of Florida, College of Medicine, Gainesville, FL 32610, USA
- University of Florida Center for Smell and Taste, Gainesville, FL 32610, USA
| | - Warren W Green
- Department of Pharmacology and Therapeutics, University of Florida, College of Medicine, Gainesville, FL 32610, USA
- University of Florida Center for Smell and Taste, Gainesville, FL 32610, USA
| | - Jordan C Moretta
- Department of Pharmacology and Therapeutics, University of Florida, College of Medicine, Gainesville, FL 32610, USA
- University of Florida Center for Smell and Taste, Gainesville, FL 32610, USA
| | - Lian Zhang
- Department of Pharmacology and Therapeutics, University of Florida, College of Medicine, Gainesville, FL 32610, USA
- University of Florida Center for Smell and Taste, Gainesville, FL 32610, USA
| | - Robert J Campbell
- Department of Pharmacology and Therapeutics, University of Florida, College of Medicine, Gainesville, FL 32610, USA
- University of Florida Center for Smell and Taste, Gainesville, FL 32610, USA
| | - Jeffrey R Martens
- Department of Pharmacology and Therapeutics, University of Florida, College of Medicine, Gainesville, FL 32610, USA
- University of Florida Center for Smell and Taste, Gainesville, FL 32610, USA
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Kim H, Mori Y, Plotkin JB. Optimality of intercellular signaling: Direct transport versus diffusion. Phys Rev E 2022; 106:054411. [PMID: 36559352 DOI: 10.1103/physreve.106.054411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 10/28/2022] [Indexed: 06/17/2023]
Abstract
Intercellular signaling has an important role in organism development, but not all communication occurs using the same mechanism. Here, we analyze the energy efficiency of intercellular signaling by two canonical mechanisms: Diffusion of signaling molecules and direct transport mediated by signaling cellular protrusions. We show that efficient contact formation for direct transport can be established by an optimal rate of projecting protrusions, which depends on the availability of information about the location of the target cell. The optimal projection rate also depends on how signaling molecules are transported along the protrusion, in particular the ratio of the energy cost for contact formation and molecule synthesis. Also, we compare the efficiency of the two signaling mechanisms, under various model parameters. We find that direct transport is favored over diffusion when transporting a large amount of signaling molecules. There is a critical number of signaling molecules at which the efficiencies of the two mechanisms are the same. The critical number is small when the distance between cells is far, which helps explain why protrusion-based mechanisms are observed in long-range cellular communications.
Collapse
Affiliation(s)
- Hyunjoong Kim
- Center for Mathematical Biology and Department of Mathematics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Yoichiro Mori
- Center for Mathematical Biology and Department of Mathematics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Joshua B Plotkin
- Center for Mathematical Biology and Department of Mathematics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| |
Collapse
|
11
|
Cilleros-Rodriguez D, Martin-Morales R, Barbeito P, Deb Roy A, Loukil A, Sierra-Rodero B, Herranz G, Pampliega O, Redrejo-Rodriguez M, Goetz SC, Izquierdo M, Inoue T, Garcia-Gonzalo FR. Multiple ciliary localization signals control INPP5E ciliary targeting. eLife 2022; 11:e78383. [PMID: 36063381 PMCID: PMC9444247 DOI: 10.7554/elife.78383] [Citation(s) in RCA: 8] [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: 03/04/2022] [Accepted: 08/21/2022] [Indexed: 12/04/2022] Open
Abstract
Primary cilia are sensory membrane protrusions whose dysfunction causes ciliopathies. INPP5E is a ciliary phosphoinositide phosphatase mutated in ciliopathies like Joubert syndrome. INPP5E regulates numerous ciliary functions, but how it accumulates in cilia remains poorly understood. Herein, we show INPP5E ciliary targeting requires its folded catalytic domain and is controlled by four conserved ciliary localization signals (CLSs): LLxPIR motif (CLS1), W383 (CLS2), FDRxLYL motif (CLS3) and CaaX box (CLS4). We answer two long-standing questions in the field. First, partial CLS1-CLS4 redundancy explains why CLS4 is dispensable for ciliary targeting. Second, the essential need for CLS2 clarifies why CLS3-CLS4 are together insufficient for ciliary accumulation. Furthermore, we reveal that some Joubert syndrome mutations perturb INPP5E ciliary targeting, and clarify how each CLS works: (i) CLS4 recruits PDE6D, RPGR and ARL13B, (ii) CLS2-CLS3 regulate association to TULP3, ARL13B, and CEP164, and (iii) CLS1 and CLS4 cooperate in ATG16L1 binding. Altogether, we shed light on the mechanisms of INPP5E ciliary targeting, revealing a complexity without known parallels among ciliary cargoes.
Collapse
Affiliation(s)
- Dario Cilleros-Rodriguez
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM)MadridSpain
- Instituto de Investigaciones Biomédicas “Alberto Sols” (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAMMadridSpain
- Instituto de Investigación del Hospital Universitario de La Paz (IdiPAZ)MadridSpain
- CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII)MadridSpain
| | - Raquel Martin-Morales
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM)MadridSpain
- Instituto de Investigaciones Biomédicas “Alberto Sols” (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAMMadridSpain
- Instituto de Investigación del Hospital Universitario de La Paz (IdiPAZ)MadridSpain
- CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII)MadridSpain
| | - Pablo Barbeito
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM)MadridSpain
- Instituto de Investigaciones Biomédicas “Alberto Sols” (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAMMadridSpain
- Instituto de Investigación del Hospital Universitario de La Paz (IdiPAZ)MadridSpain
- CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII)MadridSpain
| | - Abhijit Deb Roy
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Abdelhalim Loukil
- Department of Pharmacology and Cancer Biology, Duke University School of MedicineDurhamUnited States
| | - Belen Sierra-Rodero
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM)MadridSpain
- Instituto de Investigaciones Biomédicas “Alberto Sols” (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAMMadridSpain
- Instituto de Investigación del Hospital Universitario de La Paz (IdiPAZ)MadridSpain
- CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII)MadridSpain
| | - Gonzalo Herranz
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM)MadridSpain
- Instituto de Investigaciones Biomédicas “Alberto Sols” (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAMMadridSpain
| | - Olatz Pampliega
- Department of Neurosciences, University of the Basque Country, Achucarro Basque Center for Neuroscience-UPV/EHULeioaSpain
| | - Modesto Redrejo-Rodriguez
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM)MadridSpain
- Instituto de Investigaciones Biomédicas “Alberto Sols” (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAMMadridSpain
| | - Sarah C Goetz
- Department of Pharmacology and Cancer Biology, Duke University School of MedicineDurhamUnited States
| | - Manuel Izquierdo
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM)MadridSpain
- Instituto de Investigaciones Biomédicas “Alberto Sols” (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAMMadridSpain
| | - Takanari Inoue
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Francesc R Garcia-Gonzalo
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM)MadridSpain
- Instituto de Investigaciones Biomédicas “Alberto Sols” (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAMMadridSpain
- Instituto de Investigación del Hospital Universitario de La Paz (IdiPAZ)MadridSpain
- CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII)MadridSpain
| |
Collapse
|
12
|
Dai J, Zhang G, Alkhofash RA, Mekonnen B, Saravanan S, Xue B, Fan ZC, Betleja E, Cole DG, Liu P, Lechtreck K. Loss of ARL13 impedes BBSome-dependent cargo export from Chlamydomonas cilia. J Cell Biol 2022; 221:213429. [PMID: 36040375 PMCID: PMC9436004 DOI: 10.1083/jcb.202201050] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/12/2022] [Accepted: 07/11/2022] [Indexed: 12/25/2022] Open
Abstract
The GTPase Arl13b participates in ciliary protein transport, but its contribution to intraflagellar transport (IFT), the main motor-based protein shuttle of cilia, remains largely unknown. Chlamydomonas arl13 mutant cilia were characterized by both abnormal reduction and accumulation of select membrane-associated proteins. With respect to the latter, a similar set of proteins including phospholipase D (PLD) also accumulated in BBSome-deficient cilia. IFT and BBSome traffic were apparently normal in arl13. However, transport of PLD, which in control cells moves by BBSome-dependent IFT, was impaired in arl13, causing PLD to accumulate in cilia. ARL13 only rarely and transiently traveled by IFT, indicating that it is not a co-migrating adapter securing PLD to IFT trains. In conclusion, the loss of Chlamydomonas ARL13 impedes BBSome-dependent protein transport, resulting in overlapping biochemical defects in arl13 and bbs mutant cilia.
Collapse
Affiliation(s)
- Jin Dai
- Cellular Biology, University of Georgia, Athens, GA
| | - Gui Zhang
- Cellular Biology, University of Georgia, Athens, GA
| | | | | | | | - Bin Xue
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Zhen-Chuan Fan
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | | | | | - Peiwei Liu
- College of Life Science, Shandong Normal University, Jinan, Shandong, China
| | - Karl Lechtreck
- Cellular Biology, University of Georgia, Athens, GA,Correspondence to Karl F. Lechtreck:
| |
Collapse
|
13
|
Bentley-Ford MR, Andersen RS, Croyle MJ, Haycraft CJ, Clearman KR, Foote JB, Reiter JF, Yoder BK. ATXN10 Is Required for Embryonic Heart Development and Maintenance of Epithelial Cell Phenotypes in the Adult Kidney and Pancreas. Front Cell Dev Biol 2021; 9:705182. [PMID: 34970537 PMCID: PMC8712648 DOI: 10.3389/fcell.2021.705182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Atxn10 is a gene known for its role in cytokinesis and is associated with spinocerebellar ataxia (SCA10), a slowly progressing cerebellar syndrome caused by an intragenic pentanucleotide repeat expansion. Atxn10 is also implicated in the ciliopathy syndromes nephronophthisis (NPHP) and Joubert syndrome (JBTS), which are caused by the disruption of cilia function leading to nephron loss, impaired renal function, and cerebellar hypoplasia. How Atxn10 disruption contributes to these disorders remains unknown. Here, we generated Atxn10 congenital and conditional mutant mouse models. Our data indicate that while ATXN10 protein can be detected around the base of the cilium as well as in the cytosol, its loss does not cause overt changes in cilia formation or morphology. Congenital loss of Atxn10 results in embryonic lethality around E10.5 associated with pericardial effusion and loss of trabeculation. Similarly, tissue-specific loss of ATXN10 in the developing endothelium (Tie2-Cre) and myocardium (cTnT-Cre) also results in embryonic lethality with severe cardiac malformations occurring in the latter. Using an inducible Cagg-CreER to disrupt ATXN10 systemically at postnatal stages, we show that ATXN10 is also required for survival in adult mice. Loss of ATXN10 results in severe pancreatic and renal abnormalities leading to lethality within a few weeks post ATXN10 deletion in adult mice. Evaluation of these phenotypes further identified rapid epithelial-to-mesenchymal transition (EMT) in these tissues. In the pancreas, the phenotype includes signs of both acinar to ductal metaplasia and EMT with aberrant cilia formation and severe defects in glucose homeostasis related to pancreatic insufficiency or defects in feeding or nutrient intake. Collectively, this study identifies ATXN10 as an essential protein for survival.
Collapse
Affiliation(s)
- Melissa R. Bentley-Ford
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Reagan S. Andersen
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Mandy J. Croyle
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Courtney J. Haycraft
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Kelsey R. Clearman
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jeremy B. Foote
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jeremy F. Reiter
- Department of Biochemistry and Biophysics, University of Alabama at Birmingham, San Francisco, CA, United States
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, United States
| | - Bradley K. Yoder
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Cevik S, Kaplan OI. The Joubert syndrome protein CEP41 is excluded from the distal segment of cilia in C. elegans. MICROPUBLICATION BIOLOGY 2021; 2021:10.17912/micropub.biology.000406. [PMID: 34113804 PMCID: PMC8185565 DOI: 10.17912/micropub.biology.000406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/21/2021] [Accepted: 06/02/2021] [Indexed: 11/16/2022]
Abstract
Rare diseases are a fundamental issue in today's world, affecting more than 300 million individuals worldwide. According to data from Orphanet and OMIM, about 50-60 new conditions are added to the list of over 6,000 clinically distinct diseases each year, rendering disease diagnosis and treatment even more challenging. Ciliopathies comprise a heterogeneous category of rare diseases made up of over 35 distinct diseases, including Joubert syndrome (JBTS; OMIM 213300), that are caused by functional and structural defects in cilia. JBTS is an autosomal recessive condition characterized by a range of symptoms, including cerebellar vermis hypoplasia and poor muscle tone. There are now a total of 38 genes that cause JBTS, almost all of which encode protein products that are found in cilia and cilia-associated compartments, such as the basal body and transition zone. CEP41 is a JBTS-associated protein that is found in cilia and the basal body of mammals, but its localization in other ciliary organisms remains elusive. C. elegans is an excellent model organism for studying the molecular mechanisms of rare diseases like JBTS. We, therefore, decided to use C. elegans to identify the localization of CEP41. Our microscopy analysis revealed that CEPH-41(CEntrosomal Protein Homolog 41) not only localizes to cilia but is excluded from the distal segment of the amphid and phasmid cilia in C. elegans. Furthermore, we discovered a putative X-box motif located in the promoter of ceph-41 and the expression of ceph-41 is regulated by DAF-19, a sole Regulatory Factor X (RFX) transcription factor.
Collapse
Affiliation(s)
- Sebiha Cevik
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkey
| | - Oktay I. Kaplan
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkey
| |
Collapse
|
16
|
A complement factor H homolog, heparan sulfation, and syndecan maintain inversin compartment boundaries in C. elegans cilia. Proc Natl Acad Sci U S A 2021; 118:2016698118. [PMID: 33859044 DOI: 10.1073/pnas.2016698118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Age-related macular degeneration (AMD) is a leading cause of blindness among the elderly. Canonical disease models suggest that defective interactions between complement factor H (CFH) and cell surface heparan sulfate (HS) result in increased alternative complement pathway activity, cytolytic damage, and tissue inflammation in the retina. Although these factors are thought to contribute to increased disease risk, multiple studies indicate that noncanonical mechanisms that result from defective CFH and HS interaction may contribute to the progression of AMD as well. A total of 60 ciliated sensory neurons in the nematode Caenorhabditis elegans detect chemical, olfactory, mechanical, and thermal cues in the environment. Here, we find that a C. elegans CFH homolog localizes on CEP mechanosensory neuron cilia where it has noncanonical roles in maintaining inversin/NPHP-2 within its namesake proximal compartment and preventing inversin/NPHP-2 accumulation in distal cilia compartments in aging adults. CFH localization and maintenance of inversin/NPHP-2 compartment integrity depend on the HS 3-O sulfotransferase HST-3.1 and the transmembrane proteoglycan syndecan/SDN-1. Defective inversin/NPHP-2 localization in mouse and human photoreceptors with CFH mutations indicates that these functions and interactions may be conserved in vertebrate sensory neurons, suggesting that previously unappreciated defects in cilia structure may contribute to the progressive photoreceptor dysfunction associated with CFH loss-of-function mutations in some AMD patients.
Collapse
|
17
|
Wiegering A, Dildrop R, Vesque C, Khanna H, Schneider-Maunoury S, Gerhardt C. Rpgrip1l controls ciliary gating by ensuring the proper amount of Cep290 at the vertebrate transition zone. Mol Biol Cell 2021; 32:675-689. [PMID: 33625872 PMCID: PMC8108517 DOI: 10.1091/mbc.e20-03-0190] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A range of severe human diseases called ciliopathies is caused by the dysfunction of primary cilia. Primary cilia are cytoplasmic protrusions consisting of the basal body (BB), the axoneme, and the transition zone (TZ). The BB is a modified mother centriole from which the axoneme, the microtubule-based ciliary scaffold, is formed. At the proximal end of the axoneme, the TZ functions as the ciliary gate governing ciliary protein entry and exit. Since ciliopathies often develop due to mutations in genes encoding proteins that localize to the TZ, the understanding of the mechanisms underlying TZ function is of eminent importance. Here, we show that the ciliopathy protein Rpgrip1l governs ciliary gating by ensuring the proper amount of Cep290 at the vertebrate TZ. Further, we identified the flavonoid eupatilin as a potential agent to tackle ciliopathies caused by mutations in RPGRIP1L as it rescues ciliary gating in the absence of Rpgrip1l.
Collapse
Affiliation(s)
- Antonia Wiegering
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, 40225 Düsseldorf, Germany.,Sorbonne Université, CNRS UMR7622, INSERM U1156, Institut de Biologie Paris Seine (IBPS) - Developmental Biology Unit, 75005 Paris, France
| | - Renate Dildrop
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Christine Vesque
- Sorbonne Université, CNRS UMR7622, INSERM U1156, Institut de Biologie Paris Seine (IBPS) - Developmental Biology Unit, 75005 Paris, France
| | - Hemant Khanna
- Department of Ophthalmology and Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Sylvie Schneider-Maunoury
- Sorbonne Université, CNRS UMR7622, INSERM U1156, Institut de Biologie Paris Seine (IBPS) - Developmental Biology Unit, 75005 Paris, France
| | - Christoph Gerhardt
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, 40225 Düsseldorf, Germany
| |
Collapse
|
18
|
Lange KI, Tsiropoulou S, Kucharska K, Blacque OE. Interpreting the pathogenicity of Joubert syndrome missense variants in Caenorhabditis elegans. Dis Model Mech 2021; 14:dmm.046631. [PMID: 33234550 PMCID: PMC7859701 DOI: 10.1242/dmm.046631] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 11/13/2020] [Indexed: 12/26/2022] Open
Abstract
Ciliopathies are inherited disorders caused by defects in motile and non-motile (primary) cilia. Ciliopathy syndromes and associated gene variants are often highly pleiotropic and represent exemplars for interrogating genotype-phenotype correlations. Towards understanding disease mechanisms in the context of ciliopathy mutations, we have used a leading model organism for cilia and ciliopathy research, Caenorhabditis elegans, together with gene editing, to characterise two missense variants (P74S and G155S) in mksr-2/B9D2 associated with Joubert syndrome (JBTS). B9D2 functions within the Meckel syndrome (MKS) module at the ciliary base transition zone (TZ) compartment and regulates the molecular composition and sensory/signalling functions of the cilium. Quantitative assays of cilium/TZ structure and function, together with knock-in reporters, confirm that both variant alleles are pathogenic in worms. G155S causes a more severe overall phenotype and disrupts endogenous MKSR-2 organisation at the TZ. Recapitulation of the patient biallelic genotype shows that compound heterozygous worms phenocopy worms homozygous for P74S. The P74S and G155S alleles also reveal evidence of a very close functional association between the B9D2-associated B9 complex and MKS-2/TMEM216. Together, these data establish C. elegans as a model for interpreting JBTS mutations and provide further insight into MKS module organisation. This article has an associated First Person interview with the first author of the paper.
Collapse
Affiliation(s)
- Karen I Lange
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Sofia Tsiropoulou
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Katarzyna Kucharska
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Oliver E Blacque
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| |
Collapse
|
19
|
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.
Collapse
|
20
|
Gigante ED, Caspary T. Signaling in the primary cilium through the lens of the Hedgehog pathway. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2020; 9:e377. [PMID: 32084300 DOI: 10.1002/wdev.377] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 01/22/2020] [Accepted: 01/25/2020] [Indexed: 12/14/2022]
Abstract
Cilia are microtubule-based, cell-surface projections whose machinery is evolutionarily conserved. In vertebrates, cilia are observed on almost every cell type and are either motile or immotile. Immotile sensory, or primary cilia, are responsive to extracellular ligands and signals. Cilia can be thought of as compartments, functionally distinct from the cell that provides an environment for signaling cascades. Hedgehog is a critical developmental signaling pathway which is functionally linked to primary cilia in vertebrates. The major components of the vertebrate Hedgehog signaling pathway dynamically localize to the ciliary compartment and ciliary membrane. Critically, G-protein coupled receptor (GPCR) Smoothened, the obligate transducer of the pathway, is enriched and activated in the cilium. While Smoothened is the most intensely studied ciliary receptor, many GPCRs localize within cilia. Understanding the link between Smoothened and cilia defines common features, and distinctions, of GPCR signaling within the primary cilium. This article is categorized under: Signaling Pathways > Global Signaling Mechanisms Signaling Pathways > Cell Fate Signaling.
Collapse
Affiliation(s)
- Eduardo D Gigante
- Graduate Program in Neuroscience, Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Tamara Caspary
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| |
Collapse
|
21
|
Long H, Huang K. Transport of Ciliary Membrane Proteins. Front Cell Dev Biol 2020; 7:381. [PMID: 31998723 PMCID: PMC6970386 DOI: 10.3389/fcell.2019.00381] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 12/17/2019] [Indexed: 12/24/2022] Open
Abstract
Cilia and flagella are highly conserved organelles in eukaryotic cells that drive cell movement and act as cell antennae that receive and transmit signals. In addition to receiving and transducing external signals that activate signal cascades, cilia also secrete ciliary ectosomes that send signals to recipient cells, and thereby mediate cell–cell communication. Abnormal ciliary function leads to various ciliopathies, and the precise transport and localization of ciliary membrane proteins are essential for cilium function. This review summarizes current knowledge about the transport processes of ciliary membrane proteins after their synthesis at the endoplasmic reticulum: modification and sorting in the Golgi apparatus, transport through vesicles to the ciliary base, entrance into cilia through the diffusion barrier, and turnover by ectosome secretion. The molecular mechanisms and regulation involved in each step are also discussed. Transport of ciliary membrane proteins is a complex, precise cellular process coordinated among multiple organelles. By systematically analyzing the existing research, we identify topics that should be further investigated to promote progress in this field of research.
Collapse
Affiliation(s)
- Huan Long
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Kaiyao Huang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| |
Collapse
|
22
|
Gigante ED, Taylor MR, Ivanova AA, Kahn RA, Caspary T. ARL13B regulates Sonic hedgehog signaling from outside primary cilia. eLife 2020; 9:50434. [PMID: 32129762 PMCID: PMC7075693 DOI: 10.7554/elife.50434] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 02/25/2020] [Indexed: 01/13/2023] Open
Abstract
ARL13B is a regulatory GTPase highly enriched in cilia. Complete loss of Arl13b disrupts cilia architecture, protein trafficking and Sonic hedgehog signaling. To determine whether ARL13B is required within cilia, we knocked in a cilia-excluded variant of ARL13B (V358A) and showed it retains all known biochemical function. We found that ARL13BV358A protein was expressed but could not be detected in cilia, even when retrograde ciliary transport was blocked. We showed Arl13bV358A/V358A mice are viable and fertile with normal Shh signal transduction. However, in contrast to wild type cilia, Arl13bV358A/V358A cells displayed short cilia and lacked ciliary ARL3 and INPP5E. These data indicate that ARL13B's role within cilia can be uncoupled from its function outside of cilia. Furthermore, these data imply that the cilia defects upon complete absence of ARL13B do not underlie the alterations in Shh transduction, which is unexpected given the requirement of cilia for Shh transduction.
Collapse
Affiliation(s)
- Eduardo D Gigante
- Neuroscience Graduate Program, Emory University School of MedicineAtlantaUnited States,Department of Human Genetics, Emory University School of MedicineAtlantaUnited States
| | - Megan R Taylor
- Emory College of Arts and Sciences, Emory University School of MedicineAtlantaUnited States
| | - Anna A Ivanova
- Department of Biochemistry, Emory University School of MedicineAtlantaUnited States
| | - Richard A Kahn
- Department of Biochemistry, Emory University School of MedicineAtlantaUnited States
| | - Tamara Caspary
- Department of Human Genetics, Emory University School of MedicineAtlantaUnited States
| |
Collapse
|
23
|
ERICH3 in Primary Cilia Regulates Cilium Formation and the Localisations of Ciliary Transport and Sonic Hedgehog Signaling Proteins. Sci Rep 2019; 9:16519. [PMID: 31712586 PMCID: PMC6848114 DOI: 10.1038/s41598-019-52830-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 10/23/2019] [Indexed: 01/05/2023] Open
Abstract
Intraflagellar transport (IFT) is essential for the formation and function of the microtubule-based primary cilium, which acts as a sensory and signalling device at the cell surface. Consisting of IFT-A/B and BBSome cargo adaptors that associate with molecular motors, IFT transports protein into (anterograde IFT) and out of (retrograde IFT) the cilium. In this study, we identify the mostly uncharacterised ERICH3 protein as a component of the mammalian primary cilium. Loss of ERICH3 causes abnormally short cilia and results in the accumulation of IFT-A/B proteins at the ciliary tip, together with reduced ciliary levels of retrograde transport regulators, ARL13B, INPP5E and BBS5. We also show that ERICH3 ciliary localisations require ARL13B and BBSome components. Finally, ERICH3 loss causes positive (Smoothened) and negative (GPR161) regulators of sonic hedgehog signaling (Shh) to accumulate at abnormally high levels in the cilia of pathway-stimulated cells. Together, these findings identify ERICH3 as a novel component of the primary cilium that regulates cilium length and the ciliary levels of Shh signaling molecules. We propose that ERICH3 functions within retrograde IFT-associated pathways to remove signaling proteins from cilia.
Collapse
|
24
|
Defining the layers of a sensory cilium with STORM and cryoelectron nanoscopy. Proc Natl Acad Sci U S A 2019; 116:23562-23572. [PMID: 31690665 DOI: 10.1073/pnas.1902003116] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Primary cilia carry out numerous signaling and sensory functions, and defects in them, "ciliopathies," cause a range of symptoms, including blindness. Understanding of their nanometer-scale ciliary substructures and their disruptions in ciliopathies has been hindered by limitations of conventional microscopic techniques. We have combined cryoelectron tomography, enhanced by subtomogram averaging, with superresolution stochastic optical reconstruction microscopy (STORM) to define subdomains within the light-sensing rod sensory cilium of mouse retinas and reveal previously unknown substructures formed by resident proteins. Domains are demarcated by structural features such as the axoneme and its connections to the ciliary membrane, and are correlated with molecular markers of subcompartments, including the lumen and walls of the axoneme, the membrane glycocalyx, and the intervening cytoplasm. Within this framework, we report spatial distributions of key proteins in wild-type (WT) mice and the effects on them of genetic deficiencies in 3 models of Bardet-Biedl syndrome.
Collapse
|
25
|
Kuhns S, Seixas C, Pestana S, Tavares B, Nogueira R, Jacinto R, Ramalho JS, Simpson JC, Andersen JS, Echard A, Lopes SS, Barral DC, Blacque OE. Rab35 controls cilium length, function and membrane composition. EMBO Rep 2019; 20:e47625. [PMID: 31432619 PMCID: PMC6776896 DOI: 10.15252/embr.201847625] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 07/23/2019] [Accepted: 07/31/2019] [Indexed: 12/12/2022] Open
Abstract
Rab and Arl guanine nucleotide-binding (G) proteins regulate trafficking pathways essential for the formation, function and composition of primary cilia, which are sensory devices associated with Sonic hedgehog (Shh) signalling and ciliopathies. Here, using mammalian cells and zebrafish, we uncover ciliary functions for Rab35, a multitasking G protein with endocytic recycling, actin remodelling and cytokinesis roles. Rab35 loss via siRNAs, morpholinos or knockout reduces cilium length in mammalian cells and the zebrafish left-right organiser (Kupffer's vesicle) and causes motile cilia-associated left-right asymmetry defects. Consistent with these observations, GFP-Rab35 localises to cilia, as do GEF (DENND1B) and GAP (TBC1D10A) Rab35 regulators, which also regulate ciliary length and Rab35 ciliary localisation. Mammalian Rab35 also controls the ciliary membrane levels of Shh signalling regulators, promoting ciliary targeting of Smoothened, limiting ciliary accumulation of Arl13b and the inositol polyphosphate 5-phosphatase (INPP5E). Rab35 additionally regulates ciliary PI(4,5)P2 levels and interacts with Arl13b. Together, our findings demonstrate roles for Rab35 in regulating cilium length, function and membrane composition and implicate Rab35 in pathways controlling the ciliary levels of Shh signal regulators.
Collapse
Affiliation(s)
- Stefanie Kuhns
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublin 4Ireland
- Department of Biochemistry and Molecular BiologyUniversity of Southern DenmarkOdense MDenmark
| | - Cecília Seixas
- CEDOCNOVA Medical School|Faculdade de Ciências MédicasUniversidade NOVA de LisboaLisboaPortugal
| | - Sara Pestana
- CEDOCNOVA Medical School|Faculdade de Ciências MédicasUniversidade NOVA de LisboaLisboaPortugal
| | - Bárbara Tavares
- CEDOCNOVA Medical School|Faculdade de Ciências MédicasUniversidade NOVA de LisboaLisboaPortugal
| | - Renata Nogueira
- CEDOCNOVA Medical School|Faculdade de Ciências MédicasUniversidade NOVA de LisboaLisboaPortugal
| | - Raquel Jacinto
- CEDOCNOVA Medical School|Faculdade de Ciências MédicasUniversidade NOVA de LisboaLisboaPortugal
| | - José S Ramalho
- CEDOCNOVA Medical School|Faculdade de Ciências MédicasUniversidade NOVA de LisboaLisboaPortugal
| | - Jeremy C Simpson
- School of Biology and Environmental ScienceUniversity College DublinDublin 4Ireland
| | - Jens S Andersen
- Department of Biochemistry and Molecular BiologyUniversity of Southern DenmarkOdense MDenmark
| | | | - Susana S Lopes
- CEDOCNOVA Medical School|Faculdade de Ciências MédicasUniversidade NOVA de LisboaLisboaPortugal
| | - Duarte C Barral
- CEDOCNOVA Medical School|Faculdade de Ciências MédicasUniversidade NOVA de LisboaLisboaPortugal
| | - Oliver E Blacque
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublin 4Ireland
| |
Collapse
|
26
|
Muñoz-Estrada J, Ferland RJ. Ahi1 promotes Arl13b ciliary recruitment, regulates Arl13b stability and is required for normal cell migration. J Cell Sci 2019; 132:jcs.230680. [PMID: 31391239 DOI: 10.1242/jcs.230680] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 07/24/2019] [Indexed: 12/14/2022] Open
Abstract
Mutations in the Abelson-helper integration site 1 (AHI1) gene are associated with neurological/neuropsychiatric disorders, and cause the neurodevelopmental ciliopathy Joubert syndrome (JBTS). Here, we show that deletion of the transition zone (TZ) protein Ahi1 in mouse embryonic fibroblasts (MEFs) has a small effect on cilia formation. However, Ahi1 loss in these cells results in: (1) reduced localization of the JBTS-associated protein Arl13b to the ciliary membrane, (2) decreased sonic hedgehog signaling, (3) and an abnormally elongated ciliary axoneme accompanied by an increase in ciliary IFT88 concentrations. While no changes in Arl13b levels are detected in crude cell membrane extracts, loss of Ahi1 significantly reduced the level of non-membrane-associated Arl13b and its stability via the proteasome pathway. Exogenous expression of Ahi1-GFP in Ahi1-/- MEFs restored ciliary length, increased ciliary recruitment of Arl13b and augmented Arl13b stability. Finally, Ahi1-/- MEFs displayed defects in cell motility and Pdgfr-α-dependent migration. Overall, our findings support molecular mechanisms underlying JBTS etiology that involve: (1) disruptions at the TZ resulting in defects of membrane- and non-membrane-associated proteins to localize to primary cilia, and (2) defective cell migration.This article has an associated First Person interview with the first author of the paper.
Collapse
Affiliation(s)
- Jesús Muñoz-Estrada
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, NY 12208, USA
| | - Russell J Ferland
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, NY 12208, USA .,Department of Neurology, Albany Medical College, Albany, NY 12208, USA
| |
Collapse
|
27
|
Hor CH, Goh EL. Small GTPases in hedgehog signalling: emerging insights into the disease mechanisms of Rab23-mediated and Arl13b-mediated ciliopathies. Curr Opin Genet Dev 2019; 56:61-68. [PMID: 31465935 DOI: 10.1016/j.gde.2019.07.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 01/31/2023]
Abstract
Small GTPases are known to have pivotal roles in intracellular trafficking, and several members of the small GTPases superfamily such as Rab10 [1,2•], Rab11 [3-5], Rab34 [6•,7], Rab8 [3,8], Rab23 [9-12], RSG1 [13-15], Arl13b [16-22], and Arl6 [22,23] were recently reported to mediate primary cilia function and/or Hh signalling. Although these functions are implicated in diseases such as ciliopathies, the molecular basis underlying how these small GTPases mediate primary cilia-dependent Hh signalling and pathogenesis of ciliopathies warrants further investigations. Notably, Rab23 and Arl13b have been implicated in ciliopathy-associated human diseases and could regulate Hh signalling cascade in multifaceted manners. This review thus specifically discuss the roles of Rab23 and Arl13b in primary cilia of mammalian systems, their cilia-dependent and cilia-independent modulation of hedgehog signalling pathways and their implications in Carpenter Syndrome and Joubert Syndrome respectively.
Collapse
Affiliation(s)
- Catherine Hh Hor
- Neuroscience Academic Clinical Programme, Duke-NUS Medical School, Singapore 169857, Singapore; Department of Chemistry, Research Cluster on Health and Drug Discovery, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong
| | - Eyleen Lk Goh
- Neuroscience Academic Clinical Programme, Duke-NUS Medical School, Singapore 169857, Singapore; Department of Research, National Neuroscience Institute, Singapore 308433, Singapore; Neuroscience and Mental Health Faculty, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore; KK Research Center, KK Women's and Children's Hospital, Singapore 229899, Singapore.
| |
Collapse
|
28
|
CiliaCarta: An integrated and validated compendium of ciliary genes. PLoS One 2019; 14:e0216705. [PMID: 31095607 PMCID: PMC6522010 DOI: 10.1371/journal.pone.0216705] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 04/26/2019] [Indexed: 12/25/2022] Open
Abstract
The cilium is an essential organelle at the surface of mammalian cells whose dysfunction causes a wide range of genetic diseases collectively called ciliopathies. The current rate at which new ciliopathy genes are identified suggests that many ciliary components remain undiscovered. We generated and rigorously analyzed genomic, proteomic, transcriptomic and evolutionary data and systematically integrated these using Bayesian statistics into a predictive score for ciliary function. This resulted in 285 candidate ciliary genes. We generated independent experimental evidence of ciliary associations for 24 out of 36 analyzed candidate proteins using multiple cell and animal model systems (mouse, zebrafish and nematode) and techniques. For example, we show that OSCP1, which has previously been implicated in two distinct non-ciliary processes, causes ciliogenic and ciliopathy-associated tissue phenotypes when depleted in zebrafish. The candidate list forms the basis of CiliaCarta, a comprehensive ciliary compendium covering 956 genes. The resource can be used to objectively prioritize candidate genes in whole exome or genome sequencing of ciliopathy patients and can be accessed at http://bioinformatics.bio.uu.nl/john/syscilia/ciliacarta/.
Collapse
|
29
|
Loucks CM, Park K, Walker DS, McEwan AH, Timbers TA, Ardiel EL, Grundy LJ, Li C, Johnson JL, Kennedy J, Blacque OE, Schafer W, Rankin CH, Leroux MR. EFHC1, implicated in juvenile myoclonic epilepsy, functions at the cilium and synapse to modulate dopamine signaling. eLife 2019; 8:37271. [PMID: 30810526 PMCID: PMC6392500 DOI: 10.7554/elife.37271] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 02/06/2019] [Indexed: 01/03/2023] Open
Abstract
Neurons throughout the mammalian brain possess non-motile cilia, organelles with varied functions in sensory physiology and cellular signaling. Yet, the roles of cilia in these neurons are poorly understood. To shed light into their functions, we studied EFHC1, an evolutionarily conserved protein required for motile cilia function and linked to a common form of inherited epilepsy in humans, juvenile myoclonic epilepsy (JME). We demonstrate that C. elegans EFHC-1 functions within specialized non-motile mechanosensory cilia, where it regulates neuronal activation and dopamine signaling. EFHC-1 also localizes at the synapse, where it further modulates dopamine signaling in cooperation with the orthologue of an R-type voltage-gated calcium channel. Our findings unveil a previously undescribed dual-regulation of neuronal excitability at sites of neuronal sensory input (cilium) and neuronal output (synapse). Such a distributed regulatory mechanism may be essential for establishing neuronal activation thresholds under physiological conditions, and when impaired, may represent a novel pathomechanism for epilepsy.
Collapse
Affiliation(s)
- Catrina M Loucks
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada.,Centre for Cell Biology, Development, and Disease, Simon Fraser University, Burnaby, Canada
| | - Kwangjin Park
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada.,Centre for Cell Biology, Development, and Disease, Simon Fraser University, Burnaby, Canada
| | - Denise S Walker
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Andrea H McEwan
- Djavad Mowfaghian Centre for Brain Health, University of British Columbia, Vancouver, Canada
| | - Tiffany A Timbers
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada.,Centre for Cell Biology, Development, and Disease, Simon Fraser University, Burnaby, Canada
| | - Evan L Ardiel
- Djavad Mowfaghian Centre for Brain Health, University of British Columbia, Vancouver, Canada
| | - Laura J Grundy
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Chunmei Li
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada.,Centre for Cell Biology, Development, and Disease, Simon Fraser University, Burnaby, Canada
| | - Jacque-Lynne Johnson
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada.,Centre for Cell Biology, Development, and Disease, Simon Fraser University, Burnaby, Canada
| | - Julie Kennedy
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Oliver E Blacque
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - William Schafer
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Catharine H Rankin
- Djavad Mowfaghian Centre for Brain Health, University of British Columbia, Vancouver, Canada.,Department of Psychology, University of British Columbia, Vancouver, 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
| |
Collapse
|
30
|
Dilan TL, Moye AR, Salido EM, Saravanan T, Kolandaivelu S, Goldberg AFX, Ramamurthy V. ARL13B, a Joubert Syndrome-Associated Protein, Is Critical for Retinogenesis and Elaboration of Mouse Photoreceptor Outer Segments. J Neurosci 2019; 39:1347-1364. [PMID: 30573647 PMCID: PMC6381253 DOI: 10.1523/jneurosci.1761-18.2018] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 11/16/2018] [Accepted: 12/12/2018] [Indexed: 11/21/2022] Open
Abstract
Mutations in the Joubert syndrome-associated small GTPase ARL13B are linked to photoreceptor impairment and vision loss. To determine the role of ARL13B in the development, function, and maintenance of ciliated photoreceptors, we generated a pan-retina knock-out (Six3-Cre) and a rod photoreceptor-specific inducible conditional knock-out (Pde6g-CreERT2) of ARL13B using murine models. Embryonic deletion of ARL13B led to defects in retinal development with reduced cell proliferation. In the absence of ARL13B, photoreceptors failed to develop outer segment (OS) membranous discs and axonemes, resulting in loss of function and rapid degeneration. Additionally, the majority of photoreceptor basal bodies did not dock properly at the apical edge of the inner segments. The removal of ARL13B in adult rod photoreceptor cells after maturation of OS resulted in loss of photoresponse and vesiculation in the OS. Before changes in photoresponse, removal of ARL13B led to mislocalization of rhodopsin, prenylated phosphodiesterase-6 (PDE6), and intraflagellar transport protein-88 (IFT88). Our findings show that ARL13B is required at multiple stages of retinogenesis, including early postnatal proliferation of retinal progenitor cells, development of photoreceptor cilia, and morphogenesis of photoreceptor OS discs regardless of sex. Last, our results establish a need for ARL13B in photoreceptor maintenance and protein trafficking.SIGNIFICANCE STATEMENT The normal development of photoreceptor cilia is essential to create functional, organized outer segments with stacked membrane discs that house the phototransduction proteins necessary for sight. Our study identifies a complex role for ARL13B, a small GTPase linked to Joubert syndrome and visual impairment, at various stages of photoreceptor development. Loss of ARL13B led to defects in retinal proliferation, altered placement of basal bodies crucial for components of the cilium (transition zone) to emanate, and absence of photoreceptor-stacked discs. These defects led to extinguished visual response and dysregulated protein trafficking. Our findings show the complex role ARL13B plays in photoreceptor development, viability, and function. Our study accounts for the severe retinal impairment observed in ARL13B-linked Joubert syndrome patients.
Collapse
Affiliation(s)
- Tanya L Dilan
- Department of Ophthalmology and Neuroscience
- Department of Biochemistry
| | - Abigail R Moye
- Department of Ophthalmology and Neuroscience
- Department of Biochemistry
| | | | | | | | | | - Visvanathan Ramamurthy
- Department of Ophthalmology and Neuroscience,
- Department of Biochemistry
- WVU Rockefeller Neuroscience Institute, West Virginia University, Morgantown, West Virginia 26506, and
| |
Collapse
|
31
|
Picariello T, Brown JM, Hou Y, Swank G, Cochran DA, King OD, Lechtreck K, Pazour GJ, Witman GB. A global analysis of IFT-A function reveals specialization for transport of membrane-associated proteins into cilia. J Cell Sci 2019; 132:jcs220749. [PMID: 30659111 PMCID: PMC6382014 DOI: 10.1242/jcs.220749] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 01/02/2019] [Indexed: 12/28/2022] Open
Abstract
Intraflagellar transport (IFT), which is essential for the formation and function of cilia in most organisms, is the trafficking of IFT trains (i.e. assemblies of IFT particles) that carry cargo within the cilium. Defects in IFT cause several human diseases. IFT trains contain the complexes IFT-A and IFT-B. To dissect the functions of these complexes, we studied a Chlamydomonas mutant that is null for the IFT-A protein IFT140. The mutation had no effect on IFT-B but destabilized IFT-A, preventing flagella assembly. Therefore, IFT-A assembly requires IFT140. Truncated IFT140, which lacks the N-terminal WD repeats of the protein, partially rescued IFT and supported formation of half-length flagella that contained normal levels of IFT-B but greatly reduced amounts of IFT-A. The axonemes of these flagella had normal ultrastructure and, as investigated by SDS-PAGE, normal composition. However, composition of the flagellar 'membrane+matrix' was abnormal. Analysis of the latter fraction by mass spectrometry revealed decreases in small GTPases, lipid-anchored proteins and cell signaling proteins. Thus, IFT-A is specialized for the import of membrane-associated proteins. Abnormal levels of the latter are likely to account for the multiple phenotypes of patients with defects in IFT140.This article has an associated First Person interview with the first author of the paper.
Collapse
Affiliation(s)
- Tyler Picariello
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Jason M Brown
- Department of Biology, Salem State University, Salem, MA 01970, USA
| | - Yuqing Hou
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Gregory Swank
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Deborah A Cochran
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Oliver D King
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Karl Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Gregory J Pazour
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - George B Witman
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| |
Collapse
|
32
|
Scheidel N, Blacque OE. Intraflagellar Transport Complex A Genes Differentially Regulate Cilium Formation and Transition Zone Gating. Curr Biol 2018; 28:3279-3287.e2. [PMID: 30293716 DOI: 10.1016/j.cub.2018.08.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 06/08/2018] [Accepted: 08/07/2018] [Indexed: 02/03/2023]
Abstract
Cilia are found on most eukaryotic cell types, serving motility, environment sensing, and signaling (cell-cell) functions, and defects cause genetic diseases (ciliopathies), affecting the development of many tissues [1]. Cilia are built by intraflagellar transport (IFT), a bidirectional microtubule-based motility driven by kinesin-2 anterograde (toward ciliary tip) and IFT-dynein retrograde (toward ciliary base) motors together with IFT-A and IFT-B cargo adaptor complexes that control retrograde and anterograde IFT, respectively [2]. Ciliary composition is also facilitated by the transition zone (TZ) at the ciliary base and the associated Meckel-Gruber syndrome (MKS) and nephronophthisis (NPHP) modules that establish protein diffusion barriers and regulate cilium structure [3]. Although the molecular architecture of the IFT machine is emerging [2], how individual components contribute to cilium subtype formation and IFT remains relatively unexplored, especially in vivo. In addition, little is known about functional interactions between IFT and TZ modules. Here, in Caenorhabditis elegans (roundworms), we identify cell-type-specific mechanisms by which IFT-A sculpts the structures of discrete ciliary subtypes and regulates IFT. We also uncover differential roles for IFT-A subunits in controlling the TZ restriction of MKS module components and ciliary exclusion (gating) of periciliary membrane proteins, with IFT-140 controlling their ciliary entry and IFT-43/121/139 controlling their ciliary removal. Furthermore, we determine that IFT-A and MKS module components synergistically interact to determine cilium structure. Overall, this work provides insight into the functional architecture of a metazoan IFT-A complex in different cell types and uncovers new relationships between ciliopathy-associated IFT-A and TZ modules.
Collapse
Affiliation(s)
- Noémie Scheidel
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Oliver E Blacque
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.
| |
Collapse
|
33
|
Zhang Y, Huang Y, Srivathsan A, Lim TK, Lin Q, He CY. The unusual flagellar-targeting mechanism and functions of the trypanosome ortholog of the ciliary GTPase Arl13b. J Cell Sci 2018; 131:jcs.219071. [PMID: 30097558 PMCID: PMC6140319 DOI: 10.1242/jcs.219071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 07/28/2018] [Indexed: 12/11/2022] Open
Abstract
The small GTPase Arl13b is one of the most conserved and ancient ciliary proteins. In human and animals, Arl13b is primarily associated with the ciliary membrane, where it acts as a guanine-nucleotide-exchange factor (GEF) for Arl3 and is implicated in a variety of ciliary and cellular functions. We have identified and characterized Trypanosoma brucei (Tb)Arl13, the sole Arl13b homolog in this evolutionarily divergent, protozoan parasite. TbArl13 has conserved flagellar functions and exhibits catalytic activity towards two different TbArl3 homologs. However, TbArl13 is distinctly associated with the axoneme through a dimerization/docking (D/D) domain. Replacing the D/D domain with a sequence encoding a flagellar membrane protein created a viable alternative to the wild-type TbArl13 in our RNA interference (RNAi)-based rescue assay. Therefore, flagellar enrichment is crucial for TbArl13, but mechanisms to achieve this could be flexible. Our findings thus extend the understanding of the roles of Arl13b and Arl13b–Arl3 pathway in a divergent flagellate of medical importance. This article has an associated First Person interview with the first author of the paper. Highlighted Article: All roads lead to cilia – how the essential flagellar enrichment of Arl13 is achieved in trypanosome cells using a fundamentally different strategy compared with that of animal cells.
Collapse
Affiliation(s)
- Yiliu Zhang
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Yameng Huang
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Amrita Srivathsan
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Teck Kwang Lim
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Qingsong Lin
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Cynthia Y He
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 14 Science Drive 4, Singapore 117543
| |
Collapse
|
34
|
Dharmat R, Eblimit A, Robichaux MA, Zhang Z, Nguyen TMT, Jung SY, He F, Jain A, Li Y, Qin J, Overbeek P, Roepman R, Mardon G, Wensel TG, Chen R. SPATA7 maintains a novel photoreceptor-specific zone in the distal connecting cilium. J Cell Biol 2018; 217:2851-2865. [PMID: 29899041 PMCID: PMC6080925 DOI: 10.1083/jcb.201712117] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/09/2018] [Accepted: 05/23/2018] [Indexed: 12/25/2022] Open
Abstract
Photoreceptor-specific ciliopathies often affect a structure that is considered functionally homologous to the ciliary transition zone (TZ) called the connecting cilium (CC). However, it is unclear how mutations in certain ciliary genes disrupt the photoreceptor CC without impacting the primary cilia systemically. By applying stochastic optical reconstruction microscopy technology in different genetic models, we show that the CC can be partitioned into two regions: the proximal CC (PCC), which is homologous to the TZ of primary cilia, and the distal CC (DCC), a photoreceptor-specific extension of the ciliary TZ. This specialized distal zone of the CC in photoreceptors is maintained by SPATA7, which interacts with other photoreceptor-specific ciliary proteins such as RPGR and RPGRIP1. The absence of Spata7 results in the mislocalization of DCC proteins without affecting the PCC protein complexes. This collapse results in destabilization of the axonemal microtubules, which consequently results in photoreceptor degeneration. These data provide a novel mechanism to explain how genetic disruption of ubiquitously present ciliary proteins exerts tissue-specific ciliopathy phenotypes.
Collapse
Affiliation(s)
- Rachayata Dharmat
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Aiden Eblimit
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Michael A Robichaux
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX
| | - Zhixian Zhang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX
| | - Thanh-Minh T Nguyen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Sung Yun Jung
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX
| | - Feng He
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX
| | - Antrix Jain
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX
| | - Yumei Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Jun Qin
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX
| | - Paul Overbeek
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Ronald Roepman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Graeme Mardon
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Pathology and Immunology, Baylor College of Medicine, Houston, TX
| | - Theodore G Wensel
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX
| | - Rui Chen
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX
| |
Collapse
|
35
|
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.
Collapse
|
36
|
Lee S, Tan HY, Geneva II, Kruglov A, Calvert PD. Actin filaments partition primary cilia membranes into distinct fluid corrals. J Cell Biol 2018; 217:2831-2849. [PMID: 29945903 PMCID: PMC6080922 DOI: 10.1083/jcb.201711104] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 04/16/2018] [Accepted: 05/22/2018] [Indexed: 12/15/2022] Open
Abstract
Lee et al. examine the dynamics of membrane proteins within the ciliary membrane using quantum dots and 2P Super FRAP. They show that ciliary membrane proteins diffuse rapidly within highly fluid local membrane domains delimited by actin filaments. Physical properties of primary cilia membranes in living cells were examined using two independent, high-spatiotemporal-resolution approaches: fast tracking of single quantum dot–labeled G protein–coupled receptors and a novel two-photon super-resolution fluorescence recovery after photobleaching of protein ensemble. Both approaches demonstrated the cilium membrane to be partitioned into corralled domains spanning 274 ± 20 nm, within which the receptors are transiently confined for 0.71 ± 0.09 s. The mean membrane diffusion coefficient within the corrals, Dm1 = 2.9 ± 0.41 µm2/s, showed that the ciliary membranes were among the most fluid encountered. At longer times, the apparent membrane diffusion coefficient, Dm2 = 0.23 ± 0.05 µm2/s, showed that corral boundaries impeded receptor diffusion 13-fold. Mathematical simulations predict the probability of G protein–coupled receptors crossing corral boundaries to be 1 in 472. Remarkably, latrunculin A, cytochalasin D, and jasplakinolide treatments altered the corral permeability. Ciliary membranes are thus partitioned into highly fluid membrane nanodomains that are delimited by filamentous actin.
Collapse
Affiliation(s)
- Sungsu Lee
- Center for Vision Research and Department of Ophthalmology, State University of New York Upstate Medical University, Syracuse, NY.,Department of Neuroscience and Physiology, State University of New York Upstate Medical University, Syracuse, NY
| | - Han Yen Tan
- Center for Vision Research and Department of Ophthalmology, State University of New York Upstate Medical University, Syracuse, NY
| | - Ivayla I Geneva
- Center for Vision Research and Department of Ophthalmology, State University of New York Upstate Medical University, Syracuse, NY.,Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY
| | - Aleksandr Kruglov
- Center for Vision Research and Department of Ophthalmology, State University of New York Upstate Medical University, Syracuse, NY
| | - Peter D Calvert
- Center for Vision Research and Department of Ophthalmology, State University of New York Upstate Medical University, Syracuse, NY .,Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY.,Department of Neuroscience and Physiology, State University of New York Upstate Medical University, Syracuse, NY
| |
Collapse
|
37
|
Revenkova E, Liu Q, Gusella GL, Iomini C. The Joubert syndrome protein ARL13B binds tubulin to maintain uniform distribution of proteins along the ciliary membrane. J Cell Sci 2018; 131:jcs212324. [PMID: 29592971 PMCID: PMC5992585 DOI: 10.1242/jcs.212324] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 03/23/2018] [Indexed: 01/09/2023] Open
Abstract
Cilia-mediated signal transduction involves precise targeting and localization of selected molecules along the ciliary membrane. However, the molecular mechanism underlying these events is unclear. The Joubert syndrome protein ARL13B is a membrane-associated G-protein that localizes along the cilium and functions in protein transport and signaling. We identify tubulin as a direct interactor of ARL13B and demonstrate that the association occurs via the G-domain and independently from the GTPase activity of ARL13B. The G-domain is necessary for the interaction of ARL13B with the axoneme both in vitro and in vivo We further show that exogenously expressed mutants lacking the tubulin-binding G-domain (ARL13B-ΔGD) or whose GTPase domain is inactivated (ARL13B-T35N) retain ciliary localization, but fail to rescue ciliogenesis defects of null Arl13bhnn mouse embryonic fibroblasts (MEFs). However, while ARL13B-ΔGD and the membrane proteins Smoothened (SMO) and Somatostatin receptor-3 (SSTR3) distribute unevenly along the cilium of Arl13bhnn MEFs, ARL13B-T35N distributes evenly along the cilium and enables the uniform distribution of SMO and SSTR3. Thus, we propose a so far unknown function of ARL13B in anchoring ciliary membrane proteins to the axoneme through the direct interaction of its G-domain with tubulin.
Collapse
Affiliation(s)
- Ekaterina Revenkova
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Qing Liu
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - G Luca Gusella
- Department of Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Carlo Iomini
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| |
Collapse
|
38
|
Scheidel N, Kennedy J, Blacque OE. Endosome maturation factors Rabenosyn-5/VPS45 and caveolin-1 regulate ciliary membrane and polycystin-2 homeostasis. EMBO J 2018; 37:embj.201798248. [PMID: 29572244 DOI: 10.15252/embj.201798248] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 02/08/2018] [Accepted: 02/16/2018] [Indexed: 12/24/2022] Open
Abstract
Primary cilium structure and function relies on control of ciliary membrane homeostasis, regulated by membrane trafficking processes that deliver and retrieve ciliary components at the periciliary membrane. However, the molecular mechanisms controlling ciliary membrane establishment and maintenance, especially in relation to endocytosis, remain poorly understood. Here, using Caenorhabditis elegans, we describe closely linked functions for early endosome (EE) maturation factors RABS-5 (Rabenosyn-5) and VPS-45 (VPS45) in regulating cilium length and morphology, ciliary and periciliary membrane volume, and ciliary signalling-related sensory behaviour. We demonstrate that RABS-5 and VPS-45 control periciliary vesicle number and levels of select EE/endocytic markers (WDFY-2, CAV-1) and the ciliopathy membrane receptor PKD-2 (polycystin-2). Moreover, we show that CAV-1 (caveolin-1) also controls PKD-2 ciliary levels and associated sensory behaviour. These data link RABS-5 and VPS-45 ciliary functions to the processing of periciliary-derived endocytic vesicles and regulation of ciliary membrane homeostasis. Our findings also provide insight into the regulation of PKD-2 ciliary levels via integrated endosomal sorting and CAV-1-mediated endocytosis.
Collapse
Affiliation(s)
- Noémie Scheidel
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Julie Kennedy
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Oliver E Blacque
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| |
Collapse
|
39
|
Canning P, Park K, Gonçalves J, Li C, Howard CJ, Sharpe TD, Holt LJ, Pelletier L, Bullock AN, Leroux MR. CDKL Family Kinases Have Evolved Distinct Structural Features and Ciliary Function. Cell Rep 2018; 22:885-894. [PMID: 29420175 PMCID: PMC5846859 DOI: 10.1016/j.celrep.2017.12.083] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 11/07/2017] [Accepted: 12/22/2017] [Indexed: 12/28/2022] Open
Abstract
Various kinases, including a cyclin-dependent kinase (CDK) family member, regulate the growth and functions of primary cilia, which perform essential roles in signaling and development. Neurological disorders linked to CDK-Like (CDKL) proteins suggest that these underexplored kinases may have similar functions. Here, we present the crystal structures of human CDKL1, CDKL2, CDKL3, and CDKL5, revealing their evolutionary divergence from CDK and mitogen-activated protein kinases (MAPKs), including an unusual ?J helix important for CDKL2 and CDKL3 activity. C. elegans CDKL-1, most closely related to CDKL1-4 and localized to neuronal cilia transition zones, modulates cilium length; this depends on its kinase activity and ?J helix-containing C terminus. Human CDKL5, linked to Rett syndrome, also localizes to cilia, and it impairs ciliogenesis when overexpressed. CDKL5 patient mutations modeled in CDKL-1 cause localization and/or cilium length defects. Together, our studies establish a disease model system suggesting cilium length defects as a pathomechanism for neurological disorders, including epilepsy.
Collapse
Affiliation(s)
- Peter Canning
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Kwangjin Park
- Department of Molecular Biology and Biochemistry, and Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - João Gonçalves
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Chunmei Li
- Department of Molecular Biology and Biochemistry, and Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Conor J Howard
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Timothy D Sharpe
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Liam J Holt
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Laurence Pelletier
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Alex N Bullock
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK.
| | - Michel R Leroux
- Department of Molecular Biology and Biochemistry, and Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada.
| |
Collapse
|
40
|
Seo H, Kwon EJ, You YA, Park Y, Min BJ, Yoo K, Hwang HS, Kim JH, Kim YJ. Deleterious genetic variants in ciliopathy genes increase risk of ritodrine-induced cardiac and pulmonary side effects. BMC Med Genomics 2018; 11:4. [PMID: 29368655 PMCID: PMC5784607 DOI: 10.1186/s12920-018-0323-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 01/08/2018] [Indexed: 12/13/2022] Open
Abstract
Background Ritodrine is a commonly used tocolytic to prevent preterm labour. However, it can cause unexpected serious adverse reactions, such as pulmonary oedema, pulmonary congestion, and tachycardia. It is unknown whether such adverse reactions are associated with pharmacogenomic variants in patients. Methods Whole-exome sequencing of 13 subjects with serious ritodrine-induced cardiac and pulmonary side-effects was performed to identify causal genes and variants. The deleterious impact of nonsynonymous substitutions for all genes was computed and compared between cases (n = 13) and controls (n = 30). The significant genes were annotated with Gene Ontology (GO), and the associated disease terms were categorised into four functional classes for functional enrichment tests. To assess the impact of distributed rare variants in cases with side effects, we carried out rare variant association tests with a minor allele frequency ≤ 1% using the burden test, the sequence Kernel association test (SKAT), and optimised SKAT. Results We identified 28 genes that showed significantly lower gene-wise deleteriousness scores in cases than in controls. Three of the identified genes—CYP1A1, CYP8B1, and SERPINA7—are pharmacokinetic genes. The significantly identified genes were categorized into four functional classes: ion binding, ATP binding, Ca2+-related, and ciliopathies-related. These four classes were significantly enriched with ciliary genes according to SYSCILIA Gold Standard genes (P < 0.01), thus representing ciliary genes. Furthermore, SKAT showed a marginal trend toward significance after Bonferroni correction with Joubert Syndrome ciliopathy genes (P = 0.05). With respect to the pharmacokinetic genes, rs1048943 (CYP1A1) and rs1804495 (SERPINA7) showed a significantly higher frequency in cases than controls, as determined by Fisher’s exact test (P < 0.05 and P < 0.01, respectively). Conclusions Ritodrine-induced cardiac and pulmonary side effects may be associated with deleterious genetic variants in ciliary and pharmacokinetic genes.
Collapse
Affiliation(s)
- Heewon Seo
- Seoul National University Biomedical Informatics (SNUBI), Div. of Biomedical Informatics, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Eun Jin Kwon
- Medical Research Institute, College of Medicine, Ewha Womans University, Seoul, 07985, Korea
| | - Young-Ah You
- Medical Research Institute, College of Medicine, Ewha Womans University, Seoul, 07985, Korea
| | - Yoomi Park
- Seoul National University Biomedical Informatics (SNUBI), Div. of Biomedical Informatics, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Byung Joo Min
- Seoul National University Biomedical Informatics (SNUBI), Div. of Biomedical Informatics, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Kyunghun Yoo
- Seoul National University Biomedical Informatics (SNUBI), Div. of Biomedical Informatics, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Han-Sung Hwang
- Department of Obstetrics and Gynecology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, 05030, Korea
| | - Ju Han Kim
- Seoul National University Biomedical Informatics (SNUBI), Div. of Biomedical Informatics, Seoul National University College of Medicine, Seoul, 03080, Korea.
| | - Young Ju Kim
- Department of Obstetrics and Gynecology, College of Medicine, Ewha Womans University Mok Dong Hospital, Seoul, 07985, Korea.
| |
Collapse
|
41
|
Fu W, Wang L, Kim S, Li J, Dynlacht BD. Role for the IFT-A Complex in Selective Transport to the Primary Cilium. Cell Rep 2017; 17:1505-1517. [PMID: 27806291 DOI: 10.1016/j.celrep.2016.10.018] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 09/05/2016] [Accepted: 10/05/2016] [Indexed: 11/27/2022] Open
Abstract
Intraflagellar transport sub-complex A (IFT-A) is known to regulate retrograde IFT in the cilium. To rigorously assess its other possible roles, we knocked out an IFT-A subunit, IFT121/WDR35, in mammalian cells and screened the localization of more than 50 proteins. We found that Wdr35 regulates cilium assembly by selectively regulating transport of distinct cargoes. Beyond its role in retrograde transport, we show that Wdr35 functions in fusion of Rab8 vesicles at the nascent cilium, protein exit from the cilium, and centriolar satellite organization. Furthermore, we show that Wdr35 is essential for entry of many membrane proteins into the cilium through robust interactions with cargoes and other IFT-A subunits, but the actin network functions to dampen this transport. Wdr35 is mutated in several ciliopathies, and we find that certain disease mutations impair interactions with cargo and other IFT-A subunits. Together, our data link defects in IFT-A mediated cargo transport with disease.
Collapse
Affiliation(s)
- Wenxiang Fu
- Department of Pathology and Perlmutter Cancer Center, NYU School of Medicine, Smilow Research Building, 522 First Avenue, New York, NY 10016, USA
| | - Lei Wang
- Department of Pathology and Perlmutter Cancer Center, NYU School of Medicine, Smilow Research Building, 522 First Avenue, New York, NY 10016, USA
| | - Sehyun Kim
- Department of Pathology and Perlmutter Cancer Center, NYU School of Medicine, Smilow Research Building, 522 First Avenue, New York, NY 10016, USA
| | - Ji Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA
| | - Brian David Dynlacht
- Department of Pathology and Perlmutter Cancer Center, NYU School of Medicine, Smilow Research Building, 522 First Avenue, New York, NY 10016, USA.
| |
Collapse
|
42
|
Roy K, Jerman S, Jozsef L, McNamara T, Onyekaba G, Sun Z, Marin EP. Palmitoylation of the ciliary GTPase ARL13b is necessary for its stability and its role in cilia formation. J Biol Chem 2017; 292:17703-17717. [PMID: 28848045 PMCID: PMC5663873 DOI: 10.1074/jbc.m117.792937] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 08/18/2017] [Indexed: 01/01/2023] Open
Abstract
Primary cilia are hairlike extensions of the plasma membrane of most mammalian cells that serve specialized signaling functions. To traffic properly to cilia, multiple cilia proteins rely on palmitoylation, the post-translational attachment of a saturated 16-carbon lipid. However, details regarding the mechanism of how palmitoylation affects cilia protein localization and function are unknown. Herein, we investigated the protein ADP-ribosylation factor-like GTPase 13b (ARL13b) as a model palmitoylated ciliary protein. Using biochemical, cellular, and in vivo studies, we found that ARL13b palmitoylation occurs in vivo in mouse kidneys and that it is required for trafficking to and function within cilia. Myristoylation, a 14-carbon lipid, is shown to largely substitute for palmitoylation with regard to cilia localization of ARL13b, but not with regard to its function within cilia. The functional importance of palmitoylation results in part from a dramatic increase in ARL13b stability, which is not observed with myristoylation. Additional results show that blockade of depalmitoylation slows the degradation of ARL13b that occurs during cilia resorption, raising the possibility that the sensitivity of ARL13b stability to palmitoylation may be exploited by the cell to accelerate degradation of ARL13b by depalmitoylating it. Together, the results show that palmitoylation plays a unique and critical role in controlling the localization, stability, abundance, and thus function of ARL13b. Pharmacological manipulation of protein palmitoylation may be a strategy to alter cilia function.
Collapse
Affiliation(s)
- Kasturi Roy
- From the Department of Internal Medicine, Section of Nephrology, Yale University School of Medicine, New Haven, Connecticut 06520-8029 and
| | - Stephanie Jerman
- the Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520-8029
| | - Levente Jozsef
- From the Department of Internal Medicine, Section of Nephrology, Yale University School of Medicine, New Haven, Connecticut 06520-8029 and
| | - Thomas McNamara
- From the Department of Internal Medicine, Section of Nephrology, Yale University School of Medicine, New Haven, Connecticut 06520-8029 and
| | - Ginikanwa Onyekaba
- From the Department of Internal Medicine, Section of Nephrology, Yale University School of Medicine, New Haven, Connecticut 06520-8029 and
| | - Zhaoxia Sun
- the Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520-8029
| | - Ethan P Marin
- From the Department of Internal Medicine, Section of Nephrology, Yale University School of Medicine, New Haven, Connecticut 06520-8029 and
| |
Collapse
|
43
|
Primary Cilium Formation and Ciliary Protein Trafficking Is Regulated by the Atypical MAP Kinase MAPK15 in Caenorhabditis elegans and Human Cells. Genetics 2017; 207:1423-1440. [PMID: 29021280 DOI: 10.1534/genetics.117.300383] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/05/2017] [Indexed: 11/18/2022] Open
Abstract
Motile and immotile (or primary) cilia are microtubule-based structures that mediate multiple cellular functions, including the transduction of environmental cues, developmental signaling, cellular motility, and modulation of fluid flow. Although their core architectures are similar, motile and primary cilia exhibit marked structural differences that underlie distinct functional properties. However, the extent to which ciliogenesis mechanisms are shared between these different cilia types is not fully described. Here, we report that the atypical MAP kinase MAPK15 (ERK7/8), implicated in the formation of vertebrate motile cilia, also regulates the formation of primary cilia in Caenorhabditis elegans sensory neurons and human cells. We find that MAPK15 localizes to a basal body subdomain with the ciliopathy protein BBS7 and to cell-cell junctions. MAPK15 also regulates the localization of ciliary proteins involved in cilium structure, transport, and signaling. Our results describe a primary cilia-related role for this poorly studied member of the MAPK family in vivo, and indicate a broad requirement for MAPK15 in the formation of multiple ciliary classes across species.
Collapse
|
44
|
Drew K, Lee C, Huizar RL, Tu F, Borgeson B, McWhite CD, Ma Y, Wallingford JB, Marcotte EM. Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes. Mol Syst Biol 2017; 13:932. [PMID: 28596423 PMCID: PMC5488662 DOI: 10.15252/msb.20167490] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Macromolecular protein complexes carry out many of the essential functions of cells, and many genetic diseases arise from disrupting the functions of such complexes. Currently, there is great interest in defining the complete set of human protein complexes, but recent published maps lack comprehensive coverage. Here, through the synthesis of over 9,000 published mass spectrometry experiments, we present hu.MAP, the most comprehensive and accurate human protein complex map to date, containing > 4,600 total complexes, > 7,700 proteins, and > 56,000 unique interactions, including thousands of confident protein interactions not identified by the original publications. hu.MAP accurately recapitulates known complexes withheld from the learning procedure, which was optimized with the aid of a new quantitative metric (k‐cliques) for comparing sets of sets. The vast majority of complexes in our map are significantly enriched with literature annotations, and the map overall shows improved coverage of many disease‐associated proteins, as we describe in detail for ciliopathies. Using hu.MAP, we predicted and experimentally validated candidate ciliopathy disease genes in vivo in a model vertebrate, discovering CCDC138, WDR90, and KIAA1328 to be new cilia basal body/centriolar satellite proteins, and identifying ANKRD55 as a novel member of the intraflagellar transport machinery. By offering significant improvements to the accuracy and coverage of human protein complexes, hu.MAP (http://proteincomplexes.org) serves as a valuable resource for better understanding the core cellular functions of human proteins and helping to determine mechanistic foundations of human disease.
Collapse
Affiliation(s)
- Kevin Drew
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Chanjae Lee
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA.,Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Ryan L Huizar
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA.,Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Fan Tu
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA.,Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Blake Borgeson
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA.,Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Claire D McWhite
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA.,Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Yun Ma
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.,The Otolaryngology Hospital, The First Affiliated Hospital of Sun Yat-sen University Sun Yat-sen University, Guangzhou, China
| | - John B Wallingford
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA.,Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Edward M Marcotte
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA .,Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| |
Collapse
|
45
|
Song P, Dudinsky L, Fogerty J, Gaivin R, Perkins BD. Arl13b Interacts With Vangl2 to Regulate Cilia and Photoreceptor Outer Segment Length in Zebrafish. Invest Ophthalmol Vis Sci 2017; 57:4517-26. [PMID: 27571019 PMCID: PMC5015978 DOI: 10.1167/iovs.16-19898] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Mutations in the gene ARL13B cause the classical form of Joubert syndrome, an autosomal recessive ciliopathy with variable degrees of retinal degeneration. As second-site modifier alleles can contribute to retinal pathology in ciliopathies, animal models provide a unique platform to test how genetic interactions modulate specific phenotypes. In this study, we analyzed the zebrafish arl13b mutant for retinal degeneration and for epistatic relationships with the planar cell polarity protein (PCP) component vangl2. METHODS Photoreceptor and cilia structure was examined by light and electron microscopy. Immunohistochemistry was performed to examine ciliary markers. Genetic interactions were tested by pairwise crosses of heterozygous animals. Genetic mosaic animals were generated by blastula transplantation and analyzed by fluorescence microscopy. RESULTS At 5 days after fertilization, photoreceptor outer segments were shorter in zebrafish arl13b-/- mutants compared to wild-type larvae, no overt signs of retinal degeneration were observed by light or electron microscopy. Starting at 14 days after fertilization (dpf) and continuing through 30 dpf, cells lacking Arl13b died following transplantation into wild-type host animals. Photoreceptors of arl13b-/-;vangl2-/- mutants were more compromised than the photoreceptors of single mutants. Finally, when grown within a wild-type retina, the vangl2-/- mutant cone photoreceptors displayed normal basal body positioning. CONCLUSIONS We show that arl13b-/- mutants have shortened cilia and photoreceptor outer segments and exhibit a slow, progressive photoreceptor degeneration that occurs over weeks. The data suggest that loss of Arl13b leads to slow photoreceptor degeneration, but can be exacerbated by the loss of vangl2. Importantly, the data show that Arl13b can genetically and physically interact with Vangl2 and this association is important for normal photoreceptor structure. The loss of vangl2, however, does not affect basal body positioning.
Collapse
Affiliation(s)
- Ping Song
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio, United States
| | - Lynn Dudinsky
- Department of Biology, Texas A&M University, College Station, Texas, United States
| | - Joseph Fogerty
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio, United States
| | - Robert Gaivin
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio, United States
| | - Brian D Perkins
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio, United States 2Department of Biology, Texas A&M University, College Station, Texas, United States
| |
Collapse
|
46
|
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.
Collapse
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.
| |
Collapse
|
47
|
Nozaki S, Katoh Y, Terada M, Michisaka S, Funabashi T, Takahashi S, Kontani K, Nakayama K. Regulation of ciliary retrograde protein trafficking by the Joubert syndrome proteins ARL13B and INPP5E. J Cell Sci 2017; 130:563-576. [PMID: 27927754 DOI: 10.1242/jcs.197004] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/29/2016] [Indexed: 12/17/2022] Open
Abstract
ARL13B (a small GTPase) and INPP5E (a phosphoinositide 5-phosphatase) are ciliary proteins encoded by causative genes of Joubert syndrome. We here showed, by taking advantage of a visible immunoprecipitation assay, that ARL13B interacts with the IFT46 -: IFT56 (IFT56 is also known as TTC26) dimer of the intraflagellar transport (IFT)-B complex, which mediates anterograde ciliary protein trafficking. However, the ciliary localization of ARL13B was found to be independent of its interaction with IFT-B, but dependent on the ciliary-targeting sequence RVEP in its C-terminal region. ARL13B-knockout cells had shorter cilia than control cells and exhibited aberrant localization of ciliary proteins, including INPP5E. In particular, in ARL13B-knockout cells, the IFT-A and IFT-B complexes accumulated at ciliary tips, and GPR161 (a negative regulator of Hedgehog signaling) could not exit cilia in response to stimulation with Smoothened agonist. This abnormal phenotype was rescued by the exogenous expression of wild-type ARL13B, as well as by its mutant defective in the interaction with IFT-B, but not by its mutants defective in INPP5E binding or in ciliary localization. Thus, ARL13B regulates IFT-A-mediated retrograde protein trafficking within cilia through its interaction with INPP5E.
Collapse
Affiliation(s)
- Shohei Nozaki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yohei Katoh
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masaya Terada
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Saki Michisaka
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Teruki Funabashi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Senye Takahashi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kenji Kontani
- Department of Biochemistry, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588, Japan
| | - Kazuhisa Nakayama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| |
Collapse
|
48
|
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.
Collapse
|
49
|
Dyson JM, Conduit SE, Feeney SJ, Hakim S, DiTommaso T, Fulcher AJ, Sriratana A, Ramm G, Horan KA, Gurung R, Wicking C, Smyth I, Mitchell CA. INPP5E regulates phosphoinositide-dependent cilia transition zone function. J Cell Biol 2016; 216:247-263. [PMID: 27998989 PMCID: PMC5223597 DOI: 10.1083/jcb.201511055] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 09/19/2016] [Accepted: 12/02/2016] [Indexed: 02/07/2023] Open
Abstract
Dyson et al. demonstrate that the inositol polyphosphate 5-phosphatase INPP5E is essential for Hedgehog-dependent embryonic development. By regulating PI(4,5)P2 and PI(3,4,5)P3 signals at cilia, INPP5E contributes to cilia transition zone function and thereby Smoothened accumulation at cilia. Human ciliopathies, including Joubert syndrome (JBTS), arise from cilia dysfunction. The inositol polyphosphate 5-phosphatase INPP5E localizes to cilia and is mutated in JBTS. Murine Inpp5e ablation is embryonically lethal and recapitulates JBTS, including neural tube defects and polydactyly; however, the underlying defects in cilia signaling and the function of INPP5E at cilia are still emerging. We report Inpp5e−/− embryos exhibit aberrant Hedgehog-dependent patterning with reduced Hedgehog signaling. Using mouse genetics, we show increasing Hedgehog signaling via Smoothened M2 expression rescues some Inpp5e−/− ciliopathy phenotypes and “normalizes” Hedgehog signaling. INPP5E’s phosphoinositide substrates PI(4,5)P2 and PI(3,4,5)P3 accumulated at the transition zone (TZ) in Hedgehog-stimulated Inpp5e−/− cells, which was associated with reduced recruitment of TZ scaffolding proteins and reduced Smoothened levels at cilia. Expression of wild-type, but not 5-phosphatase-dead, INPP5E restored TZ molecular organization and Smoothened accumulation at cilia. Therefore, we identify INPP5E as an essential point of convergence between Hedgehog and phosphoinositide signaling at cilia that maintains TZ function and Hedgehog-dependent embryonic development.
Collapse
Affiliation(s)
- Jennifer M Dyson
- Cancer Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Sarah E Conduit
- Cancer Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Sandra J Feeney
- Cancer Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Sandra Hakim
- Cancer Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Tia DiTommaso
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Alex J Fulcher
- Monash Micro Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Absorn Sriratana
- Cancer Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Georg Ramm
- Monash Micro Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Kristy A Horan
- Cancer Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Rajendra Gurung
- Cancer Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Carol Wicking
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ian Smyth
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,Development and Stem Cells Program, Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Christina A Mitchell
- Cancer Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| |
Collapse
|
50
|
Mariani LE, Bijlsma MF, Ivanova AA, Suciu SK, Kahn RA, Caspary T. Arl13b regulates Shh signaling from both inside and outside the cilium. Mol Biol Cell 2016; 27:mbc.E16-03-0189. [PMID: 27682584 PMCID: PMC5170560 DOI: 10.1091/mbc.e16-03-0189] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 08/16/2016] [Accepted: 09/20/2016] [Indexed: 12/21/2022] Open
Abstract
The regulatory GTPase Arl13b localizes to primary cilia, where it regulates Sonic hedgehog (Shh) signaling. Missense mutations in ARL13B can cause the ciliopathy Joubert syndrome, while the mouse null allele is embryonic lethal. We used mouse embryonic fibroblasts as a system to determine the effects of Arl13b mutations on Shh signaling. We tested a total of seven different mutants, three JS-causing variants, two point mutants predicted to alter guanine nucleotide handling, one that disrupts cilia localization, and one that prevents palmitoylation and thus membrane binding, in assays of transcriptional and non-transcriptional Shh signaling. We found that mutations disrupting Arl13b's palmitoylation site, cilia localization signal, or GTPase handling altered the Shh response in distinct assays of transcriptional or non-transcriptional signaling. In contrast, JS-causing mutations in Arl13b did not affect Shh signaling in these same assays, suggesting these mutations result in more subtle defects, likely affecting only a subset of signaling outputs. Finally, we show that restricting Arl13b from cilia interferes with its ability to regulate Shh-stimulated chemotaxis, despite previous evidence that cilia themselves are not required for this non-transcriptional Shh response. This points to a more complex relationship between the ciliary and non-ciliary roles of this regulatory GTPase than previously envisioned.
Collapse
Affiliation(s)
- Laura E Mariani
- *Department of Human Genetics, Emory University, Atlanta, GA, USA Neuroscience Graduate Program, Emory University, Atlanta, GA, USA
| | - Maarten F Bijlsma
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Academic Medical Center and Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Anna A Ivanova
- Department of Biochemistry, Emory University, Atlanta, GA, USA
| | - Sarah K Suciu
- *Department of Human Genetics, Emory University, Atlanta, GA, USA Genetics and Molecular Biology Graduate Program, Emory University, Atlanta, GA, USA
| | - Richard A Kahn
- Department of Biochemistry, Emory University, Atlanta, GA, USA
| | - Tamara Caspary
- *Department of Human Genetics, Emory University, Atlanta, GA, USA
| |
Collapse
|