1
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Lacey SE, Graziadei A, Pigino G. Extensive structural rearrangement of intraflagellar transport trains underpins bidirectional cargo transport. Cell 2024; 187:4621-4636.e18. [PMID: 39067443 PMCID: PMC11349379 DOI: 10.1016/j.cell.2024.06.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 05/06/2024] [Accepted: 06/28/2024] [Indexed: 07/30/2024]
Abstract
Bidirectional transport in cilia is carried out by polymers of the IFTA and IFTB protein complexes, called anterograde and retrograde intraflagellar transport (IFT) trains. Anterograde trains deliver cargoes from the cell to the cilium tip, then convert into retrograde trains for cargo export. We set out to understand how the IFT complexes can perform these two directly opposing roles before and after conversion. We use cryoelectron tomography and in situ cross-linking mass spectrometry to determine the structure of retrograde IFT trains and compare it with the known structure of anterograde trains. The retrograde train is a 2-fold symmetric polymer organized around a central thread of IFTA complexes. We conclude that anterograde-to-retrograde remodeling involves global rearrangements of the IFTA/B complexes and requires complete disassembly of the anterograde train. Finally, we describe how conformational changes to cargo-binding sites facilitate unidirectional cargo transport in a bidirectional system.
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2
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Fujii T, Liang L, Nakayama K, Katoh Y. Defects in diffusion barrier function of ciliary transition zone caused by ciliopathy variations of TMEM218. Hum Mol Genet 2024; 33:1442-1453. [PMID: 38751342 DOI: 10.1093/hmg/ddae083] [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: 03/15/2024] [Revised: 05/01/2024] [Accepted: 05/07/2024] [Indexed: 08/09/2024] Open
Abstract
Primary cilia are antenna-like structures protruding from the surface of various eukaryotic cells, and have distinct protein compositions in their membranes. This distinct protein composition is maintained by the presence of the transition zone (TZ) at the ciliary base, which acts as a diffusion barrier between the ciliary and plasma membranes. Defects in cilia and the TZ are known to cause a group of disorders collectively called the ciliopathies, which demonstrate a broad spectrum of clinical features, such as perinatally lethal Meckel syndrome (MKS), relatively mild Joubert syndrome (JBTS), and nonsyndromic nephronophthisis (NPHP). Proteins constituting the TZ can be grouped into the MKS and NPHP modules. The MKS module is composed of several transmembrane proteins and three soluble proteins. TMEM218 was recently reported to be mutated in individuals diagnosed as MKS and JBTS. However, little is known about how TMEM218 mutations found in MKS and JBTS affect the functions of cilia. In this study, we found that ciliary membrane proteins were not localized to cilia in TMEM218-knockout cells, indicating impaired barrier function of the TZ. Furthermore, the exogenous expression of JBTS-associated TMEM218 variants but not MKS-associated variants in TMEM218-knockout cells restored the localization of ciliary membrane proteins. In particular, when expressed in TMEM218-knockout cells, the TMEM218(R115H) variant found in JBTS was able to restore the barrier function of cells, whereas the MKS variant TMEM218(R115C) could not. Thus, the severity of symptoms of MKS and JBTS individuals appears to correlate with the degree of their ciliary defects at the cellular level.
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Affiliation(s)
- Taiju Fujii
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Luxiaoxue Liang
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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3
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Saito M, Atsumi GI. [Mechanisms of bone formation by primary cilia]. Nihon Yakurigaku Zasshi 2024; 159:198-202. [PMID: 38684398 DOI: 10.1254/fpj.23113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Primary cilia are immotile cilia assembled from the centriole-derived basal body, and they protrude on the cell surface in almost all cell types during the cell cycle G0 phase. Due to the diffusion barrier at the ciliary base, cilia harbor selective G protein-coupled receptors, growth factor receptors, and ion channels on their membrane. Thus, cilia act as sensory organelles, regulating the proliferation and differentiation of the cells and promoting the formation and maturation of various organs including bone, brain, and kidney. It has been unveiled that malformation and dysregulation of cilia cause organ dysplasia, so-called ciliopathy, thus research on primary cilia has become active during the past 20 years. Research on the roles of cilia in bone formation and its regulatory mechanisms have also progressed. It is widely recognized that cilia of preosteoblasts receive hedgehog and promote differentiation of the cells to osteoblasts, resulting in the formation of skulls and long bones. Recently, it has been shown that a membrane-associated protein 4.1G is important in ciliogenesis, hedgehog signaling, and osteoblast differentiation in neonatal bone formation. In this review, we would like to summarize the roles of primary cilia in bone formation and their regulatory mechanisms including the contribution of 4.1G.
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Affiliation(s)
- Masaki Saito
- Department of Molecular Physiology and Pathology, Faculty of Pharmaceutical Sciences, Teikyo University
| | - Gen-Ichi Atsumi
- Department of Molecular Physiology and Pathology, Faculty of Pharmaceutical Sciences, Teikyo University
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4
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Long X, Chen L, Xiao X, Min X, Wu Y, Yang Z, Wen X. Structure, function, and research progress of primary cilia in reproductive physiology and reproductive diseases. Front Cell Dev Biol 2024; 12:1418928. [PMID: 38887518 PMCID: PMC11180893 DOI: 10.3389/fcell.2024.1418928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 05/16/2024] [Indexed: 06/20/2024] Open
Abstract
Primary cilia, serving as the central hub for cellular signal transduction, possess the remarkable ability to translate diverse extracellular signals, both chemical and mechanical, into intracellular responses. Their ubiquitous presence in the reproductive system underscores their pivotal roles in various cellular processes including development, differentiation, and migration. Emerging evidence suggests primary cilia as key players in reproductive physiology and associated pathologies. Notably, primary cilia have been identified in granulosa cells within mouse ovaries and uterine stromal cells, and perturbations in their structure and function have been implicated in a spectrum of reproductive dysfunctions and ciliary-related diseases. Furthermore, disruptions in primary cilia-mediated signal transduction pathways under pathological conditions exacerbate the onset and progression of reproductive disorders. This review provides a comprehensive overview of current research progress on primary cilia and their associated signaling pathways in reproductive physiology and diseases, with the aim of furnishing theoretical groundwork for the prevention and management of primary cilia-related structural and functional abnormalities contributing to reproductive system pathologies.
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Affiliation(s)
- Xiaochuan Long
- Clinical Veterinary Laboratory, College of Animal Science, Guizhou University, Guizhou, China
- Key Laboratory of Animal Genetic, Breeding and Reproduction in the plateau Mountainous Region, Ministry of Education, Guizhou University, Guizhou, China
| | - Li Chen
- Clinical Veterinary Laboratory, College of Animal Science, Guizhou University, Guizhou, China
- Key Laboratory of Animal Genetic, Breeding and Reproduction in the plateau Mountainous Region, Ministry of Education, Guizhou University, Guizhou, China
| | - Xinyao Xiao
- Clinical Veterinary Laboratory, College of Animal Science, Guizhou University, Guizhou, China
- Key Laboratory of Animal Genetic, Breeding and Reproduction in the plateau Mountainous Region, Ministry of Education, Guizhou University, Guizhou, China
| | - Xiayu Min
- Clinical Veterinary Laboratory, College of Animal Science, Guizhou University, Guizhou, China
- Key Laboratory of Animal Genetic, Breeding and Reproduction in the plateau Mountainous Region, Ministry of Education, Guizhou University, Guizhou, China
| | - Yao Wu
- Clinical Veterinary Laboratory, College of Animal Science, Guizhou University, Guizhou, China
- Key Laboratory of Animal Genetic, Breeding and Reproduction in the plateau Mountainous Region, Ministry of Education, Guizhou University, Guizhou, China
| | - Zengming Yang
- Key Laboratory of Animal Genetic, Breeding and Reproduction in the plateau Mountainous Region, Ministry of Education, Guizhou University, Guizhou, China
- Basic Veterinary Laboratory, College of Animal Science, Guizhou University, Guizhou, China
| | - Xin Wen
- Clinical Veterinary Laboratory, College of Animal Science, Guizhou University, Guizhou, China
- Key Laboratory of Animal Genetic, Breeding and Reproduction in the plateau Mountainous Region, Ministry of Education, Guizhou University, Guizhou, China
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5
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Ma R, Chen L, Hu N, Caplan S, Hu G. Cilia and Extracellular Vesicles in Brain Development and Disease. Biol Psychiatry 2024; 95:1020-1029. [PMID: 37956781 PMCID: PMC11087377 DOI: 10.1016/j.biopsych.2023.11.004] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/21/2023] [Accepted: 11/05/2023] [Indexed: 11/15/2023]
Abstract
Primary and motile cilia are thin, hair-like cellular projections from the cell surface involved in movement, sensing, and communication between cells. Extracellular vesicles (EVs) are small membrane-bound vesicles secreted by cells and contain various proteins, lipids, and nucleic acids that are delivered to and influence the behavior of other cells. Both cilia and EVs are essential for the normal functioning of brain cells, and their malfunction can lead to several neurological diseases. Cilia and EVs can interact with each other in several ways, and this interplay plays a crucial role in facilitating various biological processes, including cell-to-cell communication, tissue homeostasis, and pathogen defense. Cilia and EV crosstalk in the brain is an emerging area of research. Herein, we summarize the detailed molecular mechanisms of cilia and EV interplay and address the ciliary molecules that are involved in signaling and cellular dysfunction in brain development and diseases. Finally, we discuss the potential clinical use of cilia and EVs in brain diseases.
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Affiliation(s)
- Rong Ma
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska; Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Liang Chen
- Department of Computer Science, College of Engineering, Shantou University, Shantou, Guangdong, China
| | - Ningyun Hu
- Millard West High School, Omaha, Nebraska
| | - Steve Caplan
- Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska.
| | - Guoku Hu
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska.
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6
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Strobel M, Qiu L, Hofer A, Chen X. Temporal Ablation of Primary Cilia Impairs Brainwave Patterns Implicated in Memory Formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.03.587983. [PMID: 38617207 PMCID: PMC11014598 DOI: 10.1101/2024.04.03.587983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
The primary cilium is a hair-like organelle that hosts molecular machinery for various developmental and homeostatic signaling pathways. Its alteration can cause severe ciliopathies such as the Bardet-Biedl and Joubert syndromes, but is also linked to Alzheimer's disease, clinical depression, and autism spectrum disorder. These afflictions are caused by disturbances in a variety of genes but a common phenotype amongst them is cognitive impairment. Cilia-mediated neural function has generally been examined in relation to these diseases or other developmental defects, but the role of cilia in brain function and memory consolidation is unknown. To elucidate the role of cilia in neural activity and cognitive function, we temporally ablated primary cilia in adult mice before performing electroencephalogram/electromyogram (EEG/EMG) recordings. We found that cilia deficient mice had altered sleep architecture, reduced EEG power, and attenuated phase-amplitude coupling, a process that underlies memory consolidation. These results highlight the growing significance of cilia, demonstrating that they are not only necessary in early neurodevelopment, but also regulate advanced neural functions in the adult brain.
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7
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Mukhopadhyay AG, Toropova K, Daly L, Wells JN, Vuolo L, Mladenov M, Seda M, Jenkins D, Stephens DJ, Roberts AJ. Structure and tethering mechanism of dynein-2 intermediate chains in intraflagellar transport. EMBO J 2024; 43:1257-1272. [PMID: 38454149 PMCID: PMC10987677 DOI: 10.1038/s44318-024-00060-1] [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: 09/05/2023] [Revised: 02/06/2024] [Accepted: 02/09/2024] [Indexed: 03/09/2024] Open
Abstract
Dynein-2 is a large multiprotein complex that powers retrograde intraflagellar transport (IFT) of cargoes within cilia/flagella, but the molecular mechanism underlying this function is still emerging. Distinctively, dynein-2 contains two identical force-generating heavy chains that interact with two different intermediate chains (WDR34 and WDR60). Here, we dissect regulation of dynein-2 function by WDR34 and WDR60 using an integrative approach including cryo-electron microscopy and CRISPR/Cas9-enabled cell biology. A 3.9 Å resolution structure shows how WDR34 and WDR60 use surprisingly different interactions to engage equivalent sites of the two heavy chains. We show that cilia can assemble in the absence of either WDR34 or WDR60 individually, but not both subunits. Dynein-2-dependent distribution of cargoes depends more strongly on WDR60, because the unique N-terminal extension of WDR60 facilitates dynein-2 targeting to cilia. Strikingly, this N-terminal extension can be transplanted onto WDR34 and retain function, suggesting it acts as a flexible tether to the IFT "trains" that assemble at the ciliary base. We discuss how use of unstructured tethers represents an emerging theme in IFT train interactions.
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Affiliation(s)
- Aakash G Mukhopadhyay
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, UK
| | - Katerina Toropova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, UK
| | - Lydia Daly
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, UK
- Randall Centre of Cell & Molecular Biophysics, King's College London, London, UK
| | - Jennifer N Wells
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, UK
- MRC London Institute of Medical Sciences (LMS), London, UK
| | - Laura Vuolo
- Cell Biology Laboratories, School of Biochemistry, University of Bristol, Bristol, UK
| | - Miroslav Mladenov
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, UK
- Cellular Signalling and Cytoskeletal Function Laboratory, The Francis Crick Institute, London, UK
| | - Marian Seda
- UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Dagan Jenkins
- UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - David J Stephens
- Cell Biology Laboratories, School of Biochemistry, University of Bristol, Bristol, UK
| | - Anthony J Roberts
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, UK.
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8
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Moran AL, Louzao-Martinez L, Norris DP, Peters DJM, Blacque OE. Transport and barrier mechanisms that regulate ciliary compartmentalization and ciliopathies. Nat Rev Nephrol 2024; 20:83-100. [PMID: 37872350 DOI: 10.1038/s41581-023-00773-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2023] [Indexed: 10/25/2023]
Abstract
Primary cilia act as cell surface antennae, coordinating cellular responses to sensory inputs and signalling molecules that regulate developmental and homeostatic pathways. Cilia are therefore critical to physiological processes, and defects in ciliary components are associated with a large group of inherited pleiotropic disorders - known collectively as ciliopathies - that have a broad spectrum of phenotypes and affect many or most tissues, including the kidney. A central feature of the cilium is its compartmentalized structure, which imparts its unique molecular composition and signalling environment despite its membrane and cytosol being contiguous with those of the cell. Such compartmentalization is achieved via active transport pathways that bring protein cargoes to and from the cilium, as well as gating pathways at the ciliary base that establish diffusion barriers to protein exchange into and out of the organelle. Many ciliopathy-linked proteins, including those involved in kidney development and homeostasis, are components of the compartmentalizing machinery. New insights into the major compartmentalizing pathways at the cilium, namely, ciliary gating, intraflagellar transport, lipidated protein flagellar transport and ciliary extracellular vesicle release pathways, have improved our understanding of the mechanisms that underpin ciliary disease and associated renal disorders.
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Affiliation(s)
- Ailis L Moran
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Laura Louzao-Martinez
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Dorien J M Peters
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
| | - Oliver E Blacque
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland.
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9
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Udupa P, Ghosh DK. The emerging functions of intraflagellar transport 52 in ciliary transport and ciliopathies. Traffic 2024; 25:e12929. [PMID: 38272449 DOI: 10.1111/tra.12929] [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: 08/07/2023] [Revised: 10/31/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024]
Abstract
Ciliary transport in eukaryotic cells is an intricate and conserved process involving the coordinated assembly and functioning of a multiprotein intraflagellar transport (IFT) complex. Among the various IFT proteins, intraflagellar transport 52 (IFT52) plays a crucial role in ciliary transport and is implicated in various ciliopathies. IFT52 is a core component of the IFT-B complex that facilitates movement of cargoes along the ciliary axoneme. Stable binding of the IFT-B1 and IFT-B2 subcomplexes by IFT52 in the IFT-B complex regulates recycling of ciliary components and maintenance of ciliary functions such as signal transduction and molecular movement. Mutations in the IFT52 gene can disrupt ciliary trafficking, resulting in dysfunctional cilia and affecting cellular processes in ciliopathies. Such ciliopathies caused by IFT52 mutations exhibit a wide range of clinical features, including skeletal developmental abnormalities, retinal degeneration, respiratory failure and neurological abnormalities in affected individuals. Therefore, IFT52 serves as a promising biomarker for the diagnosis of various ciliopathies, including short-rib thoracic dysplasia 16 with or without polydactyly. Here, we provide an overview of the IFT52-mediated molecular mechanisms underlying ciliary transport and describe the IFT52 mutations that cause different disorders associated with cilia dysfunction.
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Affiliation(s)
- Prajna Udupa
- Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Debasish Kumar Ghosh
- Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India
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10
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Tasaki K, Zhou Z, Ishida Y, Katoh Y, Nakayama K. Compound heterozygous IFT81 variations in a skeletal ciliopathy patient cause Bardet-Biedl syndrome-like ciliary defects. Hum Mol Genet 2023; 32:2887-2900. [PMID: 37427975 DOI: 10.1093/hmg/ddad112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/04/2023] [Accepted: 07/04/2023] [Indexed: 07/11/2023] Open
Abstract
Owing to their crucial roles in development and homeostasis, defects in cilia cause ciliopathies with diverse clinical manifestations. The intraflagellar transport (IFT) machinery, containing the IFT-A and IFT-B complexes, mediates not only the intraciliary bidirectional trafficking but also import and export of ciliary proteins together with the kinesin-2 and dynein-2 motor complexes. The BBSome, containing eight subunits encoded by causative genes of Bardet-Biedl syndrome (BBS), connects the IFT machinery to ciliary membrane proteins to mediate their export from cilia. Although mutations in subunits of the IFT-A and dynein-2 complexes cause skeletal ciliopathies, mutations in some IFT-B subunits are also known to cause skeletal ciliopathies. We here show that compound heterozygous variations of an IFT-B subunit, IFT81, found in a patient with skeletal ciliopathy cause defects in its interactions with other IFT-B subunits, and in ciliogenesis and ciliary protein trafficking when one of the two variants was expressed in IFT81-knockout (KO) cells. Notably, we found that IFT81-KO cells expressing IFT81(Δ490-519), which lacks the binding site for the IFT25-IFT27 dimer, causes ciliary defects reminiscent of those found in BBS cells and those in IFT74-KO cells expressing a BBS variant of IFT74, which forms a heterodimer with IFT81. In addition, IFT81-KO cells expressing IFT81(Δ490-519) in combination with the other variant, IFT81 (L645*), which mimics the cellular conditions of the above skeletal ciliopathy patient, demonstrated essentially the same phenotype as those expressing only IFT81(Δ490-519). Thus, our data indicate that BBS-like defects can be caused by skeletal ciliopathy variants of IFT81.
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Affiliation(s)
- Koshi Tasaki
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Zhuang Zhou
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yamato Ishida
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
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11
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Ma Y, He J, Li S, Yao D, Huang C, Wu J, Lei M. Structural insight into the intraflagellar transport complex IFT-A and its assembly in the anterograde IFT train. Nat Commun 2023; 14:1506. [PMID: 36932088 PMCID: PMC10023715 DOI: 10.1038/s41467-023-37208-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
Intraflagellar transport (IFT) trains, the polymers composed of two multi-subunit complexes, IFT-A and IFT-B, carry out bidirectional intracellular transport in cilia, vital for cilia biogenesis and signaling. IFT-A plays crucial roles in the ciliary import of membrane proteins and the retrograde cargo trafficking. However, the molecular architecture of IFT-A and the assembly mechanism of the IFT-A into the IFT trains in vivo remains elusive. Here, we report the cryo-electron microscopic structures of the IFT-A complex from protozoa Tetrahymena thermophila. We find that IFT-A complexes present two distinct, elongated and folded states. Remarkably, comparison with the in situ cryo-electron tomography structure of the anterograde IFT train unveils a series of adjustments of the flexible arms in apo IFT-A when incorporated into the anterograde train. Our results provide an atomic-resolution model for the IFT-A complex and valuable insights into the assembly mechanism of anterograde IFT trains.
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Affiliation(s)
- Yuanyuan Ma
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Institute of Precision Medicine, Shanghai, 200125, China
| | - Jun He
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Institute of Precision Medicine, Shanghai, 200125, China
| | - Shaobai Li
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Institute of Precision Medicine, Shanghai, 200125, China
| | - Deqiang Yao
- Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China
| | - Chenhui Huang
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Institute of Precision Medicine, Shanghai, 200125, China
| | - Jian Wu
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.
- Shanghai Institute of Precision Medicine, Shanghai, 200125, China.
| | - Ming Lei
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.
- Shanghai Institute of Precision Medicine, Shanghai, 200125, China.
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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12
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Hiyamizu S, Qiu H, Vuolo L, Stevenson NL, Shak C, Heesom KJ, Hamada Y, Tsurumi Y, Chiba S, Katoh Y, Stephens DJ, Nakayama K. Multiple interactions of the dynein-2 complex with the IFT-B complex are required for effective intraflagellar transport. J Cell Sci 2023; 136:286934. [PMID: 36632779 PMCID: PMC10110421 DOI: 10.1242/jcs.260462] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 01/04/2023] [Indexed: 01/13/2023] Open
Abstract
The dynein-2 complex must be transported anterogradely within cilia to then drive retrograde trafficking of the intraflagellar transport (IFT) machinery containing IFT-A and IFT-B complexes. Here, we screened for potential interactions between the dynein-2 and IFT-B complexes and found multiple interactions among the dynein-2 and IFT-B subunits. In particular, WDR60 (also known as DYNC2I1) and the DYNC2H1-DYNC2LI1 dimer from dynein-2, and IFT54 (also known as TRAF3IP1) and IFT57 from IFT-B contribute to the dynein-2-IFT-B interactions. WDR60 interacts with IFT54 via a conserved region N-terminal to its light chain-binding regions. Expression of the WDR60 constructs in WDR60-knockout (KO) cells revealed that N-terminal truncation mutants lacking the IFT54-binding site fail to rescue abnormal phenotypes of WDR60-KO cells, such as aberrant accumulation of the IFT machinery around the ciliary tip and on the distal side of the transition zone. However, a WDR60 construct specifically lacking just the IFT54-binding site substantially restored the ciliary defects. In line with the current docking model of dynein-2 with the anterograde IFT trains, these results indicate that extensive interactions involving multiple subunits from the dynein-2 and IFT-B complexes participate in their connection.
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Affiliation(s)
- Shunya Hiyamizu
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hantian Qiu
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Laura Vuolo
- Cell Biology Laboratories, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Nicola L Stevenson
- Cell Biology Laboratories, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Caroline Shak
- Cell Biology Laboratories, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Kate J Heesom
- Proteomics Facility, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Yuki Hamada
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yuta Tsurumi
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shuhei Chiba
- Department of Genetic Disease Research, Graduate School of Medicine, Osaka City University, Abeno-ku, Osaka 545-8585, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - David J Stephens
- Cell Biology Laboratories, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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13
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Gonçalves-Santos F, De-Castro MJG, De-Castro ARG, Dantas TJ. Building train carriages for ciliary transport: (IFT-)A complex task. Commun Biol 2023; 6:91. [PMID: 36690675 PMCID: PMC9870902 DOI: 10.1038/s42003-023-04426-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Francisco Gonçalves-Santos
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Maria J G De-Castro
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Ana R G De-Castro
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Tiago J Dantas
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.
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14
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Lacey SE, Foster HE, Pigino G. The molecular structure of IFT-A and IFT-B in anterograde intraflagellar transport trains. Nat Struct Mol Biol 2023; 30:584-593. [PMID: 36593313 DOI: 10.1038/s41594-022-00905-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 12/01/2022] [Indexed: 01/03/2023]
Abstract
Anterograde intraflagellar transport (IFT) trains are essential for cilia assembly and maintenance. These trains are formed of 22 IFT-A and IFT-B proteins that link structural and signaling cargos to microtubule motors for import into cilia. It remains unknown how the IFT-A/-B proteins are arranged into complexes and how these complexes polymerize into functional trains. Here we use in situ cryo-electron tomography of Chlamydomonas reinhardtii cilia and AlphaFold2 protein structure predictions to generate a molecular model of the entire anterograde train. We show how the conformations of both IFT-A and IFT-B are dependent on lateral interactions with neighboring repeats, suggesting that polymerization is required to cooperatively stabilize the complexes. Following three-dimensional classification, we reveal how IFT-B extends two flexible tethers to maintain a connection with IFT-A that can withstand the mechanical stresses present in actively beating cilia. Overall, our findings provide a framework for understanding the fundamental processes that govern cilia assembly.
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15
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Hesketh SJ, Mukhopadhyay AG, Nakamura D, Toropova K, Roberts AJ. IFT-A structure reveals carriages for membrane protein transport into cilia. Cell 2022; 185:4971-4985.e16. [PMID: 36462505 DOI: 10.1016/j.cell.2022.11.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/13/2022] [Accepted: 11/09/2022] [Indexed: 12/05/2022]
Abstract
Intraflagellar transport (IFT) trains are massive molecular machines that traffic proteins between cilia and the cell body. Each IFT train is a dynamic polymer of two large complexes (IFT-A and -B) and motor proteins, posing a formidable challenge to mechanistic understanding. Here, we reconstituted the complete human IFT-A complex and obtained its structure using cryo-EM. Combined with AlphaFold prediction and genome-editing studies, our results illuminate how IFT-A polymerizes, interacts with IFT-B, and uses an array of β-propeller and TPR domains to create "carriages" of the IFT train that engage TULP adaptor proteins. We show that IFT-A⋅TULP carriages are essential for cilia localization of diverse membrane proteins, as well as ICK-the key kinase regulating IFT train turnaround. These data establish a structural link between IFT-A's distinct functions, provide a blueprint for IFT-A in the train, and shed light on how IFT evolved from a proto-coatomer ancestor.
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Affiliation(s)
- Sophie J Hesketh
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck University of London, London, WC1E 7HX, UK
| | - Aakash G Mukhopadhyay
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck University of London, London, WC1E 7HX, UK
| | - Dai Nakamura
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck University of London, London, WC1E 7HX, UK
| | - Katerina Toropova
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck University of London, London, WC1E 7HX, UK.
| | - Anthony J Roberts
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck University of London, London, WC1E 7HX, UK.
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16
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Meleppattu S, Zhou H, Dai J, Gui M, Brown A. Mechanism of IFT-A polymerization into trains for ciliary transport. Cell 2022; 185:4986-4998.e12. [PMID: 36563665 PMCID: PMC9794116 DOI: 10.1016/j.cell.2022.11.033] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/14/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022]
Abstract
Intraflagellar transport (IFT) is the highly conserved process by which proteins are transported along ciliary microtubules by a train-like polymeric assembly of IFT-A and IFT-B complexes. IFT-A is sandwiched between IFT-B and the ciliary membrane, consistent with its putative role in transporting transmembrane and membrane-associated cargoes. Here, we have used single-particle analysis electron cryomicroscopy (cryo-EM) to determine structures of native IFT-A complexes. We show that subcomplex rearrangements enable IFT-A to polymerize laterally on anterograde IFT trains, revealing a cooperative assembly mechanism. Surprisingly, we discover that binding of IFT-A to IFT-B shields the preferred lipid-binding interface from the ciliary membrane but orients an interconnected network of β-propeller domains with the capacity to accommodate diverse cargoes toward the ciliary membrane. This work provides a mechanistic basis for understanding IFT-train assembly and cargo interactions.
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Affiliation(s)
- Shimi Meleppattu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Haixia Zhou
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Jin Dai
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Miao Gui
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Alan Brown
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
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17
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Abstract
The assembly and maintenance of most cilia and eukaryotic flagella depends on intraflagellar transport (IFT), the bidirectional movement of multi-megadalton IFT trains along the axonemal microtubules. These IFT trains function as carriers, moving ciliary proteins between the cell body and the organelle. Whereas tubulin, the principal protein of cilia, binds directly to IFT particle proteins, the transport of other ciliary proteins and complexes requires adapters that link them to the trains. Large axonemal substructures, such as radial spokes, outer dynein arms and inner dynein arms, assemble in the cell body before attaching to IFT trains, using the adapters ARMC2, ODA16 and IDA3, respectively. Ciliary import of several membrane proteins involves the putative adapter tubby-like protein 3 (TULP3), whereas membrane protein export involves the BBSome, an octameric complex that co-migrates with IFT particles. Thus, cells employ a variety of adapters, each of which is substoichiometric to the core IFT machinery, to expand the cargo range of the IFT trains. This Review summarizes the individual and shared features of the known cargo adapters and discusses their possible role in regulating the transport capacity of the IFT pathway.
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Affiliation(s)
- Karl Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
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18
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Clupper M, Gill R, Elsayyid M, Touroutine D, Caplan JL, Tanis JE. Kinesin-2 motors differentially impact biogenesis of extracellular vesicle subpopulations shed from sensory cilia. iScience 2022; 25:105262. [PMID: 36304122 PMCID: PMC9593189 DOI: 10.1016/j.isci.2022.105262] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 07/13/2022] [Accepted: 09/26/2022] [Indexed: 01/21/2023] Open
Abstract
Extracellular vesicles (EVs) are bioactive lipid-bilayer enclosed particles released from nearly all cells. One specialized site for EV shedding is the primary cilium. Here, we discover the conserved ion channel CLHM-1 as a ciliary EV cargo. Imaging of EVs released from sensory neuron cilia of Caenorhabditis elegans expressing fluorescently tagged CLHM-1 and TRP polycystin-2 channel PKD-2 shows enrichment of these cargoes in distinct EV subpopulations that are differentially shed in response to mating partner availability. PKD-2 alone is present in EVs shed from the cilium distal tip, whereas CLHM-1 EVs bud from a secondary site(s), including the ciliary base. Heterotrimeric and homodimeric kinesin-2 motors have discrete impacts on PKD-2 and CLHM-1 colocalization in both cilia and EVs. Total loss of kinesin-2 activity decreases shedding of PKD-2 but not CLHM-1 EVs. Our data demonstrate that anterograde intraflagellar transport is required for selective enrichment of protein cargoes into heterogeneous EVs with different signaling potentials.
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Affiliation(s)
- Michael Clupper
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Rachael Gill
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Malek Elsayyid
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Denis Touroutine
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Jeffrey L. Caplan
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
| | - Jessica E. Tanis
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
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19
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McCafferty CL, Papoulas O, Jordan MA, Hoogerbrugge G, Nichols C, Pigino G, Taylor DW, Wallingford JB, Marcotte EM. Integrative modeling reveals the molecular architecture of the intraflagellar transport A (IFT-A) complex. eLife 2022; 11:e81977. [PMID: 36346217 PMCID: PMC9674347 DOI: 10.7554/elife.81977] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/07/2022] [Indexed: 11/10/2022] Open
Abstract
Intraflagellar transport (IFT) is a conserved process of cargo transport in cilia that is essential for development and homeostasis in organisms ranging from algae to vertebrates. In humans, variants in genes encoding subunits of the cargo-adapting IFT-A and IFT-B protein complexes are a common cause of genetic diseases known as ciliopathies. While recent progress has been made in determining the atomic structure of IFT-B, little is known of the structural biology of IFT-A. Here, we combined chemical cross-linking mass spectrometry and cryo-electron tomography with AlphaFold2-based prediction of both protein structures and interaction interfaces to model the overall architecture of the monomeric six-subunit IFT-A complex, as well as its polymeric assembly within cilia. We define monomer-monomer contacts and membrane-associated regions available for association with transported cargo, and we also use this model to provide insights into the pleiotropic nature of human ciliopathy-associated genetic variants in genes encoding IFT-A subunits. Our work demonstrates the power of integration of experimental and computational strategies both for multi-protein structure determination and for understanding the etiology of human genetic disease.
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Affiliation(s)
- Caitlyn L McCafferty
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of TexasAustinUnited States
| | - Ophelia Papoulas
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of TexasAustinUnited States
| | - Mareike A Jordan
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Gabriel Hoogerbrugge
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of TexasAustinUnited States
| | - Candice Nichols
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of TexasAustinUnited States
| | | | - David W Taylor
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of TexasAustinUnited States
| | - John B Wallingford
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of TexasAustinUnited States
| | - Edward M Marcotte
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of TexasAustinUnited States
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20
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Zhou Z, Katoh Y, Nakayama K. CEP19-RABL2-IFT-B axis controls BBSome-mediated ciliary GPCR export. Mol Biol Cell 2022; 33:ar126. [PMID: 36074075 PMCID: PMC9634966 DOI: 10.1091/mbc.e22-05-0161] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The intraflagellar transport (IFT) machinery mediates the import and export of ciliary proteins across the ciliary gate, as well as bidirectional protein trafficking within cilia. In addition to ciliary anterograde protein trafficking, the IFT-B complex participates in the export of membrane proteins together with the BBSome, which consists of eight subunits encoded by the causative genes of Bardet-Biedl syndrome (BBS). The IFT25-IFT27/BBS19 dimer in the IFT-B complex constitutes its interface with the BBSome. We show here that IFT25-IFT27 and the RABL2 GTPase bind the IFT74/BBS22-IFT81 dimer of the IFT-B complex in a mutually exclusive manner. Cells expressing GTP-locked RABL2 [RABL2(Q80L)], but not wild-type RABL2, phenocopied IFT27-knockout cells, that is, they demonstrated BBS-associated ciliary defects, including accumulation of LZTFL1/BBS17 and the BBSome within cilia and the suppression of export of the ciliary GPCRs GPR161 and Smoothened. RABL2(Q80L) enters cilia in a manner dependent on the basal body protein CEP19, but its entry into cilia is not necessary for causing BBS-associated ciliary defects. These observations suggest that GTP-bound RABL2 is likely to be required for recruitment of the IFT-B complex to the ciliary base, where it is replaced with IFT25-IFT27.
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Affiliation(s)
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan,*Address correspondence to: Kazuhisa Nakayama (); Yohei Katoh ()
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan,*Address correspondence to: Kazuhisa Nakayama (); Yohei Katoh ()
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21
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Mul W, Mitra A, Peterman EJG. Mechanisms of Regulation in Intraflagellar Transport. Cells 2022; 11:2737. [PMID: 36078145 PMCID: PMC9454703 DOI: 10.3390/cells11172737] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 11/30/2022] Open
Abstract
Cilia are eukaryotic organelles essential for movement, signaling or sensing. Primary cilia act as antennae to sense a cell's environment and are involved in a wide range of signaling pathways essential for development. Motile cilia drive cell locomotion or liquid flow around the cell. Proper functioning of both types of cilia requires a highly orchestrated bi-directional transport system, intraflagellar transport (IFT), which is driven by motor proteins, kinesin-2 and IFT dynein. In this review, we explore how IFT is regulated in cilia, focusing from three different perspectives on the issue. First, we reflect on how the motor track, the microtubule-based axoneme, affects IFT. Second, we focus on the motor proteins, considering the role motor action, cooperation and motor-train interaction plays in the regulation of IFT. Third, we discuss the role of kinases in the regulation of the motor proteins. Our goal is to provide mechanistic insights in IFT regulation in cilia and to suggest directions of future research.
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Affiliation(s)
| | | | - Erwin J. G. Peterman
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
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22
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Satoda Y, Noguchi T, Fujii T, Taniguchi A, Katoh Y, Nakayama K. BROMI/TBC1D32 together with CCRK/CDK20 and FAM149B1/JBTS36 contributes to intraflagellar transport turnaround involving ICK/CILK1. Mol Biol Cell 2022; 33:ar79. [PMID: 35609210 PMCID: PMC9582636 DOI: 10.1091/mbc.e22-03-0089] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Primary cilia are antenna-like organelles that contain specific proteins, and are crucial for tissue morphogenesis. Anterograde and retrograde trafficking of ciliary proteins are mediated by the intraflagellar transport (IFT) machinery. BROMI/TBC1D32 interacts with CCRK/CDK20, which phosphorylates and activates the intestinal cell kinase (ICK)/CILK1 kinase, to regulate the change in direction of the IFT machinery at the ciliary tip. Mutations in BROMI, CCRK, and ICK in humans cause ciliopathies, and mice defective in these genes are also known to demonstrate ciliopathy phenotypes. We show here that BROMI interacts not only with CCRK but also with CFAP20, an evolutionarily conserved ciliary protein, and with FAM149B1/ Joubert syndrome (JBTS)36, a protein in which mutations cause JBTS. In addition, we show that FAM149B1 interacts directly with CCRK as well as with BROMI. Ciliary defects observed in CCRK-knockout (KO), BROMI-KO, and FAM149B1-KO cells, including abnormally long cilia and accumulation of the IFT machinery and ICK at the ciliary tip, resembled one another, and BROMI mutants that are defective in binding to CCRK and CFAP20 were unable to rescue the ciliary defects of BROMI-KO cells. These data indicate that CCRK, BROMI, FAM149B1, and probably CFAP20 altogether regulate the IFT turnaround process under the control of ICK.
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Affiliation(s)
- Yuuki Satoda
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tatsuro Noguchi
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Taiju Fujii
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Aoi Taniguchi
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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23
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Ishida Y, Tasaki K, Katoh Y, Nakayama K. Molecular basis underlying the ciliary defects caused by IFT52 variations found in skeletal ciliopathies. Mol Biol Cell 2022; 33:ar83. [PMID: 35704471 PMCID: PMC9582644 DOI: 10.1091/mbc.e22-05-0188] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Bidirectional protein trafficking within cilia is mediated by the intraflagellar transport (IFT) machinery, which contains the IFT-A and IFT-B complexes powered by the kinesin-2 and dynein-2 motors. Mutations in genes encoding subunits of the IFT-A and dynein-2 complexes cause skeletal ciliopathies. Some subunits of the IFT-B complex, including IFT52, IFT80, and IFT172, are also mutated in skeletal ciliopathies. We here show that IFT52 variants found in individuals with short-rib polydactyly syndrome (SRPS) are compromised in terms of formation of the IFT-B holocomplex from two subcomplexes and its interaction with heterotrimeric kinesin-II. IFT52-knockout (KO) cells expressing IFT52 variants that mimic the cellular conditions of individuals with SRPS demonstrated mild ciliogenesis defects and a decrease in ciliary IFT-B level. Furthermore, in IFT52-KO cells expressing an SRPS variant of IFT52, ciliary tip localization of ICK/CILK1 and KIF17, both of which are likely to be transported to the tip via binding to the IFT-B complex, was significantly impaired. Altogether these results indicate that impaired anterograde trafficking caused by a decrease in the ciliary level of IFT-B or in its binding to kinesin-II underlies the ciliary defects found in skeletal ciliopathies caused by IFT52 variations.
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Affiliation(s)
- Yamato Ishida
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Koshi Tasaki
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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24
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Guleria VS, Parit R, Quadri N, Das R, Upadhyai P. The intraflagellar transport protein IFT52 associated with short-rib thoracic dysplasia is essential for ciliary function in osteogenic differentiation in vitro and for sensory perception in Drosophila. Exp Cell Res 2022; 418:113273. [PMID: 35839863 DOI: 10.1016/j.yexcr.2022.113273] [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: 05/16/2022] [Revised: 06/30/2022] [Accepted: 07/02/2022] [Indexed: 11/04/2022]
Abstract
Primary cilia are non-motile sensory cell-organelle that are essential for organismal development, differentiation, and postnatal homeostasis. Their biogenesis and function are mediated by the intraflagellar transport (IFT) system. Pathogenic variants in IFT52, a central component of the IFT-B complex is associated with short-rib thoracic dysplasia with or without polydactyly 16 (SRTD16), with major skeletal manifestations, in addition to other features. Here we sought to examine the role of IFT52 in osteoblast differentiation. Using lentiviral shRNA interference Ift52 was depleted in C3H10T1/2 mouse mesenchymal stem cells. This led to the disruption of the IFT-B anterograde trafficking machinery that impaired primary ciliogenesis and blocked osteogenic differentiation. In Ift52 silenced cells, Hedgehog (Hh) pathway upregulation during osteogenesis was attenuated and despite Smoothened Agonist (SAG) based Hh activation, osteogenic differentiation was incompletely restored. Further we investigated IFT52 activity in Drosophila, wherein the only ciliated somatic cells are the bipolar sensory neurons of the peripheral nervous system. Knockdown of IFT52 in Drosophila neuronal tissues reduced lifespan with the loss of embryonic chordotonal cilia, and produced severe locomotion, auditory and proprioceptive defects in larva and adults. Together these findings improve our knowledge of the role of IFT52 in various physiological contexts and its associated human disorder.
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Affiliation(s)
- Vishal Singh Guleria
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Rahul Parit
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Neha Quadri
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Ranajit Das
- Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, India
| | - Priyanka Upadhyai
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India.
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25
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Walker RV, Maranto A, Palicharla VR, Hwang SH, Mukhopadhyay S, Qian F. Cilia-Localized Counterregulatory Signals as Drivers of Renal Cystogenesis. Front Mol Biosci 2022; 9:936070. [PMID: 35832738 PMCID: PMC9272769 DOI: 10.3389/fmolb.2022.936070] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 05/30/2022] [Indexed: 12/18/2022] Open
Abstract
Primary cilia play counterregulatory roles in cystogenesis-they inhibit cyst formation in the normal renal tubule but promote cyst growth when the function of polycystins is impaired. Key upstream cilia-specific signals and components involved in driving cystogenesis have remained elusive. Recent studies of the tubby family protein, Tubby-like protein 3 (TULP3), have provided new insights into the cilia-localized mechanisms that determine cyst growth. TULP3 is a key adapter of the intraflagellar transport complex A (IFT-A) in the trafficking of multiple proteins specifically into the ciliary membrane. Loss of TULP3 results in the selective exclusion of its cargoes from cilia without affecting their extraciliary pools and without disrupting cilia or IFT-A complex integrity. Epistasis analyses have indicated that TULP3 inhibits cystogenesis independently of the polycystins during kidney development but promotes cystogenesis in adults when polycystins are lacking. In this review, we discuss the current model of the cilia-dependent cyst activation (CDCA) mechanism in autosomal dominant polycystic kidney disease (ADPKD) and consider the possible roles of ciliary and extraciliary polycystins in regulating CDCA. We then describe the limitations of this model in not fully accounting for how cilia single knockouts cause significant cystic changes either in the presence or absence of polycystins. Based on available data from TULP3/IFT-A-mediated differential regulation of cystogenesis in kidneys with deletion of polycystins either during development or in adulthood, we hypothesize the existence of cilia-localized components of CDCA (cCDCA) and cilia-localized cyst inhibition (CLCI) signals. We develop the criteria for cCDCA/CLCI signals and discuss potential TULP3 cargoes as possible cilia-localized components that determine cystogenesis in kidneys during development and in adult mice.
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Affiliation(s)
- Rebecca V. Walker
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Anthony Maranto
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | | | - Sun-Hee Hwang
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, United States
| | - Saikat Mukhopadhyay
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, United States
| | - Feng Qian
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
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26
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Senatore E, Iannucci R, Chiuso F, Delle Donne R, Rinaldi L, Feliciello A. Pathophysiology of Primary Cilia: Signaling and Proteostasis Regulation. Front Cell Dev Biol 2022; 10:833086. [PMID: 35646931 PMCID: PMC9130585 DOI: 10.3389/fcell.2022.833086] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 04/21/2022] [Indexed: 01/29/2023] Open
Abstract
Primary cilia are microtubule-based, non-motile sensory organelles present in most types of growth-arrested eukaryotic cells. They are transduction hubs that receive and transmit external signals to the cells in order to control growth, differentiation and development. Mutations of genes involved in the formation, maintenance or disassembly of ciliary structures cause a wide array of developmental genetic disorders, also known as ciliopathies. The primary cilium is formed during G1 in the cell cycle and disassembles at the G2/M transition. Following the completion of the cell division, the cilium reassembles in G1. This cycle is finely regulated at multiple levels. The ubiquitin-proteasome system (UPS) and the autophagy machinery, two main protein degradative systems in cells, play a fundamental role in cilium dynamics. Evidence indicate that UPS, autophagy and signaling pathways may act in synergy to control the ciliary homeostasis. However, the mechanisms involved and the links between these regulatory systems and cilium biogenesis, dynamics and signaling are not well defined yet. Here, we discuss the reciprocal regulation of signaling pathways and proteolytic machineries in the control of the assembly and disassembly of the primary cilium, and the impact of the derangement of these regulatory networks in human ciliopathies.
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Juhl AD, Anvarian Z, Kuhns S, Berges J, Andersen JS, Wüstner D, Pedersen LB. Transient accumulation and bidirectional movement of KIF13B in primary cilia. J Cell Sci 2022; 136:275012. [DOI: 10.1242/jcs.259257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 04/01/2022] [Indexed: 10/18/2022] Open
Abstract
Primary cilia are microtubule-based sensory organelles whose assembly and function rely on the conserved bidirectional intraflagellar transport (IFT) system, which is powered by anterograde kinesin-2 and retrograde cytoplasmic dynein 2 motors. Nematodes additionally employ a cell type-specific kinesin-3 motor, KLP-6, which moves within cilia independently of IFT and regulates ciliary content and function. Here we provide evidence that a KLP-6 homolog, KIF13B, undergoes bursts of bidirectional movement within primary cilia of cultured immortalized human retinal pigment epithelial (hTERT-RPE1) cells. Anterograde and retrograde intraciliary velocities of KIF13B were similar to those of IFT (IFT172-eGFP), but intraciliary movement of KIF13B required its own motor domain and appeared to be cell-type specific. Our work provides the first demonstration of motor-driven, intraciliary movement by a vertebrate kinesin other than kinesin-2 motors.
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Affiliation(s)
- Alice Dupont Juhl
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Zeinab Anvarian
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100 Copenhagen Ø, Denmark
| | - Stefanie Kuhns
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Julia Berges
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100 Copenhagen Ø, Denmark
- Department of Biomedicine, Facultad Ciencias Experimentales, Universidad Francisco de Vitoria, Ctra. Pozuelo-Majadahonda Km. 1.800, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Jens S. Andersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Daniel Wüstner
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Lotte B. Pedersen
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100 Copenhagen Ø, Denmark
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Thomas DC, Moorthy JD, Prabhakar V, Ajayakumar A, Pitchumani PK. Role of primary cilia and Hedgehog signaling in craniofacial features of Ellis-van Creveld syndrome. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2022; 190:36-46. [PMID: 35393766 DOI: 10.1002/ajmg.c.31969] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/13/2022] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
Ellis-van Creveld syndrome (EvC) is an autosomal recessive genetic disorder involving pathogenic variants of EVC and EVC2 genes and classified as a ciliopathy. The syndrome is caused by mutations in the EVC gene on chromosome 4p16, and EVC2 gene, located close to the EVC gene, in a head-to-head configuration. Regardless of the affliction of EVC or EVC2, the clinical features of Ellis-van Creveld syndrome are similar. Both these genes are expressed in tissues such as, but not limited to, the heart, liver, skeletal muscle, and placenta, while the predominant expression in the craniofacial tissues is that of EVC2. Biallelic mutations of EVC and EVC2 affect Hedgehog signaling and thereby ciliary function, crucial factors in vertebrate development, culminating in the phenotypical features characteristic of EvC. The clinical features of Ellis-van Creveld syndrome are consistent with significant abnormalities in morphogenesis and differentiation of the affected tissues. The robust role of primary cilia in histodifferentiation and morphodifferentiation of oral, perioral, and craniofacial tissues is becoming more evident in the most recent literature. In this review, we give a summary of the mechanistic role of primary cilia in craniofacial development, taking Ellis-van Creveld syndrome as a representative example.
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Affiliation(s)
- Davis C Thomas
- Center for TMD and Orofacial Pain, Rutgers School of Dental Medicine, Newark, New Jersey, USA
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29
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Turn RE, Hu Y, Dewees SI, Devi N, East MP, Hardin KR, Khatib T, Linnert J, Wolfrum U, Lim MJ, Casanova JE, Caspary T, Kahn RA. The ARF GAPs ELMOD1 and ELMOD3 act at the Golgi and cilia to regulate ciliogenesis and ciliary protein traffic. Mol Biol Cell 2022; 33:ar13. [PMID: 34818063 PMCID: PMC9236152 DOI: 10.1091/mbc.e21-09-0443] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 11/11/2022] Open
Abstract
ELMODs are a family of three mammalian paralogues that display GTPase-activating protein (GAP) activity toward a uniquely broad array of ADP-ribosylation factor (ARF) family GTPases that includes ARF-like (ARL) proteins. ELMODs are ubiquitously expressed in mammalian tissues, highly conserved across eukaryotes, and ancient in origin, being present in the last eukaryotic common ancestor. We described functions of ELMOD2 in immortalized mouse embryonic fibroblasts (MEFs) in the regulation of cell division, microtubules, ciliogenesis, and mitochondrial fusion. Here, using similar strategies with the paralogues ELMOD1 and ELMOD3, we identify novel functions and locations of these cell regulators and compare them to those of ELMOD2, allowing the determination of functional redundancy among the family members. We found strong similarities in phenotypes resulting from deletion of either Elmod1 or Elmod3 and marked differences from those arising in Elmod2 deletion lines. Deletion of either Elmod1 or Elmod3 results in the decreased ability of cells to form primary cilia, loss of a subset of proteins from cilia, and accumulation of some ciliary proteins at the Golgi, predicted to result from compromised traffic from the Golgi to cilia. These phenotypes are reversed upon activating mutant expression of either ARL3 or ARL16, linking their roles to ELMOD1/3 actions.
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Affiliation(s)
- Rachel E. Turn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Biochemistry, Cell & Developmental Biology Graduate Program, Emory University, Atlanta, GA 30322
- Department of Microbiology and Immunology, Stanford University, Palo Alto, CA 94305
| | - Yihan Hu
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, 410008 Hunan, China
| | - Skylar I. Dewees
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Biochemistry, Cell & Developmental Biology Graduate Program, Emory University, Atlanta, GA 30322
| | - Narra Devi
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
| | - Michael P. East
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Katherine R. Hardin
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322
- Biochemistry, Cell & Developmental Biology Graduate Program, Emory University, Atlanta, GA 30322
| | - Tala Khatib
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322
- Biochemistry, Cell & Developmental Biology Graduate Program, Emory University, Atlanta, GA 30322
| | - Joshua Linnert
- Institute of Molecular Physiology, Johannes Gutenberg University, Mainz 55128, Germany
| | - Uwe Wolfrum
- Institute of Molecular Physiology, Johannes Gutenberg University, Mainz 55128, Germany
| | - Michael J. Lim
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908
| | - James E. Casanova
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908
| | - Tamara Caspary
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Richard A. Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
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30
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Yu SS, Wang E, Chiang CY, Cheng PH, Yeh YS, Wu YY, Chiou YY, Jiang ST. Large deletion of Wdr19 in developing renal tubules disrupts primary ciliogenesis leading to polycystic kidney disease in mice. J Pathol 2022; 257:5-16. [PMID: 35007346 DOI: 10.1002/path.5863] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 12/03/2021] [Accepted: 01/06/2022] [Indexed: 11/11/2022]
Abstract
WD repeat domain 19 (Wdr19) is a major component of the intraflagellar transport (IFT) machinery, which is involved in the function of primary cilia. However, the effects of Wdr19 on primary cilia formation, cystogenesis, and polycystic kidney disease (PKD) progression remain unclear. To study these effects, we generated three lines of kidney-specific conditional knockout mice: Wdr19-knockout (Wdr19-KO, Wdr19f/- ::Cdh16-CreTg/0 ), Pkd1-knockout (Pkd1-KO, Pkd1f/- ::Cdh16-CreTg/0 ), and Wdr19/Pkd1-double knockout (Wdr19&Pkd1-dKO, Wdr19f/- ;Pkd1f/- ::Cdh16-CreTg/0 ) mice. Ultrastructural analysis using transmission electron microscopy (TEM) indicated that the primary cilia were almost absent at postnatal day 10 in Wdr19-KO mice compared with Pkd1-KO and wild-type (WT) mice. However, the primary cilia appeared structurally normal even if malfunctional in Pkd1-deficient cysts. The Pkd1-KO mice had the most severe PKD progression, including the shortest lifespan (14 days) and the largest renal cysts, among the three knockout lines. Thus, the molecular mechanism of renal cystogenesis in Wdr19-KO mice (primary cilia abrogation) was different from that in Pkd1-KO mice (primary cilia malfunction). In summary, Wdr19 deficiency leads to primary cilia abrogation and renal cyst formation. Wdr19 is primarily proposed to participate in retrograde IFT and to be crucial for the construction of primary cilia, which are critical organelles for tubulogenesis in the developing kidneys. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Shang-Shiuan Yu
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, 70457, Taiwan.,National Laboratory Animal Center, National Applied Research Laboratories, Tainan, 74147, Taiwan
| | - Ellian Wang
- Department of Physiology, National Cheng Kung University Medical College, Tainan, 70101, Taiwan
| | - Chih-Ying Chiang
- National Laboratory Animal Center, National Applied Research Laboratories, Tainan, 74147, Taiwan
| | - Po-Hao Cheng
- National Laboratory Animal Center, National Applied Research Laboratories, Tainan, 74147, Taiwan
| | - Yu-Shan Yeh
- National Laboratory Animal Center, National Applied Research Laboratories, Tainan, 74147, Taiwan
| | - Ying-Ying Wu
- National Laboratory Animal Center, National Applied Research Laboratories, Tainan, 74147, Taiwan
| | - Yuan-Yow Chiou
- National Laboratory Animal Center, National Applied Research Laboratories, Tainan, 74147, Taiwan.,Division of Pediatric Nephrology, Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 70403, Taiwan
| | - Si-Tse Jiang
- National Laboratory Animal Center, National Applied Research Laboratories, Tainan, 74147, Taiwan
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31
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Zhou Z, Qiu H, Castro-Araya RF, Takei R, Nakayama K, Katoh Y. Impaired cooperation between IFT74/BBS22-IFT81 and IFT25-IFT27/BBS19 causes Bardet-Biedl syndrome. Hum Mol Genet 2021; 31:1681-1693. [PMID: 34888642 DOI: 10.1093/hmg/ddab354] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/19/2021] [Accepted: 12/06/2021] [Indexed: 02/03/2023] Open
Abstract
The IFT-B complex mediates ciliary anterograde protein trafficking and membrane protein export together with the BBSome. Bardet-Biedl syndrome (BBS) is caused by mutations in not only all BBSome subunits, but also in some IFT-B subunits, including IFT74/BBS22 and IFT27/BBS19, which form heterodimers with IFT81 and IFT25, respectively. We found that the IFT25-IFT27 dimer bind the C-terminal region of the IFT74-IFT81 dimer, and that the IFT25-IFT27-binding region encompasses the region deleted in the BBS variants of IFT74. In addition, we found that the missense BBS variants of IFT27 are impaired in IFT74-IFT81 binding, and are unable to rescue the BBS-like phenotypes of IFT27-knockout cells. Furthermore, the BBS variants of IFT74 rescued the ciliogenesis defect of IFT74-knockout cells, but the rescued cells demonstrated BBS-like abnormal phenotypes. Taken together, we conclude that the impaired interaction between IFT74-IFT81 and IFT25-IFT27 causes the BBS-associated ciliary defects.
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Affiliation(s)
- Zhuang Zhou
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Hantian Qiu
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Roiner-Francisco Castro-Araya
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Ryota Takei
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
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32
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Noguchi T, Nakamura K, Satoda Y, Katoh Y, Nakayama K. CCRK/CDK20 regulates ciliary retrograde protein trafficking via interacting with BROMI/TBC1D32. PLoS One 2021; 16:e0258497. [PMID: 34624068 PMCID: PMC8500422 DOI: 10.1371/journal.pone.0258497] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/28/2021] [Indexed: 01/02/2023] Open
Abstract
CCRK/CDK20 was reported to interact with BROMI/TBC1D32 and regulate ciliary Hedgehog signaling. In various organisms, mutations in the orthologs of CCRK and those of the kinase ICK/CILK1, which is phosphorylated by CCRK, are known to result in cilia elongation. Furthermore, we recently showed that ICK regulates retrograde ciliary protein trafficking and/or the turnaround event at the ciliary tips, and that its mutations result in the elimination of intraflagellar transport (IFT) proteins that have overaccumulated at the bulged ciliary tips as extracellular vesicles, in addition to cilia elongation. However, how these proteins cooperate to regulate ciliary protein trafficking has remained unclear. We here show that the phenotypes of CCRK-knockout (KO) cells closely resemble those of ICK-KO cells; namely, the overaccumulation of IFT proteins at the bulged ciliary tips, which appear to be eliminated as extracellular vesicles, and the enrichment of GPR161 and Smoothened on the ciliary membrane. The abnormal phenotypes of CCRK-KO cells were rescued by the exogenous expression of wild-type CCRK but not its kinase-dead mutant or a mutant defective in BROMI binding. These results together indicate that CCRK regulates the turnaround process at the ciliary tips in concert with BROMI and probably via activating ICK.
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Affiliation(s)
- Tatsuro Noguchi
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Kentaro Nakamura
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yuuki Satoda
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
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33
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Baldi P, Alhassen W, Chen S, Nguyen H, Khoudari M, Alachkar A. Large-scale analysis reveals spatiotemporal circadian patterns of cilia transcriptomes in the primate brain. J Neurosci Res 2021; 99:2610-2624. [PMID: 34310750 PMCID: PMC11391745 DOI: 10.1002/jnr.24919] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 06/08/2021] [Accepted: 06/24/2021] [Indexed: 01/13/2023]
Abstract
Cilia are dynamic subcellular systems, with core structural and functional components operating in a highly coordinated manner. Since many environmental stimuli sensed by cilia are circadian in nature, it is reasonable to speculate that genes encoding cilia structural and functional components follow rhythmic circadian patterns of expression. Using computational methods and the largest spatiotemporal gene expression atlas of primates, we identified and analyzed the circadian rhythmic expression of cilia genes across 22 primate brain areas. We found that around 73% of cilia transcripts exhibited circadian rhythmicity across at least one of 22 brain regions. In 12 brain regions, cilia transcriptomes were significantly enriched with circadian oscillating transcripts, as compared to the rest of the transcriptome. The phase of the cilia circadian transcripts deviated from the phase of the majority of the background circadian transcripts, and transcripts coding for cilia basal body components accounted for the majority of cilia circadian transcripts. In addition, adjacent or functionally connected brain nuclei had large overlapping complements of circadian cilia genes. Most remarkably, cilia circadian transcripts shared across the basal ganglia nuclei and the prefrontal cortex peaked in these structures in sequential fashion that is similar to the sequential order of activation of the basal ganglia-cortical circuitry in connection with movement coordination, albeit on completely different timescales. These findings support a role for the circadian spatiotemporal orchestration of cilia gene expression in the normal physiology of the basal ganglia-cortical circuit and motor control. Studying orchestrated cilia rhythmicity in the basal ganglia-cortical circuits and other brain circuits may help develop better functional models, and shed light on the causal effects cilia functions have on these circuits and on the regulation of movement and other behaviors.
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Affiliation(s)
- Pierre Baldi
- Department of Computer Science, School of Information and Computer Sciences, University of California-Irvine, Irvine, CA, USA
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California-Irvine, Irvine, CA, USA
| | - Wedad Alhassen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of California-Irvine, Irvine, CA, USA
| | - Siwei Chen
- Department of Computer Science, School of Information and Computer Sciences, University of California-Irvine, Irvine, CA, USA
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California-Irvine, Irvine, CA, USA
| | - Henry Nguyen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of California-Irvine, Irvine, CA, USA
| | - Mohammad Khoudari
- Department of Pharmaceutical Sciences, School of Pharmacy, University of California-Irvine, Irvine, CA, USA
| | - Amal Alachkar
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California-Irvine, Irvine, CA, USA
- Department of Pharmaceutical Sciences, School of Pharmacy, University of California-Irvine, Irvine, CA, USA
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34
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Fujisawa S, Qiu H, Nozaki S, Chiba S, Katoh Y, Nakayama K. ARL3 and ARL13B GTPases participate in distinct steps of INPP5E targeting to the ciliary membrane. Biol Open 2021; 10:bio058843. [PMID: 34447983 PMCID: PMC8496693 DOI: 10.1242/bio.058843] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 08/19/2021] [Indexed: 01/02/2023] Open
Abstract
INPP5E, a phosphoinositide 5-phosphatase, localizes on the ciliary membrane via its C-terminal prenyl moiety, and maintains the distinct ciliary phosphoinositide composition. The ARL3 GTPase contributes to the ciliary membrane localization of INPP5E by stimulating the release of PDE6D bound to prenylated INPP5E. Another GTPase, ARL13B, which is localized on the ciliary membrane, contributes to the ciliary membrane retention of INPP5E by directly binding to its ciliary targeting sequence. However, as ARL13B was shown to act as a guanine nucleotide exchange factor (GEF) for ARL3, it is also possible that ARL13B indirectly mediates the ciliary INPP5E localization via activating ARL3. We here show that INPP5E is delocalized from cilia in both ARL3-knockout (KO) and ARL13B-KO cells. However, some of the abnormal phenotypes were different between these KO cells, while others were found to be common, indicating the parallel roles of ARL3 and ARL13B, at least concerning some cellular functions. For several variants of ARL13B, their ability to interact with INPP5E, rather than their ability as an ARL3-GEF, was associated with whether they could rescue the ciliary localization of INPP5E in ARL13B-KO cells. These observations together indicate that ARL13B determines the ciliary localization of INPP5E, mainly by its direct binding to INPP5E.
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Affiliation(s)
- Sayaka Fujisawa
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hantian Qiu
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shohei Nozaki
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shuhei Chiba
- Department of Genetic Disease Research, Graduate School of Medicine, Osaka City University, Abeno-ku, Osaka 545-8585, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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35
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Wang W, Jack BM, Wang HH, Kavanaugh MA, Maser RL, Tran PV. Intraflagellar Transport Proteins as Regulators of Primary Cilia Length. Front Cell Dev Biol 2021; 9:661350. [PMID: 34095126 PMCID: PMC8170031 DOI: 10.3389/fcell.2021.661350] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/06/2021] [Indexed: 12/21/2022] Open
Abstract
Primary cilia are small, antenna-like organelles that detect and transduce chemical and mechanical cues in the extracellular environment, regulating cell behavior and, in turn, tissue development and homeostasis. Primary cilia are assembled via intraflagellar transport (IFT), which traffics protein cargo bidirectionally along a microtubular axoneme. Ranging from 1 to 10 μm long, these organelles typically reach a characteristic length dependent on cell type, likely for optimum fulfillment of their specific roles. The importance of an optimal cilia length is underscored by the findings that perturbation of cilia length can be observed in a number of cilia-related diseases. Thus, elucidating mechanisms of cilia length regulation is important for understanding the pathobiology of ciliary diseases. Since cilia assembly/disassembly regulate cilia length, we review the roles of IFT in processes that affect cilia assembly/disassembly, including ciliary transport of structural and membrane proteins, ectocytosis, and tubulin posttranslational modification. Additionally, since the environment of a cell influences cilia length, we also review the various stimuli encountered by renal epithelia in healthy and diseased states that alter cilia length and IFT.
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Affiliation(s)
- Wei Wang
- Department of Anatomy and Cell Biology, The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, KS, United States
| | - Brittany M Jack
- Department of Anatomy and Cell Biology, The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, KS, United States
| | - Henry H Wang
- Department of Anatomy and Cell Biology, The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, KS, United States
| | - Matthew A Kavanaugh
- Department of Anatomy and Cell Biology, The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, KS, United States
| | - Robin L Maser
- Department of Clinical Laboratory Sciences, The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, KS, United States
| | - Pamela V Tran
- Department of Anatomy and Cell Biology, The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, KS, United States
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36
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Barnes CL, Malhotra H, Calvert PD. Compartmentalization of Photoreceptor Sensory Cilia. Front Cell Dev Biol 2021; 9:636737. [PMID: 33614665 PMCID: PMC7889997 DOI: 10.3389/fcell.2021.636737] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/07/2021] [Indexed: 12/12/2022] Open
Abstract
Functional compartmentalization of cells is a universal strategy for segregating processes that require specific components, undergo regulation by modulating concentrations of those components, or that would be detrimental to other processes. Primary cilia are hair-like organelles that project from the apical plasma membranes of epithelial cells where they serve as exclusive compartments for sensing physical and chemical signals in the environment. As such, molecules involved in signal transduction are enriched within cilia and regulating their ciliary concentrations allows adaptation to the environmental stimuli. The highly efficient organization of primary cilia has been co-opted by major sensory neurons, olfactory cells and the photoreceptor neurons that underlie vision. The mechanisms underlying compartmentalization of cilia are an area of intense current research. Recent findings have revealed similarities and differences in molecular mechanisms of ciliary protein enrichment and its regulation among primary cilia and sensory cilia. Here we discuss the physiological demands on photoreceptors that have driven their evolution into neurons that rely on a highly specialized cilium for signaling changes in light intensity. We explore what is known and what is not known about how that specialization appears to have driven unique mechanisms for photoreceptor protein and membrane compartmentalization.
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Affiliation(s)
| | | | - Peter D. Calvert
- Department of Ophthalmology and Visual Sciences, Center for Vision Research, SUNY Upstate Medical University, Syracuse, NY, United States
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Ishida Y, Kobayashi T, Chiba S, Katoh Y, Nakayama K. Molecular basis of ciliary defects caused by compound heterozygous IFT144/WDR19 mutations found in cranioectodermal dysplasia. Hum Mol Genet 2021; 30:213-225. [PMID: 33517396 DOI: 10.1093/hmg/ddab034] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/28/2020] [Accepted: 01/20/2021] [Indexed: 12/17/2022] Open
Abstract
Primary cilia contain specific proteins to achieve their functions as cellular antennae. Ciliary protein trafficking is mediated by the intraflagellar transport (IFT) machinery containing the IFT-A and IFT-B complexes. Mutations in genes encoding the IFT-A subunits (IFT43, IFT121/WDR35, IFT122, IFT139/TTC21B, IFT140 and IFT144/WDR19) often result in skeletal ciliopathies, including cranioectodermal dysplasia (CED). We here characterized the molecular and cellular defects of CED caused by compound heterozygous mutations in IFT144 [the missense variant IFT144(L710S) and the nonsense variant IFT144(R1103*)]. These two variants were distinct with regard to their interactions with other IFT-A subunits and with the IFT-B complex. When exogenously expressed in IFT144-knockout (KO) cells, IFT144(L710S) as well as IFT144(WT) rescued both moderately compromised ciliogenesis and the abnormal localization of ciliary proteins. As the homozygous IFT144(L710S) mutation was found to cause autosomal recessive retinitis pigmentosa, IFT144(L710S) is likely to be hypomorphic at the cellular level. In striking contrast, the exogenous expression of IFT144(R1103*) in IFT144-KO cells exacerbated the ciliogenesis defects. The expression of IFT144(R1103*) together with IFT144(WT) restored the abnormal phenotypes of IFT144-KO cells. However, the coexpression of IFT144(R1103*) with the hypomorphic IFT144(L710S) variant in IFT144-KO cells, which mimics the genotype of compound heterozygous CED patients, resulted in severe ciliogenesis defects. Taken together, these observations demonstrate that compound heterozygous mutations in IFT144 cause severe ciliary defects via a complicated mechanism, where one allele can cause severe ciliary defects when combined with a hypomorphic allele.
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Affiliation(s)
- Yamato Ishida
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takuya Kobayashi
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shuhei Chiba
- Department of Genetic Disease Research, Graduate School of Medicine, Osaka City University, Abeno-ku, Osaka 545-8585, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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Qiu H, Fujisawa S, Nozaki S, Katoh Y, Nakayama K. Interaction of INPP5E with ARL13B is essential for its ciliary membrane retention but dispensable for its ciliary entry. Biol Open 2021; 10:bio057653. [PMID: 33372066 PMCID: PMC7860134 DOI: 10.1242/bio.057653] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 12/09/2020] [Indexed: 12/11/2022] Open
Abstract
Compositions of proteins and lipids within cilia and on the ciliary membrane are maintained to be distinct from those of the cytoplasm and plasma membrane, respectively, by the presence of the ciliary gate. INPP5E is a phosphoinositide 5-phosphatase that is localized on the ciliary membrane by anchorage via its C-terminal prenyl moiety. In addition, the ciliary membrane localization of INPP5E is determined by the small GTPase ARL13B. However, it remained unclear as to how ARL13B participates in the localization of INPP5E. We here show that wild-type INPP5E, INPP5E(WT), in ARL13B-knockout cells and an INPP5E mutant defective in ARL13B binding, INPP5E(ΔCTS), in control cells were unable to show steady-state localization on the ciliary membrane. However, not only INPP5E(WT) but also INPP5E(ΔCTS) was able to rescue the abnormal localization of ciliary proteins in INPP5E-knockout cells. Analysis using the chemically induced dimerization system demonstrated that INPP5E(WT) in ARL13B-knockout cells and INPP5E(ΔCTS) in control cells were able to enter cilia, but neither was retained on the ciliary membrane due to the lack of the INPP5E-ARL13B interaction. Thus, our data demonstrate that binding of INPP5E to ARL13B is essential for its steady-state localization on the ciliary membrane but is dispensable for its entry into cilia.
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Affiliation(s)
- Hantian Qiu
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Sayaka Fujisawa
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shohei Nozaki
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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